From a9bc002b0d9e8ea7b64dbc724d90f7955927cd65 Mon Sep 17 00:00:00 2001 From: ohaanika Date: Fri, 9 Aug 2019 09:59:52 -0400 Subject: [PATCH 01/22] create usage-events.R --- demosR/usage-events.R | 282 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 282 insertions(+) create mode 100644 demosR/usage-events.R diff --git a/demosR/usage-events.R b/demosR/usage-events.R new file mode 100644 index 00000000..9e43962a --- /dev/null +++ b/demosR/usage-events.R @@ -0,0 +1,282 @@ +library(dash) +library(dashHtmlComponents) +library(dashCoreComponents) +library(dashCytoscape) +library(jsonlite) + +app <- Dash$new() + +# define elements +basic_elements = list( + list( + 'data' = list('id' = 'one', 'label' = 'Node 1'), + 'position' = list('x' = 50, 'y' = 50) + ), + list( + 'data' = list('id' = 'two', 'label' = 'Node 2'), + 'position' = list('x' = 200, 'y' = 200) + ), + list( + 'data' = list('id' = 'three', 'label' = 'Node 3'), + 'position' = list('x' = 100, 'y' = 150) + ), + list( + 'data' = list('id' = 'four', 'label' = 'Node 4'), + 'position' = list('x' = 400, 'y' = 50) + ), + list( + 'data' = list('id' = 'five', 'label' = 'Node 5'), + 'position' = list('x' = 250, 'y' = 100) + ), + list( + 'data' = list('id' = 'six', 'label' = 'Node 6', 'parent' = 'three'), + 'position' = list('x' = 150, 'y' = 150) + ), + list( + 'data' = list( + 'id' = 'one-two', + 'source' = 'one', + 'target' = 'two', + 'label' = 'Edge from Node1 to Node2' + ) + ), + list( + 'data' = list( + 'id' = 'one-five', + 'source' = 'one', + 'target' = 'five', + 'label' = 'Edge from Node 1 to Node 5' + ) + ), + list( + 'data' = list( + 'id' = 'two-four', + 'source' = 'two', + 'target' = 'four', + 'label' = 'Edge from Node 2 to Node 4' + ) + ), + list( + 'data' = list( + 'id' = 'three-five', + 'source' = 'three', + 'target' = 'five', + 'label' = 'Edge from Node 3 to Node 5' + ) + ), + list( + 'data' = list( + 'id' = 'three-two', + 'source' = 'three', + 'target' = 'two', + 'label' = 'Edge from Node 3 to Node 2' + ) + ), + list( + 'data' = list( + 'id' = 'four-four', + 'source' = 'four', + 'target' = 'four', + 'label' = 'Edge from Node 4 to Node 4' + ) + ), + list( + 'data' = list( + 'id' = 'four-six', + 'source' = 'four', + 'target' = 'six', + 'label' = 'Edge from Node 4 to Node 6' + ) + ), + list( + 'data' = list( + 'id' = 'five-one', + 'source' = 'five', + 'target' = 'one', + 'label' = 'Edge from Node 5 to Node 1' + ) + ) +) + +styles = list( + 'json-output' = list( + 'overflow-y' = 'scroll', + 'height' = 'calc(50% - 25px)', + 'border' = 'thin lightgrey solid' + ), + 'tab' = list( + 'height' = 'calc(98vh - 115px)' + ) +) + +# define app layout +app$layout( + htmlDiv( + list( + htmlDiv( + className = 'eight columns', + children = list( + cytoCytoscape( + id = 'cytoscape', + elements = basic_elements, + layout = list( + 'name' = 'preset' + ), + style = list( + 'height' = '95vh', + 'width' = '100%' + ) + ) + ) + ), + htmlDiv( + className = 'four columns', + children = list( + dccTabs( + id = 'tabs', + children = list( + dccTab( + label = 'Tap Objects', + children = list( + htmlDiv( + style = styles[['tab']], + children = list( + htmlP('Node Object JSON:'), + htmlPre( + id = 'tap-node-json-output', + style = styles[['json-output']] + ), + htmlP('Edge Object JSON:'), + htmlPre( + id = 'tap-edge-json-output', + style = styles[['json-output']] + ) + ) + ) + ) + ), + dccTab( + label = 'Tap Data', + children = list( + htmlDiv( + style = styles[['tab']], + children = list( + htmlP('Node Data JSON:'), + htmlPre( + id = 'tap-node-data-json-output', + style = styles[['json-output']] + ), + htmlP('Edge Data JSON:'), + htmlPre( + id = 'tap-edge-data-json-output', + style = styles[['json-output']] + ) + ) + ) + ) + ), + dccTab(label = 'Mouseover Data', children = list( + htmlDiv( + style = styles[['tab']], + children = list( + htmlP('Node Data JSON:'), + htmlPre( + id = 'mouseover-node-data-json-output', + style = styles[['json-output']] + ), + htmlP('Edge Data JSON:'), + htmlPre( + id = 'mouseover-edge-data-json-output', + style = styles[['json-output']] + ) + ) + ) + ) + ), + dccTab( + label = 'Selected Data', + children = list( + htmlDiv( + style = styles[['tab']], + children = list( + htmlP('Node Data JSON:'), + htmlPre( + id = 'selected-node-data-json-output', + style = styles[['json-output']] + ), + htmlP('Edge Data JSON:'), + htmlPre( + id = 'selected-edge-data-json-output', + style = styles[['json-output']] + ) + ) + ) + ) + ) + ) + ) + ) + ) + ) + ) +) + +# define callbacks +app$callback( + output = list(id = 'tap-node-json-output', property = 'children'), + params = list(input(id = 'cytoscape', property = 'tapNode')), + function(data) { + return(toJSON(data, pretty = TRUE, null = 'null')) + } +) +app$callback( + output = list(id = 'tap-edge-json-output', property = 'children'), + params = list(input(id = 'cytoscape', property = 'tapEdge')), + function(data) { + return(toJSON(data, pretty = TRUE, null = 'null')) + } +) +app$callback( + output = list(id = 'tap-node-data-json-output', property = 'children'), + params = list(input(id = 'cytoscape', property = 'tapNodeData')), + function(data) { + return(toJSON(data, pretty = TRUE, null = 'null')) + } +) +app$callback( + output = list(id = 'tap-edge-data-json-output', property = 'children'), + params = list(input(id = 'cytoscape', property = 'tapEdgeData')), + function(data) { + return(toJSON(data, pretty = TRUE, null = 'null')) + } +) +app$callback( + output = list(id = 'mouseover-node-data-json-output', property = 'children'), + params = list(input(id = 'cytoscape', property = 'mouseoverNodeData')), + function(data) { + return(toJSON(data, pretty = TRUE, null = 'null')) + } +) +app$callback( + output = list(id = 'mouseover-edge-data-json-output', property = 'children'), + params = list(input(id = 'cytoscape', property = 'mouseoverEdgeData')), + function(data) { + return(toJSON(data, pretty = TRUE, null = 'null')) + } +) +app$callback( + output = list(id = 'selected-node-data-json-output', property = 'children'), + params = list(input(id = 'cytoscape', property = 'selectedNodeData')), + function(data) { + return(toJSON(data, pretty = TRUE, null = 'null')) + } +) +app$callback( + output = list(id = 'selected-edge-data-json-output', property = 'children'), + params = list(input(id = 'cytoscape', property = 'selectedEdgeData')), + function(data) { + return(toJSON(data, pretty = TRUE, null = 'null')) + } +) + +app$run_server() From fd95add4eb08229f1e48dfdef4e475ace1bf73f1 Mon Sep 17 00:00:00 2001 From: ohaanika Date: Fri, 9 Aug 2019 12:17:06 -0400 Subject: [PATCH 02/22] create usage-multiple-instances.R --- demosR/usage-multiple-instances.R | 145 ++++++++++++++++++++++++++++++ 1 file changed, 145 insertions(+) create mode 100644 demosR/usage-multiple-instances.R diff --git a/demosR/usage-multiple-instances.R b/demosR/usage-multiple-instances.R new file mode 100644 index 00000000..6c6d6126 --- /dev/null +++ b/demosR/usage-multiple-instances.R @@ -0,0 +1,145 @@ +# original demo: http://js.cytoscape.org/demos/multiple-instances/ + +library(dash) +library(dashHtmlComponents) +library(dashCytoscape) +library(jsonlite) + +app <- Dash$new() + +# define data +elements <- list( + list('data' = list('id' = 'a', 'foo' = 3, 'bar' = 5, 'baz' = 7)), + list('data' = list('id' = 'b', 'foo' = 6, 'bar' = 1, 'baz' = 3)), + list('data' = list('id' = 'c', 'foo' = 2, 'bar' = 3, 'baz' = 6)), + list('data' = list('id' = 'd', 'foo' = 7, 'bar' = 1, 'baz' = 2)), + list('data' = list('id' = 'e', 'foo' = 2, 'bar' = 3, 'baz' = 5)), + list('data' = list('id' = 'ae', 'weight' = 1, 'source' = 'a', 'target' = 'e')), + list('data' = list('id' = 'ab', 'weight' = 3, 'source' = 'a', 'target' = 'b')), + list('data' = list('id' = 'be', 'weight' = 4, 'source' = 'b', 'target' = 'e')), + list('data' = list('id' = 'bc', 'weight' = 5, 'source' = 'b', 'target' = 'c')), + list('data' = list('id' = 'ce', 'weight' = 6, 'source' = 'c', 'target' = 'e')), + list('data' = list('id' = 'cd', 'weight' = 2, 'source' = 'c', 'target' = 'd')), + list('data' = list('id' = 'de', 'weight' = 7, 'source' = 'd', 'target' = 'e')) +) + +# define app layout +app$layout( + htmlDiv( + list( + cytoCytoscape( + id = 'cytoscape-top', + elements = elements, + layout = list( + 'name' = 'circle', + 'padding' = 10 + ), + stylesheet = list( + list( + 'selector' = 'node', + 'style' = list( + 'background-color' = '#B3767E', + 'width' = 'mapData(baz, 0, 10, 10, 40)', + 'height' = 'mapData(baz, 0, 10, 10, 40)', + 'content' = 'data(id)' + ) + ), + list( + 'selector' = 'edge', + 'style' = list( + 'line-color' = '#F2B1BA', + 'target-arrow-color' = '#F2B1BA', + 'width' = 2, + 'target-arrow-shape' = 'circle', + 'opacity' = 0.8 + ) + ), + list( + 'selector' = ':selected', + 'style' = list( + 'background-color' = 'black', + 'line-color' = 'black', + 'target-arrow-color' = 'black', + 'source-arrow-color' = 'black', + 'opacity' = 1 + ) + ), + list( + 'selector' = '.faded', + 'style' = list( + 'opacity' = 0.25, + 'text-opacity' = 0 + ) + ) + ), + style = list( + 'width' = '100%', + 'height' = '50%', + 'position' = 'absolute', + 'background-color' = '#FAEDEF', + 'left' = 0, + 'top' = 0 + ) + ), + cytoCytoscape( + id = 'cytoscape-bottom', + elements = elements, + layout = list( + 'name' = 'breadthfirst', + 'directed' = TRUE, + 'padding' = 10 + ), + stylesheet = list( + list( + 'selector' = 'node', + 'style' = list( + 'background-color' = '#6272A3', + 'shape' = 'rectangle', + 'width' = 'mapData(foo, 0, 10, 10, 30)', + 'height' = 'mapData(bar, 0, 10, 10, 50)', + 'content' = 'data(id)' + ) + ), + list( + 'selector' = 'edge', + 'style' = list( + 'width' = 'mapData(weight, 0, 10, 3, 9)', + 'line-color' = '#B1C1F2', + 'target-arrow-color' = '#B1C1F2', + 'target-arrow-shape' = 'triangle', + 'opacity' = 0.8 + ) + ), + list( + 'selector' = ':selected', + 'style' = list( + 'background-color' = 'black', + 'line-color' = 'black', + 'target-arrow-color' = 'black', + 'source-arrow-color' = 'black', + 'opacity' = 1 + ) + ), + list( + 'selector' = '.faded', + 'style' = list( + 'opacity' = 0.25, + 'text-opacity' = 0 + ) + ) + ), + style = list( + 'width' = '100%', + 'height' = '50%', + 'position' = 'absolute', + 'background-color' = '#EDF1FA', + 'left' = 0, + 'top' = '50%', + 'border-top' = '1px solid #ccc' + ) + ) + ) + ) +) + +app$run_server(debug = TRUE) From 7c06cacb7f03af97be6899702bd2ed7fddeaf61d Mon Sep 17 00:00:00 2001 From: ohaanika Date: Fri, 9 Aug 2019 12:18:02 -0400 Subject: [PATCH 03/22] create usage-grid-layout.R --- demosR/usage-grid-layout.R | 54 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 demosR/usage-grid-layout.R diff --git a/demosR/usage-grid-layout.R b/demosR/usage-grid-layout.R new file mode 100644 index 00000000..f55f4445 --- /dev/null +++ b/demosR/usage-grid-layout.R @@ -0,0 +1,54 @@ +# original demo: http://js.cytoscape.org/demos/grid-layout/ + +library(dash) +library(dashHtmlComponents) +library(dashCytoscape) +library(jsonlite) + +app <- Dash$new() + +# load data +elements <- fromJSON("demos/data/grid-layout/data.json") + +# define app layout +app$layout( + htmlDiv( + list( + cytoCytoscape( + id = 'cytoscape', + elements = elements, + layout = list('name' = 'grid'), + stylesheet = list( + list( + 'selector' = 'node', + 'style' = list( + 'height' = 20, + 'width' = 20, + 'background-color' = '#18e018' + ) + ), + list( + 'selector' = 'edge', + 'style' = list( + 'curve-style' = 'haystack', + 'haystack-radius' = 0, + 'width' = 5, + 'opacity' = 0.5, + 'line-color' = '#a2efa2' + ) + ) + ), + style = list( + 'width' = '100%', + 'height' = '100%', + 'position' = 'absolute', + 'left' = 0, + 'top' = 0, + 'z-index' = 999 + ) + ) + ) + ) +) + +app$run_server(debug = TRUE) From c58dc1512cb884513095ab46681487bea5167971 Mon Sep 17 00:00:00 2001 From: ohaanika Date: Fri, 9 Aug 2019 12:18:19 -0400 Subject: [PATCH 04/22] create usage-circle-layout.R --- demosR/usage-circle-layout.R | 54 ++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 demosR/usage-circle-layout.R diff --git a/demosR/usage-circle-layout.R b/demosR/usage-circle-layout.R new file mode 100644 index 00000000..cc642b0b --- /dev/null +++ b/demosR/usage-circle-layout.R @@ -0,0 +1,54 @@ +# original demo: http://js.cytoscape.org/demos/circle-layout/ + +library(dash) +library(dashHtmlComponents) +library(dashCytoscape) +library(jsonlite) + +app <- Dash$new() + +# load data +elements <- fromJSON("demos/data/circle-layout/data.json") + +# define app layout +app$layout( + htmlDiv( + list( + cytoCytoscape( + id = 'cytoscape', + elements = elements, + layout = list('name' = 'circle'), + stylesheet = list( + list( + 'selector' = 'node', + 'style' = list( + 'height' = 20, + 'width' = 20, + 'background-color' = '#e8e406' + ) + ), + list( + 'selector' = 'edge', + 'style' = list( + 'curve-style' = 'haystack', + 'haystack-radius' = 0, + 'width' = 5, + 'opacity' = 0.5, + 'line-color' = '#f2f08c' + ) + ) + ), + style = list( + 'width' = '100%', + 'height' = '100%', + 'position' = 'absolute', + 'left' = 0, + 'top' = 0, + 'z-index' = 999 + ) + ) + ) + ) +) + +app$run_server(debug = TRUE) From 613105cb5aa8e9cc4a2c59f29b716aad4b840f92 Mon Sep 17 00:00:00 2001 From: ohaanika Date: Fri, 9 Aug 2019 12:19:09 -0400 Subject: [PATCH 05/22] create usage-breadthfirst-layout.R --- demosR/usage-breadthfirst-layout.R | 129 +++++++++++++++++++++++++++++ 1 file changed, 129 insertions(+) create mode 100644 demosR/usage-breadthfirst-layout.R diff --git a/demosR/usage-breadthfirst-layout.R b/demosR/usage-breadthfirst-layout.R new file mode 100644 index 00000000..f9bae1d9 --- /dev/null +++ b/demosR/usage-breadthfirst-layout.R @@ -0,0 +1,129 @@ +# original demo: http://js.cytoscape.org/demos/images-breadthfirst-layout/ +# +# note: click animation is not implemented + +library(dash) +library(dashHtmlComponents) +library(dashCytoscape) +library(jsonlite) + +app <- Dash$new() + +# define data +elements <- list( + list('data' = list('id' = 'cat')), + list('data' = list('id' = 'bird')), + list('data' = list('id' = 'ladybug')), + list('data' = list('id' = 'aphid')), + list('data' = list('id' = 'rose')), + list('data' = list('id' = 'grasshopper')), + list('data' = list('id' = 'plant')), + list('data' = list('id' = 'wheat')), + list('data' = list('source' = 'cat', 'target' = 'bird')), + list('data' = list('source' = 'bird', 'target' = 'ladybug')), + list('data' = list('source' = 'bird', 'target' = 'grasshopper')), + list('data' = list('source' = 'grasshopper', 'target' = 'plant')), + list('data' = list('source' = 'grasshopper', 'target' = 'wheat')), + list('data' = list('source' = 'ladybug', 'target' = 'aphid')), + list('data' = list('source' = 'aphid', 'target' = 'rose')) +) + +# define stylesheet +stylesheet <- list( + list( + 'selector' = 'node', + 'style' = list( + 'height' = 80, + 'width' = 80, + 'background-fit' = 'cover', + 'border-color' = '#000', + 'border-width' = 3, + 'border-opacity' = 0.5 + ) + ), + list( + 'selector' = 'edge', + 'style' = list( + 'curve-style' = 'bezier', + 'width' = 6, + 'target-arrow-shape' = 'triangle', + 'line-color' = '#ffaaaa', + 'target-arrow-color' = '#ffaaaa' + ) + ), + list( + 'selector' = '#bird', + 'style' = list( + 'background-image' = 'https://farm8.staticflickr.com/7272/7633179468_3e19e45a0c_b.jpg' + ) + ), + list( + 'selector' = '#cat', + 'style' = list( + 'background-image' = 'https://farm2.staticflickr.com/1261/1413379559_412a540d29_b.jpg' + ) + ), + list( + 'selector' = '#ladybug', + 'style' = list( + 'background-image' = 'https://farm4.staticflickr.com/3063/2751740612_af11fb090b_b.jpg' + ) + ), + list( + 'selector' = '#aphid', + 'style' = list( + 'background-image' = 'https://farm9.staticflickr.com/8316/8003798443_32d01257c8_b.jpg' + ) + ), + list( + 'selector' = '#rose', + 'style' = list( + 'background-image' = 'https://farm6.staticflickr.com/5109/5817854163_eaccd688f5_b.jpg' + ) + ), + list( + 'selector' = '#grasshopper', + 'style' = list( + 'background-image' = 'https://farm7.staticflickr.com/6098/6224655456_f4c3c98589_b.jpg' + ) + ), + list( + 'selector' = '#plant', + 'style' = list( + 'background-image' = 'https://farm1.staticflickr.com/231/524893064_f49a4d1d10_z.jpg' + ) + ), + list( + 'selector' = '#wheat', + 'style' = list( + 'background-image' = 'https://farm3.staticflickr.com/2660/3715569167_7e978e8319_b.jpg' + ) + ) +) + +# define app layout +app$layout( + htmlDiv( + list( + cytoCytoscape( + id = 'cytoscape', + elements = elements, + stylesheet = stylesheet, + layout = list( + 'name' = 'breadthfirst', + 'directed' = TRUE, + 'padding' = 10 + ), + style = list( + 'width' = '100%', + 'height' = '100%', + 'position' = 'absolute', + 'left' = 0, + 'top' = 0 + ) + ) + ) + ) +) + +app$run_server(debug = TRUE) From eb1f4dccc6d7433e559e4b778b75412c9a460947 Mon Sep 17 00:00:00 2001 From: ohaanika Date: Fri, 9 Aug 2019 12:22:05 -0400 Subject: [PATCH 06/22] create usage-animated-bfs.R --- demosR/usage-animated-bfs.R | 72 +++++++++++++++++++++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 demosR/usage-animated-bfs.R diff --git a/demosR/usage-animated-bfs.R b/demosR/usage-animated-bfs.R new file mode 100644 index 00000000..2ea1f5d1 --- /dev/null +++ b/demosR/usage-animated-bfs.R @@ -0,0 +1,72 @@ +# original demo: http://js.cytoscape.org/demos/animated-bfs/ +# code: https://github.com/cytoscape/cytoscape.js/tree/master/documentation/demos/animated-bfs +# +# note: animation not implemented yet, please refer to code. + +library(dash) +library(dashHtmlComponents) +library(dashCytoscape) +library(jsonlite) + +app <- Dash$new() + +# define data +elements <- list( + list('data' = list('id' = 'a')), + list('data' = list('id' = 'b')), + list('data' = list('id' = 'c')), + list('data' = list('id' = 'd')), + list('data' = list('id' = 'e')), + list('data' = list('id' = 'a"e', 'weight' = 1, 'source' = 'a', 'target' = 'e')), + list('data' = list('id' = 'ab', 'weight' = 3, 'source' = 'a', 'target' = 'b')), + list('data' = list('id' = 'be', 'weight' = 4, 'source' = 'b', 'target' = 'e')), + list('data' = list('id' = 'bc', 'weight' = 5, 'source' = 'b', 'target' = 'c')), + list('data' = list('id' = 'ce', 'weight' = 6, 'source' = 'c', 'target' = 'e')), + list('data' = list('id' = 'cd', 'weight' = 2, 'source' = 'c', 'target' = 'd')), + list('data' = list('id' = 'de', 'weight' = 7, 'source' = 'd', 'target' = 'e')) +) + +# define app layout +app$layout( + htmlDiv( + list( + cytoCytoscape( + id = 'cytoscape', + elements = elements, + layout = list( + 'name' = 'breadthfirst', + 'directed' = TRUE, + 'roots' = '#a', + 'padding' = 10 + ), + stylesheet = list( + list( + 'selector' = 'node', + 'style' = list( + 'content' = 'data(id)' + ) + ), list( + 'selector' = 'edge', + 'style' = list( + 'curve-style' = 'bezier', + 'target-arrow-shape' = 'triangle', + 'width' = 4, + 'line-color' = '#ddd', + 'target-arrow-color' = '#ddd' + ) + ) + ), + style = list( + 'width' = '100%', + 'height' = '100%', + 'position' = 'absolute', + 'left' = 0, + 'top' = 0, + 'z-index' = 999 + ) + ) + ) + ) +) + +app$run_server(debug = TRUE) From 345cd14780f26ec5f066c12d3534f177970edf09 Mon Sep 17 00:00:00 2001 From: ohaanika Date: Fri, 9 Aug 2019 12:22:31 -0400 Subject: [PATCH 07/22] create usage-pie-style.R --- demosR/usage-pie-style.R | 92 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 92 insertions(+) create mode 100644 demosR/usage-pie-style.R diff --git a/demosR/usage-pie-style.R b/demosR/usage-pie-style.R new file mode 100644 index 00000000..eee5ab04 --- /dev/null +++ b/demosR/usage-pie-style.R @@ -0,0 +1,92 @@ +# original demo: http://js.cytoscape.org/demos/pie-style/ + +library(dash) +library(dashHtmlComponents) +library(dashCytoscape) +library(jsonlite) + +app <- Dash$new() + +# define data +elements <- list( + list('data' = list('id' = 'a', 'foo' = 3, 'bar' = 5, 'baz' = 2)), + list('data' = list('id' = 'b', 'foo' = 6, 'bar' = 1, 'baz' = 3)), + list('data' = list('id' = 'c', 'foo' = 2, 'bar' = 3, 'baz' = 5)), + list('data' = list('id' = 'd', 'foo' = 7, 'bar' = 1, 'baz' = 2)), + list('data' = list('id' = 'e', 'foo' = 2, 'bar' = 3, 'baz' = 5)), + list('data' = list('id' = 'ae', 'weight' = 1, 'source' = 'a', 'target' = 'e')), + list('data' = list('id' = 'ab', 'weight' = 3, 'source' = 'a', 'target' = 'b')), + list('data' = list('id' = 'be', 'weight' = 4, 'source' = 'b', 'target' = 'e')), + list('data' = list('id' = 'bc', 'weight' = 5, 'source' = 'b', 'target' = 'c')), + list('data' = list('id' = 'ce', 'weight' = 6, 'source' = 'c', 'target' = 'e')), + list('data' = list('id' = 'cd', 'weight' = 2, 'source' = 'c', 'target' = 'd')), + list('data' = list('id' = 'de', 'weight' = 7, 'source' = 'd', 'target' = 'e')) +) + +# define app layout +app$layout( + htmlDiv( + list( + cytoCytoscape( + id = 'cytoscape', + elements = elements, + layout = list( + 'name' = 'circle', + 'padding' = 10 + ), + stylesheet = list( + list( + 'selector' = 'node', + 'style' = list( + 'width' = '60px', + 'height' = '60px', + 'content' = 'data(id)', + 'pie-size' = '80%', + 'pie-1-background-color' = '#E8747C', + 'pie-1-background-size' = 'mapData(foo, 0, 10, 0, 100)', + 'pie-2-background-color' = '#74CBE8', + 'pie-2-background-size' = 'mapData(bar, 0, 10, 0, 100)', + 'pie-3-background-color' = '#74E883', + 'pie-3-background-size' = 'mapData(baz, 0, 10, 0, 100)' + ) + ), + list( + 'selector' = 'edge', + 'style' = list( + 'curve-style' = 'bezier', + 'width' = 4, + 'target-arrow-shape' = 'triangle', + 'opacity' = 0.5 + ) + ), + list( + 'selector' = ':selected', + 'style' = list( + 'background-color' = 'black', + 'line-color' = 'black', + 'target-arrow-color' = 'black', + 'source-arrow-color' = 'black', + 'opacity' = 1 + ) + ), + list( + 'selector' = '.faded', + 'style' = list( + 'opacity' = 0.25, + 'text-opacity' = 0 + ) + ) + ), + style = list( + 'width' = '100%', + 'height' = '100%', + 'position' = 'absolute', + 'left' = 0, + 'top' = 0 + ) + ) + ) + ) +) + +app$run_server(debug = TRUE) From 24121b8033e9aa60880de21c5ff24f7a1873661e Mon Sep 17 00:00:00 2001 From: ohaanika Date: Fri, 9 Aug 2019 12:34:57 -0400 Subject: [PATCH 08/22] create usage-compound-nodes.R --- demosR/usage-compound-nodes.R | 85 +++++++++++++++++++++++++++++++++++ 1 file changed, 85 insertions(+) create mode 100644 demosR/usage-compound-nodes.R diff --git a/demosR/usage-compound-nodes.R b/demosR/usage-compound-nodes.R new file mode 100644 index 00000000..935ea831 --- /dev/null +++ b/demosR/usage-compound-nodes.R @@ -0,0 +1,85 @@ +# original demo: http://js.cytoscape.org/demos/compound-nodes/ +# +# note: the Dash version is also uncentered, and otherwise it works + +library(dash) +library(dashHtmlComponents) +library(dashCytoscape) + +app <- Dash$new() + +# define data +elements <- list( + list('data' = list('id' = 'a', 'parent' = 'b'), 'position' = list('x' = 215, 'y' = 85)), + list('data' = list('id' = 'b')), + list('data' = list('id' = 'c', 'parent' = 'b'), 'position' = list('x' = 300, 'y' = 85)), + list('data' = list('id' = 'd'), 'position' = list('x' = 215, 'y' = 175)), + list('data' = list('id' = 'e')), + list('data' = list('id' = 'f', 'parent' = 'e'), 'position' = list('x' = 300, 'y' = 175)), + list('data' = list('id' = 'ad', 'source' = 'a', 'target' = 'd')), + list('data' = list('id' = 'eb', 'source' = 'e', 'target' = 'b')) +) + +# define app layout +app$layout( + htmlDiv( + list( + cytoCytoscape( + id = 'cytoscape', + elements = elements, + boxSelectionEnabled = FALSE, + autounselectify = TRUE, + layout = list( + 'name' = 'preset', + 'padding' = 5 + ), + stylesheet = list( + list( + 'selector' = 'node', + 'style' = list( + 'content' = 'data(id)', + 'text-valign' = 'center', + 'text-halign' = 'center' + ) + ), + list( + 'selector' = '$node > node', + 'style' = list( + 'padding-top' = '10px', + 'padding-left' = '10px', + 'padding-bottom' = '10px', + 'padding-right' = '10px', + 'text-valign' = 'top', + 'text-halign' = 'center', + 'background-color' = '#bbb' + ) + ), + list( + 'selector' = ':selected', + 'style' = list( + 'background-color' = 'black', + 'line-color' = 'black', + 'target-arrow-color' = 'black', + 'source-arrow-color' = 'black' + ) + ), + list( + 'selector' = 'edge', + 'style' = list( + 'target-arrow-shape' = 'triangle' + ) + ) + ), + style = list( + 'width' = '100%', + 'height' = '100%', + 'position' = 'absolute', + 'left' = 0, + 'top' = 0 + ) + ) + ) + ) +) + +app$run_server(debug = TRUE) From 4da049694ef4e2632371e796ac032bc47467bc8c Mon Sep 17 00:00:00 2001 From: ohaanika Date: Fri, 9 Aug 2019 12:45:33 -0400 Subject: [PATCH 09/22] create usage-visual-style.R --- demosR/usage-visual-style.R | 98 +++++++++++++++++++++++++++++++++++++ 1 file changed, 98 insertions(+) create mode 100644 demosR/usage-visual-style.R diff --git a/demosR/usage-visual-style.R b/demosR/usage-visual-style.R new file mode 100644 index 00000000..1f3d00d1 --- /dev/null +++ b/demosR/usage-visual-style.R @@ -0,0 +1,98 @@ +# original demo: http://js.cytoscape.org/demos/visual-style/ + +library(dash) +library(dashHtmlComponents) +library(dashCytoscape) + +app <- Dash$new() + +# define elements +elements <- list( + list('data' = list('id' = 'j', 'name' = 'Jerry', 'weight' = 65, 'faveColor' = '#6FB1FC', 'faveShape' = 'triangle')), + list('data' = list('id' = 'e', 'name' = 'Elaine', 'weight' = 45, 'faveColor' = '#EDA1ED', 'faveShape' = 'ellipse')), + list('data' = list('id' = 'k', 'name' = 'Kramer', 'weight' = 75, 'faveColor' = '#86B342', 'faveShape' = 'octagon')), + list('data' = list('id' = 'g', 'name' = 'George', 'weight' = 70, 'faveColor' = '#F5A45D', 'faveShape' = 'rectangle')), + list('data' = list('source' = 'j', 'target' = 'e', 'faveColor' = '#6FB1FC', 'strength' = 90)), + list('data' = list('source' = 'j', 'target' = 'k', 'faveColor' = '#6FB1FC', 'strength' = 70)), + list('data' = list('source' = 'j', 'target' = 'g', 'faveColor' = '#6FB1FC', 'strength' = 80)), + list('data' = list('source' = 'e', 'target' = 'j', 'faveColor' = '#EDA1ED', 'strength' = 95)), + list('data' = list('source' = 'e', 'target' = 'k', 'faveColor' = '#EDA1ED', 'strength' = 60), 'classes' = 'questionable'), + list('data' = list('source' = 'k', 'target' = 'j', 'faveColor' = '#86B342', 'strength' = 100)), + list('data' = list('source' = 'k', 'target' = 'e', 'faveColor' = '#86B342', 'strength' = 100)), + list('data' = list('source' = 'k', 'target' = 'g', 'faveColor' = '#86B342', 'strength' = 100)), + list('data' = list('source' = 'g', 'target' = 'j', 'faveColor' = '#F5A45D', 'strength' = 90)) +) + +# define app layout +app$layout( + htmlDiv( + list( + cytoCytoscape( + id = 'cytoscape', + elements = elements, + layout = list( + 'name' = 'cose', + 'padding' = 10 + ), + stylesheet = list( + list( + 'selector' = 'node', + 'style' = list( + 'shape' = 'data(faveShape)', + 'width' = 'mapData(weight, 40, 80, 20, 60)', + 'content' = 'data(name)', + 'text-valign' = 'center', + 'text-outline-width' = 2, + 'text-outline-color' = 'data(faveColor)', + 'background-color' = 'data(faveColor)', + 'color' = '#fff' + ) + ), + list( + 'selector' = 'edge', + 'style' = list( + 'curve-style' = 'bezier', + 'opacity' = 0.666, + 'width' = 'mapData(strength, 70, 100, 2, 6)', + 'target-arrow-shape' = 'triangle', + 'source-arrow-shape' = 'circle', + 'line-color' = 'data(faveColor)', + 'source-arrow-color' = 'data(faveColor)', + 'target-arrow-color' = 'data(faveColor)' + ) + ), + list( + 'selector' = ':selected', + 'style' = list( + 'border-width' = 3, + 'border-color' = '#333' + ) + ), + list( + 'selector' = 'edge.questionable', + 'style' = list( + 'line-style' = 'dotted', + 'target-arrow-shape' = 'diamond' + ) + ), + list( + 'selector' = '.faded', + 'style' = list( + 'opacity' = 0.25, + 'text-opacity' = 0 + ) + ) + ), + style = list( + 'width' = '100%', + 'height' = '100%', + 'position' = 'absolute', + 'left' = 0, + 'top' = 0 + ) + ) + ) + ) +) + +app$run_server(debug = TRUE) From 1b473f498cc69058443337d362f5792fd8584560 Mon Sep 17 00:00:00 2001 From: ohaanika Date: Sat, 10 Aug 2019 17:05:51 -0400 Subject: [PATCH 10/22] start usage-phylogeny.R --- demosR/usage-phylogeny.R | 86 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 demosR/usage-phylogeny.R diff --git a/demosR/usage-phylogeny.R b/demosR/usage-phylogeny.R new file mode 100644 index 00000000..645700cf --- /dev/null +++ b/demosR/usage-phylogeny.R @@ -0,0 +1,86 @@ +library(dash) +library(dashHtmlComponents) +library(dashCytoscape) +# library(XML) +# library(methods) +# library(ape) +# library(rphyloxml) + +app <- Dash$new() + +# result <- xmlParse(file = "demosR/data/apaf.xml") +# print(result) + +# xml_file <- system.file("phyloxml/amphibian_tree_of_life_Frost_DR_2006.xml", package="rphyloxml") +# xml_tree <- read_phyloxml(xml_file) +# print(xml_tree) + +layout <- list('name' = 'preset') + +stylesheet <- list( + list( + 'selector' = '.nonterminal', + 'style' = list( + 'label' = 'data(confidence)', + 'background-opacity' = 0, + "text-halign" = "left", + "text-valign" = "top", + ) + ), + list( + 'selector' = '.support', + 'style' = list('background-opacity' = 0) + ), + list( + 'selector' = 'edge', + 'style' = list( + "source-endpoint" = "inside-to-node", + "target-endpoint" = "inside-to-node", + ) + ), + list( + 'selector' = '.terminal', + 'style' = list( + 'label' = 'data(name)', + 'width' = 10, + 'height' = 10, + "text-valign" = "center", + "text-halign" = "right", + 'background-color' = '#222222' + ) + ) +) + +app$layout( + htmlDiv( + list( + cytoCytoscape( + id = 'cytoscape', + elements = elements, + stylesheet = stylesheet, + layout = layout, + style = list( + 'height' = '95vh', + 'width' = '100%' + ) + ) + ) + ) +) + +app$callback( + output = list(id = 'cytoscape', property = 'stylesheet'), + params = list( + input(id = 'cytoscape', property = 'mouseoverEdgeData') + ), + function(data) { + if (is.null(data)) { + return(stylesheet) + } + return( + "" + ) + } +) + +app$run_server() From a17e9245e3358467791026ab39a742f546ec0894 Mon Sep 17 00:00:00 2001 From: ohaanika Date: Sat, 10 Aug 2019 22:30:31 -0400 Subject: [PATCH 11/22] update usage-phylogeny.R --- demosR/usage-phylogeny.R | 23 ++++++++++------------- 1 file changed, 10 insertions(+), 13 deletions(-) diff --git a/demosR/usage-phylogeny.R b/demosR/usage-phylogeny.R index 645700cf..6068a3db 100644 --- a/demosR/usage-phylogeny.R +++ b/demosR/usage-phylogeny.R @@ -1,19 +1,16 @@ library(dash) library(dashHtmlComponents) library(dashCytoscape) -# library(XML) -# library(methods) -# library(ape) -# library(rphyloxml) +library(XML) app <- Dash$new() -# result <- xmlParse(file = "demosR/data/apaf.xml") -# print(result) +result <- xmlParse(file = "demos/data/apaf.xml") +# print(typeof(result)) -# xml_file <- system.file("phyloxml/amphibian_tree_of_life_Frost_DR_2006.xml", package="rphyloxml") -# xml_tree <- read_phyloxml(xml_file) -# print(xml_tree) +tree <- xmlToList(result) +# print(typeof(tree)) +str(tree) layout <- list('name' = 'preset') @@ -24,7 +21,7 @@ stylesheet <- list( 'label' = 'data(confidence)', 'background-opacity' = 0, "text-halign" = "left", - "text-valign" = "top", + "text-valign" = "top" ) ), list( @@ -35,7 +32,7 @@ stylesheet <- list( 'selector' = 'edge', 'style' = list( "source-endpoint" = "inside-to-node", - "target-endpoint" = "inside-to-node", + "target-endpoint" = "inside-to-node" ) ), list( @@ -56,7 +53,7 @@ app$layout( list( cytoCytoscape( id = 'cytoscape', - elements = elements, + elements = list(), # change to 'elements' once defined stylesheet = stylesheet, layout = layout, style = list( @@ -83,4 +80,4 @@ app$callback( } ) -app$run_server() +#app$run_server() From 81b67fad6a550a226c6e9c96c4c989483ab3d159 Mon Sep 17 00:00:00 2001 From: ohaanika Date: Sun, 11 Aug 2019 07:09:50 -0400 Subject: [PATCH 12/22] update usage-phylogeny.R --- demosR/usage-phylogeny.R | 170 +++++++++++++++++++++++++++++++++++++-- 1 file changed, 163 insertions(+), 7 deletions(-) diff --git a/demosR/usage-phylogeny.R b/demosR/usage-phylogeny.R index 6068a3db..c07a76b5 100644 --- a/demosR/usage-phylogeny.R +++ b/demosR/usage-phylogeny.R @@ -5,12 +5,168 @@ library(XML) app <- Dash$new() -result <- xmlParse(file = "demos/data/apaf.xml") -# print(typeof(result)) +tree <- xmlToList(xmlParse(file = "demos/data/apaf.xml"))$phylogeny +capture.output(tree, file = "demosR/tree.txt", append = FALSE) -tree <- xmlToList(result) -# print(typeof(tree)) -str(tree) +# nodes: 31 terminal, 31 support; 30 nonterminal, 29 support (root has no support) + +generate_elements <- function(tree, xlen=30, ylen=30, grabbable=False) { + organize_tree <- function(tree, terminals=list(), nonterminals=list(), i=list(), t=0, n=0) { + + explore_child <- function(child, id) { + if (class(child) == "list") { + if (!is.null(child$name)) { + t <<- t+1 + id <- paste0(id, "c", i[[length(i)]]) + i[[length(i)]] <<- i[[length(i)]]+1 + terminals[[t]] <<- list( + id = id, + tmpID = paste0("t-", t), + name = child$name, + branch_length = child$branch_length, + classes = "terminal" + ) + } else { + if (!is.null(child$confidence$text)) { + n <<- n+1 + id <- paste0(id, "c", i[[length(i)]]) + i[[length(i)]] <<- i[[length(i)]]+1 + nonterminals[[n]] <<- list( + id = id, + tmpID = paste0("n-", n), + confidence = child$confidence$text, + branch_length = child$branch_length, + classes = "nonterminal" + ) + } + i[[length(i)+1]] <<- 0 + lapply(child, explore_child, id=id) + i <<- i[-length(i)] + } + } + } + lapply(tree, explore_child, id="r") + + # CORRECT SO FAR + # explore_child <- function(child, id) { + # if (class(child) == "list") { + # #i <<- i+1 + # #id <- paste0(id, "c", i) + # if (!is.null(child$name)) { + # t <<- t+1 + # terminals[[t]] <<- list( + # #id = id, + # tmpID = paste0("t-", t), + # name = child$name, + # branch_length = child$branch_length, + # classes = "terminal" + # ) + # } else { + # if (!is.null(child$confidence$text)) { + # n <<- n+1 + # nonterminals[[n]] <<- list( + # #id = id, + # tmpID = paste0("n-", n), + # confidence = child$confidence$text, + # branch_length = child$branch_length, + # classes = "nonterminal" + # ) + # } + # lapply(child, explore_child, id=id) + # } + # #i <<- i-1 + # } + # } + # lapply(tree, explore_child, id="r") + + # FAILED ATTEMPT + # explore_child <- function(child) { + # if (class(child) == "list") { + # if (!is.null(child$name)) { + # return( + # list( + # id = paste("t-", child$name), + # name = child$name, + # branch_length = child$branch_length, + # classes = "terminal" + # ) + # ) + # } else if (!is.null(child$confidence$text)) { + # return( + # list( + # id = paste("n-", child$confidence$text), + # confidence = child$confidence$text, + # branch_length = child$branch_length, + # classes = "nonterminal", + # child = lapply(child, explore_child) + # ) + # ) + # } else { + # return(lapply(child, explore_child)) + # } + # } + # } + # nodes <- lapply(tree, explore_child) + + # print("TERMINALS") + # str(terminals) + # print(paste("SIZE", length(terminals))) + # print("NONTERMINALS") + # str(nonterminals) + # print(paste("SIZE", length(nonterminals))) + + return(list(terminals = terminals, nonterminals = nonterminals)) + } + + get_terminals <- function(tree, terminals=list()) { + get_name <- function(child) { + if (class(child) == "list") { + if (!is.null(child$name)) { + terminals[[length(terminals)+1]] <<- list( + name = child$name, + branch_length = child$branch_length + ) + } else { + lapply(child, get_name) + } + } + } + lapply(tree, get_name) + return(terminals) + } + + get_col_positions <- function(tree, taxa, column_width=80) { + # note constants for drawing calculations + max_label_width <- max(unlist(lapply(taxa, function(taxon) return(nchar(taxon$name))))) + drawing_width <- column_width - max_label_width - 1 + + return(list()) + } + + get_row_positions <- function(tree, taxa) { + positions <- lapply(1:length(taxa), function(id) return(2*(id-1))) + names(positions) <- lapply(taxa, function(taxon) return(taxon$name)) + + return(list()) + } + + clean_tree <- organize_tree(tree) + taxa <- get_terminals(tree) + col_positions <- get_col_positions(tree, taxa) + row_positions <- get_row_positions(tree, taxa) + + nodes <- list() + edges <- list() + + # TODO: remove dummy data to not overwrite outputs using functions above + nodes <- list(1,2,3) + edges <- list(4,5,6) + elements <- c(nodes, edges) + + return (elements) +} + +elements <- generate_elements(tree) layout <- list('name' = 'preset') @@ -53,7 +209,7 @@ app$layout( list( cytoCytoscape( id = 'cytoscape', - elements = list(), # change to 'elements' once defined + elements = list(), # TODO: change to 'elements' once defined stylesheet = stylesheet, layout = layout, style = list( @@ -80,4 +236,4 @@ app$callback( } ) -#app$run_server() +# app$run_server() From 04f3642958516a84ece6f2a6d24e49f9e3fad5b0 Mon Sep 17 00:00:00 2001 From: ohaanika Date: Sun, 11 Aug 2019 08:01:42 -0400 Subject: [PATCH 13/22] update usage-phylogeny.R --- demosR/usage-phylogeny.R | 196 ++++++++++++++++----------------------- 1 file changed, 80 insertions(+), 116 deletions(-) diff --git a/demosR/usage-phylogeny.R b/demosR/usage-phylogeny.R index c07a76b5..6c850507 100644 --- a/demosR/usage-phylogeny.R +++ b/demosR/usage-phylogeny.R @@ -8,114 +8,78 @@ app <- Dash$new() tree <- xmlToList(xmlParse(file = "demos/data/apaf.xml"))$phylogeny capture.output(tree, file = "demosR/tree.txt", append = FALSE) -# nodes: 31 terminal, 31 support; 30 nonterminal, 29 support (root has no support) - generate_elements <- function(tree, xlen=30, ylen=30, grabbable=False) { - organize_tree <- function(tree, terminals=list(), nonterminals=list(), i=list(), t=0, n=0) { - - explore_child <- function(child, id) { + # there are 31 "terminal" nodes with their respective 31 "support" nodes + # and 30 "nonterminal" nodes with their respective 29 "support" nodes + # since the root node does not require a preceding "support" node; + # each "support" node has the same x position as the parent clade, + # and the same y position as the child clade; it is used to create + # the 90 degree angle between the parent and the children; + # edge config: parent -> support -> child + + organize_tree <- function(tree, nodes=list(), edges=list(), i=list(), n=1) { + # append root element + nodes[[n]] <- list( + data = list(id = "r"), + position = list(x = 30, y = 1200), + classes = "nonterminal", + grabbable = FALSE + ) + # function to append all nodes and respective support nodes + explore_child <- function(child, child_id) { if (class(child) == "list") { if (!is.null(child$name)) { - t <<- t+1 - id <- paste0(id, "c", i[[length(i)]]) - i[[length(i)]] <<- i[[length(i)]]+1 - terminals[[t]] <<- list( - id = id, - tmpID = paste0("t-", t), - name = child$name, - branch_length = child$branch_length, - classes = "terminal" + support_id <- paste0(child_id, "s", i[[length(i)]]) + child_id <- paste0(child_id, "c", i[[length(i)]]) + n <<- n+2 + nodes[[n-1]] <<- list( + data = list(id = support_id), + # TODO: edit (x,y) according to branch_length = child$branch_length + position = list(x = 0, y = 0), + classes = "support", + grabbable = FALSE + ) + nodes[[n]] <<- list( + data = list(id = child_id, name = child$name), + # TODO: edit (x,y) according to branch_length = child$branch_length + position = list(x = 0, y = 0), + classes = "terminal", + grabbable = FALSE ) + i[[length(i)]] <<- i[[length(i)]]+1 } else { if (!is.null(child$confidence$text)) { - n <<- n+1 - id <- paste0(id, "c", i[[length(i)]]) - i[[length(i)]] <<- i[[length(i)]]+1 - nonterminals[[n]] <<- list( - id = id, - tmpID = paste0("n-", n), - confidence = child$confidence$text, - branch_length = child$branch_length, - classes = "nonterminal" + support_id <- paste0(child_id, "s", i[[length(i)]]) + child_id <- paste0(child_id, "c", i[[length(i)]]) + n <<- n+2 + nodes[[n-1]] <<- list( + data = list(id = support_id), + # TODO: edit (x,y) according to branch_length = child$branch_length + position = list(x = 0, y = 0), + classes = "support", + grabbable = FALSE + ) + nodes[[n]] <<- list( + data = list(id = child_id, confidence = child$confidence$text), + # TODO: edit (x,y) according to branch_length = child$branch_length + position = list(x = 0, y = 0), + classes = "nonterminal", + grabbable = FALSE ) + i[[length(i)]] <<- i[[length(i)]]+1 } i[[length(i)+1]] <<- 0 - lapply(child, explore_child, id=id) + lapply(child, explore_child, child_id=child_id) i <<- i[-length(i)] } } } - lapply(tree, explore_child, id="r") - - # CORRECT SO FAR - # explore_child <- function(child, id) { - # if (class(child) == "list") { - # #i <<- i+1 - # #id <- paste0(id, "c", i) - # if (!is.null(child$name)) { - # t <<- t+1 - # terminals[[t]] <<- list( - # #id = id, - # tmpID = paste0("t-", t), - # name = child$name, - # branch_length = child$branch_length, - # classes = "terminal" - # ) - # } else { - # if (!is.null(child$confidence$text)) { - # n <<- n+1 - # nonterminals[[n]] <<- list( - # #id = id, - # tmpID = paste0("n-", n), - # confidence = child$confidence$text, - # branch_length = child$branch_length, - # classes = "nonterminal" - # ) - # } - # lapply(child, explore_child, id=id) - # } - # #i <<- i-1 - # } - # } - # lapply(tree, explore_child, id="r") - - # FAILED ATTEMPT - # explore_child <- function(child) { - # if (class(child) == "list") { - # if (!is.null(child$name)) { - # return( - # list( - # id = paste("t-", child$name), - # name = child$name, - # branch_length = child$branch_length, - # classes = "terminal" - # ) - # ) - # } else if (!is.null(child$confidence$text)) { - # return( - # list( - # id = paste("n-", child$confidence$text), - # confidence = child$confidence$text, - # branch_length = child$branch_length, - # classes = "nonterminal", - # child = lapply(child, explore_child) - # ) - # ) - # } else { - # return(lapply(child, explore_child)) - # } - # } - # } - # nodes <- lapply(tree, explore_child) - - # print("TERMINALS") - # str(terminals) - # print(paste("SIZE", length(terminals))) - # print("NONTERMINALS") - # str(nonterminals) - # print(paste("SIZE", length(nonterminals))) - - return(list(terminals = terminals, nonterminals = nonterminals)) + lapply(tree, explore_child, child_id="r") + + str(nodes) + print(paste("SIZE", length(nodes))) + + return(nodes) } get_terminals <- function(tree, terminals=list()) { @@ -168,38 +132,38 @@ generate_elements <- function(tree, xlen=30, ylen=30, grabbable=False) { elements <- generate_elements(tree) -layout <- list('name' = 'preset') +layout <- list("name" = "preset") stylesheet <- list( list( - 'selector' = '.nonterminal', - 'style' = list( - 'label' = 'data(confidence)', - 'background-opacity' = 0, + "selector" = ".nonterminal", + "style" = list( + "label" = "data(confidence)", + "background-opacity" = 0, "text-halign" = "left", "text-valign" = "top" ) ), list( - 'selector' = '.support', - 'style' = list('background-opacity' = 0) + "selector" = ".support", + "style" = list("background-opacity" = 0) ), list( - 'selector' = 'edge', - 'style' = list( + "selector" = "edge", + "style" = list( "source-endpoint" = "inside-to-node", "target-endpoint" = "inside-to-node" ) ), list( - 'selector' = '.terminal', - 'style' = list( - 'label' = 'data(name)', - 'width' = 10, - 'height' = 10, + "selector" = ".terminal", + "style" = list( + "label" = "data(name)", + "width" = 10, + "height" = 10, "text-valign" = "center", "text-halign" = "right", - 'background-color' = '#222222' + "background-color" = "#222222" ) ) ) @@ -208,13 +172,13 @@ app$layout( htmlDiv( list( cytoCytoscape( - id = 'cytoscape', - elements = list(), # TODO: change to 'elements' once defined + id = "cytoscape", + elements = list(), # TODO: change to "elements" once defined stylesheet = stylesheet, layout = layout, style = list( - 'height' = '95vh', - 'width' = '100%' + "height" = "95vh", + "width" = "100%" ) ) ) @@ -222,9 +186,9 @@ app$layout( ) app$callback( - output = list(id = 'cytoscape', property = 'stylesheet'), + output = list(id = "cytoscape", property = "stylesheet"), params = list( - input(id = 'cytoscape', property = 'mouseoverEdgeData') + input(id = "cytoscape", property = "mouseoverEdgeData") ), function(data) { if (is.null(data)) { From 38c381a9c7928279e6b6f98debb60bfd48a9729d Mon Sep 17 00:00:00 2001 From: ohaanika Date: Sun, 11 Aug 2019 08:09:18 -0400 Subject: [PATCH 14/22] update usage-phylogeny.R --- demosR/usage-phylogeny.R | 174 +++++++++++++++++++-------------------- 1 file changed, 87 insertions(+), 87 deletions(-) diff --git a/demosR/usage-phylogeny.R b/demosR/usage-phylogeny.R index 6c850507..0e8834f5 100644 --- a/demosR/usage-phylogeny.R +++ b/demosR/usage-phylogeny.R @@ -8,7 +8,9 @@ app <- Dash$new() tree <- xmlToList(xmlParse(file = "demos/data/apaf.xml"))$phylogeny capture.output(tree, file = "demosR/tree.txt", append = FALSE) -generate_elements <- function(tree, xlen=30, ylen=30, grabbable=False) { +generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, + nodes=list(), edges=list(), i=list(), n=1) { + # there are 31 "terminal" nodes with their respective 31 "support" nodes # and 30 "nonterminal" nodes with their respective 29 "support" nodes # since the root node does not require a preceding "support" node; @@ -17,117 +19,115 @@ generate_elements <- function(tree, xlen=30, ylen=30, grabbable=False) { # the 90 degree angle between the parent and the children; # edge config: parent -> support -> child - organize_tree <- function(tree, nodes=list(), edges=list(), i=list(), n=1) { - # append root element - nodes[[n]] <- list( - data = list(id = "r"), - position = list(x = 30, y = 1200), - classes = "nonterminal", - grabbable = FALSE - ) - # function to append all nodes and respective support nodes - explore_child <- function(child, child_id) { - if (class(child) == "list") { - if (!is.null(child$name)) { + # append root element + nodes[[n]] <- list( + data = list(id = "r"), + position = list(x = 30, y = 1200), + classes = "nonterminal", + grabbable = FALSE + ) + # function to append all nodes and respective support nodes + explore_child <- function(child, child_id) { + if (class(child) == "list") { + if (!is.null(child$name)) { + support_id <- paste0(child_id, "s", i[[length(i)]]) + child_id <- paste0(child_id, "c", i[[length(i)]]) + n <<- n+2 + nodes[[n-1]] <<- list( + data = list(id = support_id), + # TODO: edit (x,y) according to branch_length = child$branch_length + # position = list(x = 0, y = 0), + classes = "support", + grabbable = FALSE + ) + nodes[[n]] <<- list( + data = list(id = child_id, name = child$name), + # TODO: edit (x,y) according to branch_length = child$branch_length + # position = list(x = 0, y = 0), + classes = "terminal", + grabbable = FALSE + ) + i[[length(i)]] <<- i[[length(i)]]+1 + } else { + if (!is.null(child$confidence$text)) { support_id <- paste0(child_id, "s", i[[length(i)]]) child_id <- paste0(child_id, "c", i[[length(i)]]) n <<- n+2 nodes[[n-1]] <<- list( data = list(id = support_id), # TODO: edit (x,y) according to branch_length = child$branch_length - position = list(x = 0, y = 0), + # position = list(x = 0, y = 0), classes = "support", grabbable = FALSE ) nodes[[n]] <<- list( - data = list(id = child_id, name = child$name), + data = list(id = child_id, confidence = child$confidence$text), # TODO: edit (x,y) according to branch_length = child$branch_length - position = list(x = 0, y = 0), - classes = "terminal", + # position = list(x = 0, y = 0), + classes = "nonterminal", grabbable = FALSE ) i[[length(i)]] <<- i[[length(i)]]+1 - } else { - if (!is.null(child$confidence$text)) { - support_id <- paste0(child_id, "s", i[[length(i)]]) - child_id <- paste0(child_id, "c", i[[length(i)]]) - n <<- n+2 - nodes[[n-1]] <<- list( - data = list(id = support_id), - # TODO: edit (x,y) according to branch_length = child$branch_length - position = list(x = 0, y = 0), - classes = "support", - grabbable = FALSE - ) - nodes[[n]] <<- list( - data = list(id = child_id, confidence = child$confidence$text), - # TODO: edit (x,y) according to branch_length = child$branch_length - position = list(x = 0, y = 0), - classes = "nonterminal", - grabbable = FALSE - ) - i[[length(i)]] <<- i[[length(i)]]+1 - } - i[[length(i)+1]] <<- 0 - lapply(child, explore_child, child_id=child_id) - i <<- i[-length(i)] } + i[[length(i)+1]] <<- 0 + lapply(child, explore_child, child_id=child_id) + i <<- i[-length(i)] } } - lapply(tree, explore_child, child_id="r") - - str(nodes) - print(paste("SIZE", length(nodes))) - - return(nodes) } + lapply(tree, explore_child, child_id="r") - get_terminals <- function(tree, terminals=list()) { - get_name <- function(child) { - if (class(child) == "list") { - if (!is.null(child$name)) { - terminals[[length(terminals)+1]] <<- list( - name = child$name, - branch_length = child$branch_length - ) - } else { - lapply(child, get_name) - } - } - } - lapply(tree, get_name) - return(terminals) - } - - get_col_positions <- function(tree, taxa, column_width=80) { - # note constants for drawing calculations - max_label_width <- max(unlist(lapply(taxa, function(taxon) return(nchar(taxon$name))))) - drawing_width <- column_width - max_label_width - 1 - - return(list()) - } - - get_row_positions <- function(tree, taxa) { - positions <- lapply(1:length(taxa), function(id) return(2*(id-1))) - names(positions) <- lapply(taxa, function(taxon) return(taxon$name)) - - return(list()) - } - - clean_tree <- organize_tree(tree) - taxa <- get_terminals(tree) - col_positions <- get_col_positions(tree, taxa) - row_positions <- get_row_positions(tree, taxa) - - nodes <- list() - edges <- list() + print("NODES") + str(nodes) + print(paste("SIZE", length(nodes))) + print("EDGES") + str(edges) + print(paste("SIZE", length(edges))) # TODO: remove dummy data to not overwrite outputs using functions above nodes <- list(1,2,3) edges <- list(4,5,6) + elements <- c(nodes, edges) + return(elements) + + # TODO: remove these drafts + # get_terminals <- function(tree, terminals=list()) { + # get_name <- function(child) { + # if (class(child) == "list") { + # if (!is.null(child$name)) { + # terminals[[length(terminals)+1]] <<- list( + # name = child$name, + # branch_length = child$branch_length + # ) + # } else { + # lapply(child, get_name) + # } + # } + # } + # lapply(tree, get_name) + # return(terminals) + # } + # + # get_col_positions <- function(tree, taxa, column_width=80) { + # # note constants for drawing calculations + # max_label_width <- max(unlist(lapply(taxa, function(taxon) return(nchar(taxon$name))))) + # drawing_width <- column_width - max_label_width - 1 + # + # return(list()) + # } + # + # get_row_positions <- function(tree, taxa) { + # positions <- lapply(1:length(taxa), function(id) return(2*(id-1))) + # names(positions) <- lapply(taxa, function(taxon) return(taxon$name)) + # + # return(list()) + # } + # + # taxa <- get_terminals(tree) + # col_positions <- get_col_positions(tree, taxa) + # row_positions <- get_row_positions(tree, taxa) - return (elements) } elements <- generate_elements(tree) From 6cd7fa2a9e6340b8a9b4b88f6313737b67e88bd1 Mon Sep 17 00:00:00 2001 From: ohaanika Date: Sun, 11 Aug 2019 09:28:12 -0400 Subject: [PATCH 15/22] update usage-phylogeny.R --- demosR/usage-phylogeny.R | 126 ++++++++++++++++++++++++++------------- 1 file changed, 85 insertions(+), 41 deletions(-) diff --git a/demosR/usage-phylogeny.R b/demosR/usage-phylogeny.R index 0e8834f5..829a1163 100644 --- a/demosR/usage-phylogeny.R +++ b/demosR/usage-phylogeny.R @@ -2,15 +2,14 @@ library(dash) library(dashHtmlComponents) library(dashCytoscape) library(XML) +source("demosR/dummyData.R") app <- Dash$new() tree <- xmlToList(xmlParse(file = "demos/data/apaf.xml"))$phylogeny -capture.output(tree, file = "demosR/tree.txt", append = FALSE) - -generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, - nodes=list(), edges=list(), i=list(), n=1) { +capture.output(tree, file = "demosR/treeR.txt", append = FALSE) +generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, i=list(), n=1) { # there are 31 "terminal" nodes with their respective 31 "support" nodes # and 30 "nonterminal" nodes with their respective 29 "support" nodes # since the root node does not require a preceding "support" node; @@ -18,6 +17,8 @@ generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, # and the same y position as the child clade; it is used to create # the 90 degree angle between the parent and the children; # edge config: parent -> support -> child + nodes <- list() + edges <- list() # append root element nodes[[n]] <- list( @@ -26,13 +27,16 @@ generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, classes = "nonterminal", grabbable = FALSE ) - # function to append all nodes and respective support nodes - explore_child <- function(child, child_id) { + + # append all child nodes/edges and respective support nodes/edges + explore_child <- function(child, child_id, branch_length) { if (class(child) == "list") { if (!is.null(child$name)) { + clade_id <- child_id support_id <- paste0(child_id, "s", i[[length(i)]]) child_id <- paste0(child_id, "c", i[[length(i)]]) n <<- n+2 + # support node and edge nodes[[n-1]] <<- list( data = list(id = support_id), # TODO: edit (x,y) according to branch_length = child$branch_length @@ -40,6 +44,14 @@ generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, classes = "support", grabbable = FALSE ) + edges[[n-2]] <<- list( + data = list( + source = clade_id, + target = support_id, + sourceCladeId = clade_id + ) + ) + # terminal node and edge nodes[[n]] <<- list( data = list(id = child_id, name = child$name), # TODO: edit (x,y) according to branch_length = child$branch_length @@ -47,12 +59,22 @@ generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, classes = "terminal", grabbable = FALSE ) + edges[[n-1]] <<- list( + data = list( + source = support_id, + target = child_id, + length = branch_length, + sourceCladeId = clade_id + ) + ) i[[length(i)]] <<- i[[length(i)]]+1 } else { if (!is.null(child$confidence$text)) { + clade_id <- child_id support_id <- paste0(child_id, "s", i[[length(i)]]) child_id <- paste0(child_id, "c", i[[length(i)]]) n <<- n+2 + # support node and edge nodes[[n-1]] <<- list( data = list(id = support_id), # TODO: edit (x,y) according to branch_length = child$branch_length @@ -60,6 +82,14 @@ generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, classes = "support", grabbable = FALSE ) + edges[[n-2]] <<- list( + data = list( + source = clade_id, + target = support_id, + sourceCladeId = clade_id + ) + ) + # nonterminal node and edge nodes[[n]] <<- list( data = list(id = child_id, confidence = child$confidence$text), # TODO: edit (x,y) according to branch_length = child$branch_length @@ -67,26 +97,30 @@ generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, classes = "nonterminal", grabbable = FALSE ) + edges[[n-1]] <<- list( + data = list( + source = support_id, + target = child_id, + length = branch_length, + sourceCladeId = clade_id + ) + ) i[[length(i)]] <<- i[[length(i)]]+1 } i[[length(i)+1]] <<- 0 - lapply(child, explore_child, child_id=child_id) + lapply(child, explore_child, child_id=child_id, branch_length=child$branch_length) i <<- i[-length(i)] } } } - lapply(tree, explore_child, child_id="r") + lapply(tree, explore_child, child_id="r", branch_length=0) - print("NODES") - str(nodes) - print(paste("SIZE", length(nodes))) - print("EDGES") - str(edges) - print(paste("SIZE", length(edges))) - - # TODO: remove dummy data to not overwrite outputs using functions above - nodes <- list(1,2,3) - edges <- list(4,5,6) + # print("NODES") + # str(nodes) + # print(paste("SIZE", length(nodes))) + # print("EDGES") + # str(edges) + # print(paste("SIZE", length(edges))) elements <- c(nodes, edges) return(elements) @@ -131,38 +165,41 @@ generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, } elements <- generate_elements(tree) - -layout <- list("name" = "preset") +# print("ELEMENTS") +# str(elements) +# print(paste("SIZE", length(elements))) stylesheet <- list( list( - "selector" = ".nonterminal", + "selector" = "edge", "style" = list( - "label" = "data(confidence)", - "background-opacity" = 0, - "text-halign" = "left", - "text-valign" = "top" + "source-endpoint" = "inside-to-node", + "target-endpoint" = "inside-to-node" ) ), list( "selector" = ".support", - "style" = list("background-opacity" = 0) + "style" = list( + "background-opacity" = 0 + ) ), list( - "selector" = "edge", + "selector" = ".nonterminal", "style" = list( - "source-endpoint" = "inside-to-node", - "target-endpoint" = "inside-to-node" + "label" = "data(confidence)", + "text-valign" = "top", + "text-halign" = "left", + "background-opacity" = 0 ) ), list( "selector" = ".terminal", "style" = list( "label" = "data(name)", - "width" = 10, - "height" = 10, "text-valign" = "center", "text-halign" = "right", + "width" = 10, + "height" = 10, "background-color" = "#222222" ) ) @@ -173,9 +210,11 @@ app$layout( list( cytoCytoscape( id = "cytoscape", - elements = list(), # TODO: change to "elements" once defined + elements = dummyElements, # TODO: change to "elements" once defined stylesheet = stylesheet, - layout = layout, + layout = list( + "name" = "preset" + ), style = list( "height" = "95vh", "width" = "100%" @@ -187,17 +226,22 @@ app$layout( app$callback( output = list(id = "cytoscape", property = "stylesheet"), - params = list( - input(id = "cytoscape", property = "mouseoverEdgeData") - ), - function(data) { - if (is.null(data)) { + params = list(input(id = "cytoscape", property = "mouseoverEdgeData")), + function(edgeData) { + if (is.null(edgeData)) { return(stylesheet) } - return( - "" + val <- ifelse(grepl("s", edgeData$source), strsplit(edgeData$source, "s")[[1]], edgeData$source) + children_style = list( + list( + selector = sprintf("edge[source *= '%s']", val), + style = list( + 'line-color' = 'blue' + ) + ) ) + return(c(stylesheet, children_style)) } ) -# app$run_server() +app$run_server(port = "8080", debug = TRUE) From 8ee1c00464c240ce3c839bf3dca53d572928a072 Mon Sep 17 00:00:00 2001 From: ohaanika Date: Sun, 11 Aug 2019 09:35:21 -0400 Subject: [PATCH 16/22] update usage-phylogeny.R --- demosR/usage-phylogeny.R | 26 +++++++++++++++----------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/demosR/usage-phylogeny.R b/demosR/usage-phylogeny.R index 829a1163..09bd13c9 100644 --- a/demosR/usage-phylogeny.R +++ b/demosR/usage-phylogeny.R @@ -115,17 +115,7 @@ generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, i=list(), } lapply(tree, explore_child, child_id="r", branch_length=0) - # print("NODES") - # str(nodes) - # print(paste("SIZE", length(nodes))) - # print("EDGES") - # str(edges) - # print(paste("SIZE", length(edges))) - - elements <- c(nodes, edges) - return(elements) - - # TODO: remove these drafts + # TODO: remove these draft functions and respective outputs # get_terminals <- function(tree, terminals=list()) { # get_name <- function(child) { # if (class(child) == "list") { @@ -162,9 +152,23 @@ generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, i=list(), # col_positions <- get_col_positions(tree, taxa) # row_positions <- get_row_positions(tree, taxa) + # TODO: delete test print statements + # print("NODES") + # str(nodes) + # print(paste("SIZE", length(nodes))) + # print("EDGES") + # str(edges) + # print(paste("SIZE", length(edges))) + + # TODO: add remaining attributes for nodes (i.e. position) in function the explore_child + elements <- c(nodes, edges) + + return(elements) } elements <- generate_elements(tree) + +# TODO: delete test print statements # print("ELEMENTS") # str(elements) # print(paste("SIZE", length(elements))) From a6b8eacf84549994e0f379b8adf98f9c20a67b88 Mon Sep 17 00:00:00 2001 From: ohaanika Date: Sun, 11 Aug 2019 09:45:26 -0400 Subject: [PATCH 17/22] update usage-phylogeny.R, add temporary files --- demosR/phylogeny/dummyData.R | 248 +++ demosR/phylogeny/elementsPy.txt | 254 +++ demosR/phylogeny/elementsR.txt | 248 +++ demosR/phylogeny/treePy.txt | 140 ++ demosR/phylogeny/treeR.txt | 2881 +++++++++++++++++++++++++++++++ demosR/usage-phylogeny.R | 5 +- 6 files changed, 3774 insertions(+), 2 deletions(-) create mode 100644 demosR/phylogeny/dummyData.R create mode 100644 demosR/phylogeny/elementsPy.txt create mode 100644 demosR/phylogeny/elementsR.txt create mode 100644 demosR/phylogeny/treePy.txt create mode 100644 demosR/phylogeny/treeR.txt diff --git a/demosR/phylogeny/dummyData.R b/demosR/phylogeny/dummyData.R new file mode 100644 index 00000000..88dd34aa --- /dev/null +++ b/demosR/phylogeny/dummyData.R @@ -0,0 +1,248 @@ +dummyNodes <- list( + list(data = list(id = 'r'), position = list('x' = 30, 'y' = 1200), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rs0'), position = list('x' = 30, 'y' = 840), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0', confidence = 89.0), position = list('x' = 180, 'y' = 840), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0s0'), position = list('x' = 180, 'y' = 660), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0', confidence = 32.0), position = list('x' = 240, 'y' = 660), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0s0'), position = list('x' = 240, 'y' = 540), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0', confidence = 100.0), position = list('x' = 450, 'y' = 540), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0s0'), position = list('x' = 450, 'y' = 390), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0', confidence = 89.0), position = list('x' = 630, 'y' = 390), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0s0'), position = list('x' = 630, 'y' = 270), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0', confidence = 100.0), position = list('x' = 870, 'y' = 270), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0s0'), position = list('x' = 870, 'y' = 180), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0', confidence = 100.0), position = list('x' = 930, 'y' = 180), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0s0'), position = list('x' = 930, 'y' = 120), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0', confidence = 43.0), position = list('x' = 960, 'y' = 120), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0s0'), position = list('x' = 960, 'y' = 60), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0', confidence = 100.0), position = list('x' = 1020, 'y' = 60), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0s0'), position = list('x' = 1020, 'y' = 30), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0c0', confidence = 88.0), position = list('x' = 1020, 'y' = 30), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0c0s0'), position = list('x' = 1020, 'y' = 0), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0c0c0', name = '22_MOUSE'), position = list('x' = 1080, 'y' = 0), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0c0s1'), position = list('x' = 1020, 'y' = 60), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0c0c1', name = 'Apaf-1_HUMAN'), position = list('x' = 1050, 'y' = 60), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0s1'), position = list('x' = 1020, 'y' = 120), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0c1', name = '12_CANFA'), position = list('x' = 1050, 'y' = 120), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0s1'), position = list('x' = 960, 'y' = 180), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c1', name = '11_CHICK'), position = list('x' = 1080, 'y' = 180), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0s1'), position = list('x' = 930, 'y' = 240), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c1', name = '16_XENLA'), position = list('x' = 1290, 'y' = 240), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0s1'), position = list('x' = 870, 'y' = 360), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1', confidence = 100.0), position = list('x' = 1020, 'y' = 360), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1s0'), position = list('x' = 1020, 'y' = 330), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1c0', confidence = 100.0), position = list('x' = 1110, 'y' = 330), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1c0s0'), position = list('x' = 1110, 'y' = 300), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1c0c0', name = '14_FUGRU'), position = list('x' = 1140, 'y' = 300), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1c0s1'), position = list('x' = 1110, 'y' = 360), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1c0c1', name = '15_TETNG'), position = list('x' = 1200, 'y' = 360), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1s1'), position = list('x' = 1020, 'y' = 420), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1c1', name = '17_BRARE'), position = list('x' = 1170, 'y' = 420), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0s1'), position = list('x' = 630, 'y' = 540), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1', confidence = 53.0), position = list('x' = 660, 'y' = 540), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1s0'), position = list('x' = 660, 'y' = 510), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1c0', confidence = 68.0), position = list('x' = 750, 'y' = 510), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1c0s0'), position = list('x' = 750, 'y' = 480), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1c0c0', name = '1_BRAFL'), position = list('x' = 960, 'y' = 480), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1c0s1'), position = list('x' = 750, 'y' = 540), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1c0c1', name = '18_NEMVE'), position = list('x' = 1050, 'y' = 540), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1s1'), position = list('x' = 660, 'y' = 600), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1c1', name = '23_STRPU'), position = list('x' = 1050, 'y' = 600), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0s1'), position = list('x' = 450, 'y' = 690), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c1', confidence = 100.0), position = list('x' = 750, 'y' = 690), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c1s0'), position = list('x' = 750, 'y' = 660), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c1c0', name = '26_STRPU'), position = list('x' = 1050, 'y' = 660), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c1s1'), position = list('x' = 750, 'y' = 720), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c1c1', name = '25_STRPU'), position = list('x' = 1020, 'y' = 720), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0s1'), position = list('x' = 240, 'y' = 810), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c1', confidence = 100.0), position = list('x' = 1320, 'y' = 810), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c1s0'), position = list('x' = 1320, 'y' = 780), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c1c0', name = 'CED4_CAEEL'), position = list('x' = 1440, 'y' = 780), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c1s1'), position = list('x' = 1320, 'y' = 840), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c1c1', name = '31_CAEBR'), position = list('x' = 1380, 'y' = 840), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0s1'), position = list('x' = 180, 'y' = 1020), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c1', confidence = 45.0), position = list('x' = 270, 'y' = 1020), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c1s0'), position = list('x' = 270, 'y' = 960), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c1c0', confidence = 95.0), position = list('x' = 480, 'y' = 960), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c1c0s0'), position = list('x' = 480, 'y' = 930), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c1c0c0', confidence = 100.0), position = list('x' = 1140, 'y' = 930), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c1c0c0s0'), position = list('x' = 1140, 'y' = 900), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c1c0c0c0', name = '28_DROPS'), position = list('x' = 1260, 'y' = 900), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c1c0c0s1'), position = list('x' = 1140, 'y' = 960), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c1c0c0c1', name = 'Dark_DROME'), position = list('x' = 1290, 'y' = 960), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c1c0s1'), position = list('x' = 480, 'y' = 1020), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c1c0c1', name = '29_AEDAE'), position = list('x' = 1200, 'y' = 1020), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c1s1'), position = list('x' = 270, 'y' = 1080), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c1c1', name = '30_TRICA'), position = list('x' = 1080, 'y' = 1080), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rs1'), position = list('x' = 30, 'y' = 1590), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1', confidence = 89.0), position = list('x' = 180, 'y' = 1590), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1s0'), position = list('x' = 180, 'y' = 1440), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0', confidence = 64.0), position = list('x' = 300, 'y' = 1440), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c0s0'), position = list('x' = 300, 'y' = 1350), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0', confidence = 100.0), position = list('x' = 750, 'y' = 1350), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0s0'), position = list('x' = 750, 'y' = 1260), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0', confidence = 46.0), position = list('x' = 840, 'y' = 1260), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0s0'), position = list('x' = 840, 'y' = 1200), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0', confidence = 61.0), position = list('x' = 1020, 'y' = 1200), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0s0'), position = list('x' = 1020, 'y' = 1170), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0c0', confidence = 100.0), position = list('x' = 1800, 'y' = 1170), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0c0s0'), position = list('x' = 1800, 'y' = 1140), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0c0c0', name = '34_BRAFL'), position = list('x' = 1860, 'y' = 1140), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0c0s1'), position = list('x' = 1800, 'y' = 1200), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0c0c1', name = '35_BRAFL'), position = list('x' = 1860, 'y' = 1200), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0s1'), position = list('x' = 1020, 'y' = 1260), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0c1', name = '8_BRAFL'), position = list('x' = 1500, 'y' = 1260), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0s1'), position = list('x' = 840, 'y' = 1350), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c1', confidence = 84.0), position = list('x' = 1080, 'y' = 1350), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c1s0'), position = list('x' = 1080, 'y' = 1320), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c1c0', name = '20_NEMVE'), position = list('x' = 1680, 'y' = 1320), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c1s1'), position = list('x' = 1080, 'y' = 1380), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c1c1', name = '21_NEMVE'), position = list('x' = 1890, 'y' = 1380), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0s1'), position = list('x' = 750, 'y' = 1440), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c1', name = '9_BRAFL'), position = list('x' = 1680, 'y' = 1440), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c0s1'), position = list('x' = 300, 'y' = 1560), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c1', confidence = 98.0), position = list('x' = 600, 'y' = 1560), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c1s0'), position = list('x' = 600, 'y' = 1530), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c1c0', confidence = 95.0), position = list('x' = 780, 'y' = 1530), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c1c0s0'), position = list('x' = 780, 'y' = 1500), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c1c0c0', name = '3_BRAFL'), position = list('x' = 1200, 'y' = 1500), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c1c0s1'), position = list('x' = 780, 'y' = 1560), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c1c0c1', name = '2_BRAFL'), position = list('x' = 1320, 'y' = 1560), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c1s1'), position = list('x' = 600, 'y' = 1620), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c1c1', name = '19_NEMVE'), position = list('x' = 1080, 'y' = 1620), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1s1'), position = list('x' = 180, 'y' = 1740), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c1', confidence = 92.0), position = list('x' = 540, 'y' = 1740), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c1s0'), position = list('x' = 540, 'y' = 1710), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c1c0', confidence = 100.0), position = list('x' = 1290, 'y' = 1710), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c1c0s0'), position = list('x' = 1290, 'y' = 1680), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c1c0c0', name = '37_BRAFL'), position = list('x' = 1470, 'y' = 1680), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c1c0s1'), position = list('x' = 1290, 'y' = 1740), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c1c0c1', name = '36_BRAFL'), position = list('x' = 1440, 'y' = 1740), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c1s1'), position = list('x' = 540, 'y' = 1800), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c1c1', name = '33_BRAFL'), position = list('x' = 1230, 'y' = 1800), classes = 'terminal', grabbable = FALSE) +) + +dummyEdges <- list( + list(data = list(source = 'r', target = 'rs0', sourceCladeId = 'r')), + list(data = list(source = 'rs0', target = 'rc0', length = 0, sourceCladeId = 'r')), + list(data = list(source = 'rc0', target = 'rc0s0', sourceCladeId = 'rc0')), + list(data = list(source = 'rc0s0', target = 'rc0c0', length = 0.18105, sourceCladeId = 'rc0')), + list(data = list(source = 'rc0c0', target = 'rc0c0s0', sourceCladeId = 'rc0c0')), + list(data = list(source = 'rc0c0s0', target = 'rc0c0c0', length = 0.07466, sourceCladeId = 'rc0c0')), + list(data = list(source = 'rc0c0c0', target = 'rc0c0c0s0', sourceCladeId = 'rc0c0c0')), + list(data = list(source = 'rc0c0c0s0', target = 'rc0c0c0c0', length = 0.26168, sourceCladeId = 'rc0c0c0')), + list(data = list(source = 'rc0c0c0c0', target = 'rc0c0c0c0s0', sourceCladeId = 'rc0c0c0c0')), + list(data = list(source = 'rc0c0c0c0s0', target = 'rc0c0c0c0c0', length = 0.22058, sourceCladeId = 'rc0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0', target = 'rc0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0s0', target = 'rc0c0c0c0c0c0', length = 0.28901, sourceCladeId = 'rc0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0', target = 'rc0c0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0s0', target = 'rc0c0c0c0c0c0c0', length = 0.06584, sourceCladeId = 'rc0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0s0', target = 'rc0c0c0c0c0c0c0c0', length = 0.02309, sourceCladeId = 'rc0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0c0s0', target = 'rc0c0c0c0c0c0c0c0c0', length = 0.0746, sourceCladeId = 'rc0c0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0c0c0s0', target = 'rc0c0c0c0c0c0c0c0c0c0', length = 0.02365, sourceCladeId = 'rc0c0c0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0c0c0s1', target = 'rc0c0c0c0c0c0c0c0c0c1', length = 0.02365, sourceCladeId = 'rc0c0c0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0c0s1', target = 'rc0c0c0c0c0c0c0c0c1', length = 0.0746, sourceCladeId = 'rc0c0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0s1', target = 'rc0c0c0c0c0c0c0c1', length = 0.02309, sourceCladeId = 'rc0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0', target = 'rc0c0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0s1', target = 'rc0c0c0c0c0c0c1', length = 0.06584, sourceCladeId = 'rc0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0', target = 'rc0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0s1', target = 'rc0c0c0c0c0c1', length = 0.28901, sourceCladeId = 'rc0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c1', target = 'rc0c0c0c0c0c1s0', sourceCladeId = 'rc0c0c0c0c0c1')), + list(data = list(source = 'rc0c0c0c0c0c1s0', target = 'rc0c0c0c0c0c1c0', length = 0.17031, sourceCladeId = 'rc0c0c0c0c0c1')), + list(data = list(source = 'rc0c0c0c0c0c1c0', target = 'rc0c0c0c0c0c1c0s0', sourceCladeId = 'rc0c0c0c0c0c1c0')), + list(data = list(source = 'rc0c0c0c0c0c1c0s0', target = 'rc0c0c0c0c0c1c0c0', length = 0.10929, sourceCladeId = 'rc0c0c0c0c0c1c0')), + list(data = list(source = 'rc0c0c0c0c0c1c0', target = 'rc0c0c0c0c0c1c0s1', sourceCladeId = 'rc0c0c0c0c0c1c0')), + list(data = list(source = 'rc0c0c0c0c0c1c0s1', target = 'rc0c0c0c0c0c1c0c1', length = 0.10929, sourceCladeId = 'rc0c0c0c0c0c1c0')), + list(data = list(source = 'rc0c0c0c0c0c1', target = 'rc0c0c0c0c0c1s1', sourceCladeId = 'rc0c0c0c0c0c1')), + list(data = list(source = 'rc0c0c0c0c0c1s1', target = 'rc0c0c0c0c0c1c1', length = 0.17031, sourceCladeId = 'rc0c0c0c0c0c1')), + list(data = list(source = 'rc0c0c0c0', target = 'rc0c0c0c0s1', sourceCladeId = 'rc0c0c0c0')), + list(data = list(source = 'rc0c0c0c0s1', target = 'rc0c0c0c0c1', length = 0.22058, sourceCladeId = 'rc0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c1', target = 'rc0c0c0c0c1s0', sourceCladeId = 'rc0c0c0c0c1')), + list(data = list(source = 'rc0c0c0c0c1s0', target = 'rc0c0c0c0c1c0', length = 0.01594, sourceCladeId = 'rc0c0c0c0c1')), + list(data = list(source = 'rc0c0c0c0c1c0', target = 'rc0c0c0c0c1c0s0', sourceCladeId = 'rc0c0c0c0c1c0')), + list(data = list(source = 'rc0c0c0c0c1c0s0', target = 'rc0c0c0c0c1c0c0', length = 0.10709, sourceCladeId = 'rc0c0c0c0c1c0')), + list(data = list(source = 'rc0c0c0c0c1c0', target = 'rc0c0c0c0c1c0s1', sourceCladeId = 'rc0c0c0c0c1c0')), + list(data = list(source = 'rc0c0c0c0c1c0s1', target = 'rc0c0c0c0c1c0c1', length = 0.10709, sourceCladeId = 'rc0c0c0c0c1c0')), + list(data = list(source = 'rc0c0c0c0c1', target = 'rc0c0c0c0c1s1', sourceCladeId = 'rc0c0c0c0c1')), + list(data = list(source = 'rc0c0c0c0c1s1', target = 'rc0c0c0c0c1c1', length = 0.01594, sourceCladeId = 'rc0c0c0c0c1')), + list(data = list(source = 'rc0c0c0', target = 'rc0c0c0s1', sourceCladeId = 'rc0c0c0')), + list(data = list(source = 'rc0c0c0s1', target = 'rc0c0c0c1', length = 0.26168, sourceCladeId = 'rc0c0c0')), + list(data = list(source = 'rc0c0c0c1', target = 'rc0c0c0c1s0', sourceCladeId = 'rc0c0c0c1')), + list(data = list(source = 'rc0c0c0c1s0', target = 'rc0c0c0c1c0', length = 0.34475, sourceCladeId = 'rc0c0c0c1')), + list(data = list(source = 'rc0c0c0c1', target = 'rc0c0c0c1s1', sourceCladeId = 'rc0c0c0c1')), + list(data = list(source = 'rc0c0c0c1s1', target = 'rc0c0c0c1c1', length = 0.34475, sourceCladeId = 'rc0c0c0c1')), + list(data = list(source = 'rc0c0', target = 'rc0c0s1', sourceCladeId = 'rc0c0')), + list(data = list(source = 'rc0c0s1', target = 'rc0c0c1', length = 0.07466, sourceCladeId = 'rc0c0')), + list(data = list(source = 'rc0c0c1', target = 'rc0c0c1s0', sourceCladeId = 'rc0c0c1')), + list(data = list(source = 'rc0c0c1s0', target = 'rc0c0c1c0', length = 1.31498, sourceCladeId = 'rc0c0c1')), + list(data = list(source = 'rc0c0c1', target = 'rc0c0c1s1', sourceCladeId = 'rc0c0c1')), + list(data = list(source = 'rc0c0c1s1', target = 'rc0c0c1c1', length = 1.31498, sourceCladeId = 'rc0c0c1')), + list(data = list(source = 'rc0', target = 'rc0s1', sourceCladeId = 'rc0')), + list(data = list(source = 'rc0s1', target = 'rc0c1', length = 0.18105, sourceCladeId = 'rc0')), + list(data = list(source = 'rc0c1', target = 'rc0c1s0', sourceCladeId = 'rc0c1')), + list(data = list(source = 'rc0c1s0', target = 'rc0c1c0', length = 0.13172, sourceCladeId = 'rc0c1')), + list(data = list(source = 'rc0c1c0', target = 'rc0c1c0s0', sourceCladeId = 'rc0c1c0')), + list(data = list(source = 'rc0c1c0s0', target = 'rc0c1c0c0', length = 0.24915, sourceCladeId = 'rc0c1c0')), + list(data = list(source = 'rc0c1c0c0', target = 'rc0c1c0c0s0', sourceCladeId = 'rc0c1c0c0')), + list(data = list(source = 'rc0c1c0c0s0', target = 'rc0c1c0c0c0', length = 0.76898, sourceCladeId = 'rc0c1c0c0')), + list(data = list(source = 'rc0c1c0c0', target = 'rc0c1c0c0s1', sourceCladeId = 'rc0c1c0c0')), + list(data = list(source = 'rc0c1c0c0s1', target = 'rc0c1c0c0c1', length = 0.76898, sourceCladeId = 'rc0c1c0c0')), + list(data = list(source = 'rc0c1c0', target = 'rc0c1c0s1', sourceCladeId = 'rc0c1c0')), + list(data = list(source = 'rc0c1c0s1', target = 'rc0c1c0c1', length = 0.24915, sourceCladeId = 'rc0c1c0')), + list(data = list(source = 'rc0c1', target = 'rc0c1s1', sourceCladeId = 'rc0c1')), + list(data = list(source = 'rc0c1s1', target = 'rc0c1c1', length = 0.13172, sourceCladeId = 'rc0c1')), + list(data = list(source = 'r', target = 'rs1', sourceCladeId = 'r')), + list(data = list(source = 'rs1', target = 'rc1', length = 0, sourceCladeId = 'r')), + list(data = list(source = 'rc1', target = 'rc1s0', sourceCladeId = 'rc1')), + list(data = list(source = 'rc1s0', target = 'rc1c0', length = 0.18105, sourceCladeId = 'rc1')), + list(data = list(source = 'rc1c0', target = 'rc1c0s0', sourceCladeId = 'rc1c0')), + list(data = list(source = 'rc1c0s0', target = 'rc1c0c0', length = 0.15891, sourceCladeId = 'rc1c0')), + list(data = list(source = 'rc1c0c0', target = 'rc1c0c0s0', sourceCladeId = 'rc1c0c0')), + list(data = list(source = 'rc1c0c0s0', target = 'rc1c0c0c0', length = 0.54836, sourceCladeId = 'rc1c0c0')), + list(data = list(source = 'rc1c0c0c0', target = 'rc1c0c0c0s0', sourceCladeId = 'rc1c0c0c0')), + list(data = list(source = 'rc1c0c0c0s0', target = 'rc1c0c0c0c0', length = 0.09305, sourceCladeId = 'rc1c0c0c0')), + list(data = list(source = 'rc1c0c0c0c0', target = 'rc1c0c0c0c0s0', sourceCladeId = 'rc1c0c0c0c0')), + list(data = list(source = 'rc1c0c0c0c0s0', target = 'rc1c0c0c0c0c0', length = 0.21648, sourceCladeId = 'rc1c0c0c0c0')), + list(data = list(source = 'rc1c0c0c0c0c0', target = 'rc1c0c0c0c0c0s0', sourceCladeId = 'rc1c0c0c0c0c0')), + list(data = list(source = 'rc1c0c0c0c0c0s0', target = 'rc1c0c0c0c0c0c0', length = 0.93134, sourceCladeId = 'rc1c0c0c0c0c0')), + list(data = list(source = 'rc1c0c0c0c0c0', target = 'rc1c0c0c0c0c0s1', sourceCladeId = 'rc1c0c0c0c0c0')), + list(data = list(source = 'rc1c0c0c0c0c0s1', target = 'rc1c0c0c0c0c0c1', length = 0.93134, sourceCladeId = 'rc1c0c0c0c0c0')), + list(data = list(source = 'rc1c0c0c0c0', target = 'rc1c0c0c0c0s1', sourceCladeId = 'rc1c0c0c0c0')), + list(data = list(source = 'rc1c0c0c0c0s1', target = 'rc1c0c0c0c0c1', length = 0.21648, sourceCladeId = 'rc1c0c0c0c0')), + list(data = list(source = 'rc1c0c0c0', target = 'rc1c0c0c0s1', sourceCladeId = 'rc1c0c0c0')), + list(data = list(source = 'rc1c0c0c0s1', target = 'rc1c0c0c0c1', length = 0.09305, sourceCladeId = 'rc1c0c0c0')), + list(data = list(source = 'rc1c0c0c0c1', target = 'rc1c0c0c0c1s0', sourceCladeId = 'rc1c0c0c0c1')), + list(data = list(source = 'rc1c0c0c0c1s0', target = 'rc1c0c0c0c1c0', length = 0.28437, sourceCladeId = 'rc1c0c0c0c1')), + list(data = list(source = 'rc1c0c0c0c1', target = 'rc1c0c0c0c1s1', sourceCladeId = 'rc1c0c0c0c1')), + list(data = list(source = 'rc1c0c0c0c1s1', target = 'rc1c0c0c0c1c1', length = 0.28437, sourceCladeId = 'rc1c0c0c0c1')), + list(data = list(source = 'rc1c0c0', target = 'rc1c0c0s1', sourceCladeId = 'rc1c0c0')), + list(data = list(source = 'rc1c0c0s1', target = 'rc1c0c0c1', length = 0.54836, sourceCladeId = 'rc1c0c0')), + list(data = list(source = 'rc1c0', target = 'rc1c0s1', sourceCladeId = 'rc1c0')), + list(data = list(source = 'rc1c0s1', target = 'rc1c0c1', length = 0.15891, sourceCladeId = 'rc1c0')), + list(data = list(source = 'rc1c0c1', target = 'rc1c0c1s0', sourceCladeId = 'rc1c0c1')), + list(data = list(source = 'rc1c0c1s0', target = 'rc1c0c1c0', length = 0.34914, sourceCladeId = 'rc1c0c1')), + list(data = list(source = 'rc1c0c1c0', target = 'rc1c0c1c0s0', sourceCladeId = 'rc1c0c1c0')), + list(data = list(source = 'rc1c0c1c0s0', target = 'rc1c0c1c0c0', length = 0.22189, sourceCladeId = 'rc1c0c1c0')), + list(data = list(source = 'rc1c0c1c0', target = 'rc1c0c1c0s1', sourceCladeId = 'rc1c0c1c0')), + list(data = list(source = 'rc1c0c1c0s1', target = 'rc1c0c1c0c1', length = 0.22189, sourceCladeId = 'rc1c0c1c0')), + list(data = list(source = 'rc1c0c1', target = 'rc1c0c1s1', sourceCladeId = 'rc1c0c1')), + list(data = list(source = 'rc1c0c1s1', target = 'rc1c0c1c1', length = 0.34914, sourceCladeId = 'rc1c0c1')), + list(data = list(source = 'rc1', target = 'rc1s1', sourceCladeId = 'rc1')), + list(data = list(source = 'rc1s1', target = 'rc1c1', length = 0.18105, sourceCladeId = 'rc1')), + list(data = list(source = 'rc1c1', target = 'rc1c1s0', sourceCladeId = 'rc1c1')), + list(data = list(source = 'rc1c1s0', target = 'rc1c1c0', length = 0.43438, sourceCladeId = 'rc1c1')), + list(data = list(source = 'rc1c1c0', target = 'rc1c1c0s0', sourceCladeId = 'rc1c1c0')), + list(data = list(source = 'rc1c1c0s0', target = 'rc1c1c0c0', length = 0.92214, sourceCladeId = 'rc1c1c0')), + list(data = list(source = 'rc1c1c0', target = 'rc1c1c0s1', sourceCladeId = 'rc1c1c0')), + list(data = list(source = 'rc1c1c0s1', target = 'rc1c1c0c1', length = 0.92214, sourceCladeId = 'rc1c1c0')), + list(data = list(source = 'rc1c1', target = 'rc1c1s1', sourceCladeId = 'rc1c1')), + list(data = list(source = 'rc1c1s1', target = 'rc1c1c1', length = 0.43438, sourceCladeId = 'rc1c1')) +) + +dummyElements <- c(dummyNodes, dummyEdges) diff --git a/demosR/phylogeny/elementsPy.txt b/demosR/phylogeny/elementsPy.txt new file mode 100644 index 00000000..7dc27e18 --- /dev/null +++ b/demosR/phylogeny/elementsPy.txt @@ -0,0 +1,254 @@ +[ + +# NODES +{'data': {'id': 'r'}, 'position': {'x': 30, 'y': 1200}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rs0'}, 'position': {'x': 30, 'y': 840}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0', 'confidence': 89.0}, 'position': {'x': 180, 'y': 840}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0s0'}, 'position': {'x': 180, 'y': 660}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0', 'confidence': 32.0}, 'position': {'x': 240, 'y': 660}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0c0s0'}, 'position': {'x': 240, 'y': 540}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0', 'confidence': 100.0}, 'position': {'x': 450, 'y': 540}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0s0'}, 'position': {'x': 450, 'y': 390}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0', 'confidence': 89.0}, 'position': {'x': 630, 'y': 390}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0s0'}, 'position': {'x': 630, 'y': 270}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c0', 'confidence': 100.0}, 'position': {'x': 870, 'y': 270}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c0s0'}, 'position': {'x': 870, 'y': 180}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c0c0', 'confidence': 100.0}, 'position': {'x': 930, 'y': 180}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c0c0s0'}, 'position': {'x': 930, 'y': 120}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c0c0c0', 'confidence': 43.0}, 'position': {'x': 960, 'y': 120}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c0c0c0s0'}, 'position': {'x': 960, 'y': 60}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c0c0c0c0', 'confidence': 100.0}, 'position': {'x': 1020, 'y': 60}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c0c0c0c0s0'}, 'position': {'x': 1020, 'y': 30}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c0c0c0c0c0', 'confidence': 88.0}, 'position': {'x': 1020, 'y': 30}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c0c0c0c0c0s0'}, 'position': {'x': 1020, 'y': 0}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c0c0c0c0c0c0', 'name': '22_MOUSE'}, 'position': {'x': 1080, 'y': 0}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c0c0c0c0c0s1'}, 'position': {'x': 1020, 'y': 60}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c0c0c0c0c0c1', 'name': 'Apaf-1_HUMAN'}, 'position': {'x': 1050, 'y': 60}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c0c0c0c0s1'}, 'position': {'x': 1020, 'y': 120}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c0c0c0c0c1', 'name': '12_CANFA'}, 'position': {'x': 1050, 'y': 120}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c0c0c0s1'}, 'position': {'x': 960, 'y': 180}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c0c0c0c1', 'name': '11_CHICK'}, 'position': {'x': 1080, 'y': 180}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c0c0s1'}, 'position': {'x': 930, 'y': 240}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c0c0c1', 'name': '16_XENLA'}, 'position': {'x': 1290, 'y': 240}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c0s1'}, 'position': {'x': 870, 'y': 360}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c0c1', 'confidence': 100.0}, 'position': {'x': 1020, 'y': 360}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c0c1s0'}, 'position': {'x': 1020, 'y': 330}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c0c1c0', 'confidence': 100.0}, 'position': {'x': 1110, 'y': 330}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c0c1c0s0'}, 'position': {'x': 1110, 'y': 300}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c0c1c0c0', 'name': '14_FUGRU'}, 'position': {'x': 1140, 'y': 300}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c0c1c0s1'}, 'position': {'x': 1110, 'y': 360}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c0c1c0c1', 'name': '15_TETNG'}, 'position': {'x': 1200, 'y': 360}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c0c1s1'}, 'position': {'x': 1020, 'y': 420}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c0c1c1', 'name': '17_BRARE'}, 'position': {'x': 1170, 'y': 420}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0s1'}, 'position': {'x': 630, 'y': 540}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c1', 'confidence': 53.0}, 'position': {'x': 660, 'y': 540}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c1s0'}, 'position': {'x': 660, 'y': 510}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c1c0', 'confidence': 68.0}, 'position': {'x': 750, 'y': 510}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c1c0s0'}, 'position': {'x': 750, 'y': 480}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c1c0c0', 'name': '1_BRAFL'}, 'position': {'x': 960, 'y': 480}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c1c0s1'}, 'position': {'x': 750, 'y': 540}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c1c0c1', 'name': '18_NEMVE'}, 'position': {'x': 1050, 'y': 540}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c0c1s1'}, 'position': {'x': 660, 'y': 600}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c0c1c1', 'name': '23_STRPU'}, 'position': {'x': 1050, 'y': 600}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0s1'}, 'position': {'x': 450, 'y': 690}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c1', 'confidence': 100.0}, 'position': {'x': 750, 'y': 690}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c1s0'}, 'position': {'x': 750, 'y': 660}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c1c0', 'name': '26_STRPU'}, 'position': {'x': 1050, 'y': 660}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c0c1s1'}, 'position': {'x': 750, 'y': 720}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c0c1c1', 'name': '25_STRPU'}, 'position': {'x': 1020, 'y': 720}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0c0s1'}, 'position': {'x': 240, 'y': 810}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c1', 'confidence': 100.0}, 'position': {'x': 1320, 'y': 810}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c1s0'}, 'position': {'x': 1320, 'y': 780}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c1c0', 'name': 'CED4_CAEEL'}, 'position': {'x': 1440, 'y': 780}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0c0c1s1'}, 'position': {'x': 1320, 'y': 840}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c0c1c1', 'name': '31_CAEBR'}, 'position': {'x': 1380, 'y': 840}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0s1'}, 'position': {'x': 180, 'y': 1020}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c1', 'confidence': 45.0}, 'position': {'x': 270, 'y': 1020}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0c1s0'}, 'position': {'x': 270, 'y': 960}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c1c0', 'confidence': 95.0}, 'position': {'x': 480, 'y': 960}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0c1c0s0'}, 'position': {'x': 480, 'y': 930}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c1c0c0', 'confidence': 100.0}, 'position': {'x': 1140, 'y': 930}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc0c1c0c0s0'}, 'position': {'x': 1140, 'y': 900}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c1c0c0c0', 'name': '28_DROPS'}, 'position': {'x': 1260, 'y': 900}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0c1c0c0s1'}, 'position': {'x': 1140, 'y': 960}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c1c0c0c1', 'name': 'Dark_DROME'}, 'position': {'x': 1290, 'y': 960}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0c1c0s1'}, 'position': {'x': 480, 'y': 1020}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c1c0c1', 'name': '29_AEDAE'}, 'position': {'x': 1200, 'y': 1020}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc0c1s1'}, 'position': {'x': 270, 'y': 1080}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc0c1c1', 'name': '30_TRICA'}, 'position': {'x': 1080, 'y': 1080}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rs1'}, 'position': {'x': 30, 'y': 1590}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1', 'confidence': 89.0}, 'position': {'x': 180, 'y': 1590}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc1s0'}, 'position': {'x': 180, 'y': 1440}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c0', 'confidence': 64.0}, 'position': {'x': 300, 'y': 1440}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc1c0s0'}, 'position': {'x': 300, 'y': 1350}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c0c0', 'confidence': 100.0}, 'position': {'x': 750, 'y': 1350}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc1c0c0s0'}, 'position': {'x': 750, 'y': 1260}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c0c0c0', 'confidence': 46.0}, 'position': {'x': 840, 'y': 1260}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc1c0c0c0s0'}, 'position': {'x': 840, 'y': 1200}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c0c0c0c0', 'confidence': 61.0}, 'position': {'x': 1020, 'y': 1200}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc1c0c0c0c0s0'}, 'position': {'x': 1020, 'y': 1170}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c0c0c0c0c0', 'confidence': 100.0}, 'position': {'x': 1800, 'y': 1170}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc1c0c0c0c0c0s0'}, 'position': {'x': 1800, 'y': 1140}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c0c0c0c0c0c0', 'name': '34_BRAFL'}, 'position': {'x': 1860, 'y': 1140}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc1c0c0c0c0c0s1'}, 'position': {'x': 1800, 'y': 1200}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c0c0c0c0c0c1', 'name': '35_BRAFL'}, 'position': {'x': 1860, 'y': 1200}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc1c0c0c0c0s1'}, 'position': {'x': 1020, 'y': 1260}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c0c0c0c0c1', 'name': '8_BRAFL'}, 'position': {'x': 1500, 'y': 1260}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc1c0c0c0s1'}, 'position': {'x': 840, 'y': 1350}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c0c0c0c1', 'confidence': 84.0}, 'position': {'x': 1080, 'y': 1350}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc1c0c0c0c1s0'}, 'position': {'x': 1080, 'y': 1320}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c0c0c0c1c0', 'name': '20_NEMVE'}, 'position': {'x': 1680, 'y': 1320}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc1c0c0c0c1s1'}, 'position': {'x': 1080, 'y': 1380}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c0c0c0c1c1', 'name': '21_NEMVE'}, 'position': {'x': 1890, 'y': 1380}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc1c0c0s1'}, 'position': {'x': 750, 'y': 1440}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c0c0c1', 'name': '9_BRAFL'}, 'position': {'x': 1680, 'y': 1440}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc1c0s1'}, 'position': {'x': 300, 'y': 1560}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c0c1', 'confidence': 98.0}, 'position': {'x': 600, 'y': 1560}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc1c0c1s0'}, 'position': {'x': 600, 'y': 1530}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c0c1c0', 'confidence': 95.0}, 'position': {'x': 780, 'y': 1530}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc1c0c1c0s0'}, 'position': {'x': 780, 'y': 1500}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c0c1c0c0', 'name': '3_BRAFL'}, 'position': {'x': 1200, 'y': 1500}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc1c0c1c0s1'}, 'position': {'x': 780, 'y': 1560}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c0c1c0c1', 'name': '2_BRAFL'}, 'position': {'x': 1320, 'y': 1560}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc1c0c1s1'}, 'position': {'x': 600, 'y': 1620}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c0c1c1', 'name': '19_NEMVE'}, 'position': {'x': 1080, 'y': 1620}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc1s1'}, 'position': {'x': 180, 'y': 1740}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c1', 'confidence': 92.0}, 'position': {'x': 540, 'y': 1740}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc1c1s0'}, 'position': {'x': 540, 'y': 1710}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c1c0', 'confidence': 100.0}, 'position': {'x': 1290, 'y': 1710}, 'classes': 'nonterminal', 'grabbable': False}, +{'data': {'id': 'rc1c1c0s0'}, 'position': {'x': 1290, 'y': 1680}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c1c0c0', 'name': '37_BRAFL'}, 'position': {'x': 1470, 'y': 1680}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc1c1c0s1'}, 'position': {'x': 1290, 'y': 1740}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c1c0c1', 'name': '36_BRAFL'}, 'position': {'x': 1440, 'y': 1740}, 'classes': 'terminal', 'grabbable': False}, +{'data': {'id': 'rc1c1s1'}, 'position': {'x': 540, 'y': 1800}, 'grabbable': False, 'classes': 'support'}, +{'data': {'id': 'rc1c1c1', 'name': '33_BRAFL'}, 'position': {'x': 1230, 'y': 1800}, 'classes': 'terminal', 'grabbable': False}, + +# EDGES +{'data': {'source': 'r', 'target': 'rs0', 'sourceCladeId': 'r'}}, +{'data': {'source': 'rs0', 'target': 'rc0', 'length': None, 'sourceCladeId': 'r'}}, +{'data': {'source': 'rc0', 'target': 'rc0s0', 'sourceCladeId': 'rc0'}}, +{'data': {'source': 'rc0s0', 'target': 'rc0c0', 'length': 0.18105, 'sourceCladeId': 'rc0'}}, +{'data': {'source': 'rc0c0', 'target': 'rc0c0s0', 'sourceCladeId': 'rc0c0'}}, +{'data': {'source': 'rc0c0s0', 'target': 'rc0c0c0', 'length': 0.07466, 'sourceCladeId': 'rc0c0'}}, +{'data': {'source': 'rc0c0c0', 'target': 'rc0c0c0s0', 'sourceCladeId': 'rc0c0c0'}}, +{'data': {'source': 'rc0c0c0s0', 'target': 'rc0c0c0c0', 'length': 0.26168, 'sourceCladeId': 'rc0c0c0'}}, +{'data': {'source': 'rc0c0c0c0', 'target': 'rc0c0c0c0s0', 'sourceCladeId': 'rc0c0c0c0'}}, +{'data': {'source': 'rc0c0c0c0s0', 'target': 'rc0c0c0c0c0', 'length': 0.22058, 'sourceCladeId': 'rc0c0c0c0'}}, +{'data': {'source': 'rc0c0c0c0c0', 'target': 'rc0c0c0c0c0s0', 'sourceCladeId': 'rc0c0c0c0c0'}}, +{'data': {'source': 'rc0c0c0c0c0s0', 'target': 'rc0c0c0c0c0c0', 'length': 0.28901, 'sourceCladeId': 'rc0c0c0c0c0'}}, +{'data': {'source': 'rc0c0c0c0c0c0', 'target': 'rc0c0c0c0c0c0s0', 'sourceCladeId': 'rc0c0c0c0c0c0'}}, +{'data': {'source': 'rc0c0c0c0c0c0s0', 'target': 'rc0c0c0c0c0c0c0', 'length': 0.06584, 'sourceCladeId': 'rc0c0c0c0c0c0'}}, +{'data': {'source': 'rc0c0c0c0c0c0c0', 'target': 'rc0c0c0c0c0c0c0s0', 'sourceCladeId': 'rc0c0c0c0c0c0c0'}}, +{'data': {'source': 'rc0c0c0c0c0c0c0s0', 'target': 'rc0c0c0c0c0c0c0c0', 'length': 0.02309, 'sourceCladeId': 'rc0c0c0c0c0c0c0'}}, +{'data': {'source': 'rc0c0c0c0c0c0c0c0', 'target': 'rc0c0c0c0c0c0c0c0s0', 'sourceCladeId': 'rc0c0c0c0c0c0c0c0'}}, +{'data': {'source': 'rc0c0c0c0c0c0c0c0s0', 'target': 'rc0c0c0c0c0c0c0c0c0', 'length': 0.0746, 'sourceCladeId': 'rc0c0c0c0c0c0c0c0'}}, +{'data': {'source': 'rc0c0c0c0c0c0c0c0c0', 'target': 'rc0c0c0c0c0c0c0c0c0s0', 'sourceCladeId': 'rc0c0c0c0c0c0c0c0c0'}}, +{'data': {'source': 'rc0c0c0c0c0c0c0c0c0s0', 'target': 'rc0c0c0c0c0c0c0c0c0c0', 'length': 0.02365, 'sourceCladeId': 'rc0c0c0c0c0c0c0c0c0'}}, +{'data': {'source': 'rc0c0c0c0c0c0c0c0c0', 'target': 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{'source': 'rc1c1', 'target': 'rc1c1s1', 'sourceCladeId': 'rc1c1'}}, +{'data': {'source': 'rc1c1s1', 'target': 'rc1c1c1', 'length': 0.43438, 'sourceCladeId': 'rc1c1'}} + +] + + + + + + diff --git a/demosR/phylogeny/elementsR.txt b/demosR/phylogeny/elementsR.txt new file mode 100644 index 00000000..6f180a78 --- /dev/null +++ b/demosR/phylogeny/elementsR.txt @@ -0,0 +1,248 @@ +dummyNodes <- list( + list(data = list(id = 'r'), position = list('x' = 30, 'y' = 1200), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rs0'), position = list('x' = 30, 'y' = 840), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0', confidence = 89.0), position = list('x' = 180, 'y' = 840), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0s0'), position = list('x' = 180, 'y' = 660), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0', confidence = 32.0), position = list('x' = 240, 'y' = 660), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0s0'), position = list('x' = 240, 'y' = 540), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0', confidence = 100.0), position = list('x' = 450, 'y' = 540), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0s0'), position = list('x' = 450, 'y' = 390), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0', confidence = 89.0), position = list('x' = 630, 'y' = 390), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0s0'), position = list('x' = 630, 'y' = 270), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0', confidence = 100.0), position = list('x' = 870, 'y' = 270), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0s0'), position = list('x' = 870, 'y' = 180), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0', confidence = 100.0), position = list('x' = 930, 'y' = 180), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0s0'), position = list('x' = 930, 'y' = 120), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0', confidence = 43.0), position = list('x' = 960, 'y' = 120), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0s0'), position = list('x' = 960, 'y' = 60), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0', confidence = 100.0), position = list('x' = 1020, 'y' = 60), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0s0'), position = list('x' = 1020, 'y' = 30), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0c0', confidence = 88.0), position = list('x' = 1020, 'y' = 30), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0c0s0'), position = list('x' = 1020, 'y' = 0), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0c0c0', name = '22_MOUSE'), position = list('x' = 1080, 'y' = 0), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0c0s1'), position = list('x' = 1020, 'y' = 60), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0c0c1', name = 'Apaf-1_HUMAN'), position = list('x' = 1050, 'y' = 60), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0s1'), position = list('x' = 1020, 'y' = 120), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c0c1', name = '12_CANFA'), position = list('x' = 1050, 'y' = 120), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0s1'), position = list('x' = 960, 'y' = 180), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c0c1', name = '11_CHICK'), position = list('x' = 1080, 'y' = 180), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0s1'), position = list('x' = 930, 'y' = 240), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c0c1', name = '16_XENLA'), position = list('x' = 1290, 'y' = 240), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0s1'), position = list('x' = 870, 'y' = 360), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1', confidence = 100.0), position = list('x' = 1020, 'y' = 360), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1s0'), position = list('x' = 1020, 'y' = 330), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1c0', confidence = 100.0), position = list('x' = 1110, 'y' = 330), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1c0s0'), position = list('x' = 1110, 'y' = 300), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1c0c0', name = '14_FUGRU'), position = list('x' = 1140, 'y' = 300), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1c0s1'), position = list('x' = 1110, 'y' = 360), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1c0c1', name = '15_TETNG'), position = list('x' = 1200, 'y' = 360), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1s1'), position = list('x' = 1020, 'y' = 420), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c0c1c1', name = '17_BRARE'), position = list('x' = 1170, 'y' = 420), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0s1'), position = list('x' = 630, 'y' = 540), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1', confidence = 53.0), position = list('x' = 660, 'y' = 540), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1s0'), position = list('x' = 660, 'y' = 510), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1c0', confidence = 68.0), position = list('x' = 750, 'y' = 510), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1c0s0'), position = list('x' = 750, 'y' = 480), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1c0c0', name = '1_BRAFL'), position = list('x' = 960, 'y' = 480), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1c0s1'), position = list('x' = 750, 'y' = 540), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1c0c1', name = '18_NEMVE'), position = list('x' = 1050, 'y' = 540), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1s1'), position = list('x' = 660, 'y' = 600), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c0c1c1', name = '23_STRPU'), position = list('x' = 1050, 'y' = 600), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0s1'), position = list('x' = 450, 'y' = 690), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c1', confidence = 100.0), position = list('x' = 750, 'y' = 690), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c1s0'), position = list('x' = 750, 'y' = 660), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c1c0', name = '26_STRPU'), position = list('x' = 1050, 'y' = 660), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c1s1'), position = list('x' = 750, 'y' = 720), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c0c1c1', name = '25_STRPU'), position = list('x' = 1020, 'y' = 720), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0s1'), position = list('x' = 240, 'y' = 810), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c1', confidence = 100.0), position = list('x' = 1320, 'y' = 810), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c1s0'), position = list('x' = 1320, 'y' = 780), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c1c0', name = 'CED4_CAEEL'), position = list('x' = 1440, 'y' = 780), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c0c1s1'), position = list('x' = 1320, 'y' = 840), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c0c1c1', name = '31_CAEBR'), position = list('x' = 1380, 'y' = 840), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0s1'), position = list('x' = 180, 'y' = 1020), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c1', confidence = 45.0), position = list('x' = 270, 'y' = 1020), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c1s0'), position = list('x' = 270, 'y' = 960), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c1c0', confidence = 95.0), position = list('x' = 480, 'y' = 960), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c1c0s0'), position = list('x' = 480, 'y' = 930), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c1c0c0', confidence = 100.0), position = list('x' = 1140, 'y' = 930), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc0c1c0c0s0'), position = list('x' = 1140, 'y' = 900), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c1c0c0c0', name = '28_DROPS'), position = list('x' = 1260, 'y' = 900), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c1c0c0s1'), position = list('x' = 1140, 'y' = 960), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c1c0c0c1', name = 'Dark_DROME'), position = list('x' = 1290, 'y' = 960), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c1c0s1'), position = list('x' = 480, 'y' = 1020), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c1c0c1', name = '29_AEDAE'), position = list('x' = 1200, 'y' = 1020), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc0c1s1'), position = list('x' = 270, 'y' = 1080), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc0c1c1', name = '30_TRICA'), position = list('x' = 1080, 'y' = 1080), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rs1'), position = list('x' = 30, 'y' = 1590), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1', confidence = 89.0), position = list('x' = 180, 'y' = 1590), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1s0'), position = list('x' = 180, 'y' = 1440), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0', confidence = 64.0), position = list('x' = 300, 'y' = 1440), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c0s0'), position = list('x' = 300, 'y' = 1350), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0', confidence = 100.0), position = list('x' = 750, 'y' = 1350), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0s0'), position = list('x' = 750, 'y' = 1260), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0', confidence = 46.0), position = list('x' = 840, 'y' = 1260), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0s0'), position = list('x' = 840, 'y' = 1200), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0', confidence = 61.0), position = list('x' = 1020, 'y' = 1200), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0s0'), position = list('x' = 1020, 'y' = 1170), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0c0', confidence = 100.0), position = list('x' = 1800, 'y' = 1170), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0c0s0'), position = list('x' = 1800, 'y' = 1140), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0c0c0', name = '34_BRAFL'), position = list('x' = 1860, 'y' = 1140), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0c0s1'), position = list('x' = 1800, 'y' = 1200), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0c0c1', name = '35_BRAFL'), position = list('x' = 1860, 'y' = 1200), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0s1'), position = list('x' = 1020, 'y' = 1260), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c0c1', name = '8_BRAFL'), position = list('x' = 1500, 'y' = 1260), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0s1'), position = list('x' = 840, 'y' = 1350), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c1', confidence = 84.0), position = list('x' = 1080, 'y' = 1350), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c1s0'), position = list('x' = 1080, 'y' = 1320), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c1c0', name = '20_NEMVE'), position = list('x' = 1680, 'y' = 1320), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c1s1'), position = list('x' = 1080, 'y' = 1380), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c0c1c1', name = '21_NEMVE'), position = list('x' = 1890, 'y' = 1380), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c0s1'), position = list('x' = 750, 'y' = 1440), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c0c1', name = '9_BRAFL'), position = list('x' = 1680, 'y' = 1440), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c0s1'), position = list('x' = 300, 'y' = 1560), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c1', confidence = 98.0), position = list('x' = 600, 'y' = 1560), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c1s0'), position = list('x' = 600, 'y' = 1530), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c1c0', confidence = 95.0), position = list('x' = 780, 'y' = 1530), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c1c0s0'), position = list('x' = 780, 'y' = 1500), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c1c0c0', name = '3_BRAFL'), position = list('x' = 1200, 'y' = 1500), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c1c0s1'), position = list('x' = 780, 'y' = 1560), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c1c0c1', name = '2_BRAFL'), position = list('x' = 1320, 'y' = 1560), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c0c1s1'), position = list('x' = 600, 'y' = 1620), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c0c1c1', name = '19_NEMVE'), position = list('x' = 1080, 'y' = 1620), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1s1'), position = list('x' = 180, 'y' = 1740), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c1', confidence = 92.0), position = list('x' = 540, 'y' = 1740), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c1s0'), position = list('x' = 540, 'y' = 1710), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c1c0', confidence = 100.0), position = list('x' = 1290, 'y' = 1710), classes = 'nonterminal', grabbable = FALSE), + list(data = list(id = 'rc1c1c0s0'), position = list('x' = 1290, 'y' = 1680), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c1c0c0', name = '37_BRAFL'), position = list('x' = 1470, 'y' = 1680), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c1c0s1'), position = list('x' = 1290, 'y' = 1740), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c1c0c1', name = '36_BRAFL'), position = list('x' = 1440, 'y' = 1740), classes = 'terminal', grabbable = FALSE), + list(data = list(id = 'rc1c1s1'), position = list('x' = 540, 'y' = 1800), classes = 'support', grabbable = FALSE), + list(data = list(id = 'rc1c1c1', name = '33_BRAFL'), position = list('x' = 1230, 'y' = 1800), classes = 'terminal', grabbable = FALSE) +) + +dummyEdges <- list( + list(data = list(source = 'r', target = 'rs0', sourceCladeId = 'r')), + list(data = list(source = 'rs0', target = 'rc0', length = 0, sourceCladeId = 'r')), + list(data = list(source = 'rc0', target = 'rc0s0', sourceCladeId = 'rc0')), + list(data = list(source = 'rc0s0', target = 'rc0c0', length = 0.18105, sourceCladeId = 'rc0')), + list(data = list(source = 'rc0c0', target = 'rc0c0s0', sourceCladeId = 'rc0c0')), + list(data = list(source = 'rc0c0s0', target = 'rc0c0c0', length = 0.07466, sourceCladeId = 'rc0c0')), + list(data = list(source = 'rc0c0c0', target = 'rc0c0c0s0', sourceCladeId = 'rc0c0c0')), + list(data = list(source = 'rc0c0c0s0', target = 'rc0c0c0c0', length = 0.26168, sourceCladeId = 'rc0c0c0')), + list(data = list(source = 'rc0c0c0c0', target = 'rc0c0c0c0s0', sourceCladeId = 'rc0c0c0c0')), + list(data = list(source = 'rc0c0c0c0s0', target = 'rc0c0c0c0c0', length = 0.22058, sourceCladeId = 'rc0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0', target = 'rc0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0s0', target = 'rc0c0c0c0c0c0', length = 0.28901, sourceCladeId = 'rc0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0', target = 'rc0c0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0s0', target = 'rc0c0c0c0c0c0c0', length = 0.06584, sourceCladeId = 'rc0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0s0', target = 'rc0c0c0c0c0c0c0c0', length = 0.02309, sourceCladeId = 'rc0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0c0s0', target = 'rc0c0c0c0c0c0c0c0c0', length = 0.0746, sourceCladeId = 'rc0c0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0c0c0s0', target = 'rc0c0c0c0c0c0c0c0c0c0', length = 0.02365, sourceCladeId = 'rc0c0c0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0c0c0s1', target = 'rc0c0c0c0c0c0c0c0c0c1', length = 0.02365, sourceCladeId = 'rc0c0c0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0c0s1', target = 'rc0c0c0c0c0c0c0c0c1', length = 0.0746, sourceCladeId = 'rc0c0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0c0s1', target = 'rc0c0c0c0c0c0c0c1', length = 0.02309, sourceCladeId = 'rc0c0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0', target = 'rc0c0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c0s1', target = 'rc0c0c0c0c0c0c1', length = 0.06584, sourceCladeId = 'rc0c0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0', target = 'rc0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0s1', target = 'rc0c0c0c0c0c1', length = 0.28901, sourceCladeId = 'rc0c0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c0c1', target = 'rc0c0c0c0c0c1s0', sourceCladeId = 'rc0c0c0c0c0c1')), + list(data = list(source = 'rc0c0c0c0c0c1s0', target = 'rc0c0c0c0c0c1c0', length = 0.17031, sourceCladeId = 'rc0c0c0c0c0c1')), + list(data = list(source = 'rc0c0c0c0c0c1c0', target = 'rc0c0c0c0c0c1c0s0', sourceCladeId = 'rc0c0c0c0c0c1c0')), + list(data = list(source = 'rc0c0c0c0c0c1c0s0', target = 'rc0c0c0c0c0c1c0c0', length = 0.10929, sourceCladeId = 'rc0c0c0c0c0c1c0')), + list(data = list(source = 'rc0c0c0c0c0c1c0', target = 'rc0c0c0c0c0c1c0s1', sourceCladeId = 'rc0c0c0c0c0c1c0')), + list(data = list(source = 'rc0c0c0c0c0c1c0s1', target = 'rc0c0c0c0c0c1c0c1', length = 0.10929, sourceCladeId = 'rc0c0c0c0c0c1c0')), + list(data = list(source = 'rc0c0c0c0c0c1', target = 'rc0c0c0c0c0c1s1', sourceCladeId = 'rc0c0c0c0c0c1')), + list(data = list(source = 'rc0c0c0c0c0c1s1', target = 'rc0c0c0c0c0c1c1', length = 0.17031, sourceCladeId = 'rc0c0c0c0c0c1')), + list(data = list(source = 'rc0c0c0c0', target = 'rc0c0c0c0s1', sourceCladeId = 'rc0c0c0c0')), + list(data = list(source = 'rc0c0c0c0s1', target = 'rc0c0c0c0c1', length = 0.22058, sourceCladeId = 'rc0c0c0c0')), + list(data = list(source = 'rc0c0c0c0c1', target = 'rc0c0c0c0c1s0', sourceCladeId = 'rc0c0c0c0c1')), + list(data = list(source = 'rc0c0c0c0c1s0', target = 'rc0c0c0c0c1c0', length = 0.01594, sourceCladeId = 'rc0c0c0c0c1')), + list(data = list(source = 'rc0c0c0c0c1c0', target = 'rc0c0c0c0c1c0s0', sourceCladeId = 'rc0c0c0c0c1c0')), + list(data = list(source = 'rc0c0c0c0c1c0s0', target = 'rc0c0c0c0c1c0c0', length = 0.10709, sourceCladeId = 'rc0c0c0c0c1c0')), + list(data = list(source = 'rc0c0c0c0c1c0', target = 'rc0c0c0c0c1c0s1', sourceCladeId = 'rc0c0c0c0c1c0')), + list(data = list(source = 'rc0c0c0c0c1c0s1', target = 'rc0c0c0c0c1c0c1', length = 0.10709, sourceCladeId = 'rc0c0c0c0c1c0')), + list(data = list(source = 'rc0c0c0c0c1', target = 'rc0c0c0c0c1s1', sourceCladeId = 'rc0c0c0c0c1')), + list(data = list(source = 'rc0c0c0c0c1s1', target = 'rc0c0c0c0c1c1', length = 0.01594, sourceCladeId = 'rc0c0c0c0c1')), + list(data = list(source = 'rc0c0c0', target = 'rc0c0c0s1', sourceCladeId = 'rc0c0c0')), + list(data = list(source = 'rc0c0c0s1', target = 'rc0c0c0c1', length = 0.26168, sourceCladeId = 'rc0c0c0')), + list(data = list(source = 'rc0c0c0c1', target = 'rc0c0c0c1s0', sourceCladeId = 'rc0c0c0c1')), + list(data = list(source = 'rc0c0c0c1s0', target = 'rc0c0c0c1c0', length = 0.34475, sourceCladeId = 'rc0c0c0c1')), + list(data = list(source = 'rc0c0c0c1', target = 'rc0c0c0c1s1', sourceCladeId = 'rc0c0c0c1')), + list(data = list(source = 'rc0c0c0c1s1', target = 'rc0c0c0c1c1', length = 0.34475, sourceCladeId = 'rc0c0c0c1')), + list(data = list(source = 'rc0c0', target = 'rc0c0s1', sourceCladeId = 'rc0c0')), + list(data = list(source = 'rc0c0s1', target = 'rc0c0c1', length = 0.07466, sourceCladeId = 'rc0c0')), + list(data = list(source = 'rc0c0c1', target = 'rc0c0c1s0', sourceCladeId = 'rc0c0c1')), + list(data = list(source = 'rc0c0c1s0', target = 'rc0c0c1c0', length = 1.31498, sourceCladeId = 'rc0c0c1')), + list(data = list(source = 'rc0c0c1', target = 'rc0c0c1s1', sourceCladeId = 'rc0c0c1')), + list(data = list(source = 'rc0c0c1s1', target = 'rc0c0c1c1', length = 1.31498, sourceCladeId = 'rc0c0c1')), + list(data = list(source = 'rc0', target = 'rc0s1', sourceCladeId = 'rc0')), + list(data = list(source = 'rc0s1', target = 'rc0c1', length = 0.18105, sourceCladeId = 'rc0')), + list(data = list(source = 'rc0c1', target = 'rc0c1s0', sourceCladeId = 'rc0c1')), + list(data = list(source = 'rc0c1s0', target = 'rc0c1c0', length = 0.13172, sourceCladeId = 'rc0c1')), + list(data = list(source = 'rc0c1c0', target = 'rc0c1c0s0', sourceCladeId = 'rc0c1c0')), + list(data = list(source = 'rc0c1c0s0', target = 'rc0c1c0c0', length = 0.24915, sourceCladeId = 'rc0c1c0')), + list(data = list(source = 'rc0c1c0c0', target = 'rc0c1c0c0s0', sourceCladeId = 'rc0c1c0c0')), + list(data = list(source = 'rc0c1c0c0s0', target = 'rc0c1c0c0c0', length = 0.76898, sourceCladeId = 'rc0c1c0c0')), + list(data = list(source = 'rc0c1c0c0', target = 'rc0c1c0c0s1', sourceCladeId = 'rc0c1c0c0')), + list(data = list(source = 'rc0c1c0c0s1', target = 'rc0c1c0c0c1', length = 0.76898, sourceCladeId = 'rc0c1c0c0')), + list(data = list(source = 'rc0c1c0', target = 'rc0c1c0s1', sourceCladeId = 'rc0c1c0')), + list(data = list(source = 'rc0c1c0s1', target = 'rc0c1c0c1', length = 0.24915, sourceCladeId = 'rc0c1c0')), + list(data = list(source = 'rc0c1', target = 'rc0c1s1', sourceCladeId = 'rc0c1')), + list(data = list(source = 'rc0c1s1', target = 'rc0c1c1', length = 0.13172, sourceCladeId = 'rc0c1')), + list(data = list(source = 'r', target = 'rs1', sourceCladeId = 'r')), + list(data = list(source = 'rs1', target = 'rc1', length = 0, sourceCladeId = 'r')), + list(data = list(source = 'rc1', target = 'rc1s0', sourceCladeId = 'rc1')), + list(data = list(source = 'rc1s0', target = 'rc1c0', length = 0.18105, sourceCladeId = 'rc1')), + list(data = list(source = 'rc1c0', target = 'rc1c0s0', sourceCladeId = 'rc1c0')), + list(data = list(source = 'rc1c0s0', target = 'rc1c0c0', length = 0.15891, sourceCladeId = 'rc1c0')), + list(data = list(source = 'rc1c0c0', target = 'rc1c0c0s0', sourceCladeId = 'rc1c0c0')), + list(data = list(source = 'rc1c0c0s0', target = 'rc1c0c0c0', length = 0.54836, sourceCladeId = 'rc1c0c0')), + list(data = list(source = 'rc1c0c0c0', target = 'rc1c0c0c0s0', sourceCladeId = 'rc1c0c0c0')), + list(data = list(source = 'rc1c0c0c0s0', target = 'rc1c0c0c0c0', length = 0.09305, sourceCladeId = 'rc1c0c0c0')), + list(data = list(source = 'rc1c0c0c0c0', target = 'rc1c0c0c0c0s0', sourceCladeId = 'rc1c0c0c0c0')), + list(data = list(source = 'rc1c0c0c0c0s0', target = 'rc1c0c0c0c0c0', length = 0.21648, sourceCladeId = 'rc1c0c0c0c0')), + list(data = list(source = 'rc1c0c0c0c0c0', target = 'rc1c0c0c0c0c0s0', sourceCladeId = 'rc1c0c0c0c0c0')), + list(data = list(source = 'rc1c0c0c0c0c0s0', target = 'rc1c0c0c0c0c0c0', length = 0.93134, sourceCladeId = 'rc1c0c0c0c0c0')), + list(data = list(source = 'rc1c0c0c0c0c0', target = 'rc1c0c0c0c0c0s1', sourceCladeId = 'rc1c0c0c0c0c0')), + list(data = list(source = 'rc1c0c0c0c0c0s1', target = 'rc1c0c0c0c0c0c1', length = 0.93134, sourceCladeId = 'rc1c0c0c0c0c0')), + list(data = list(source = 'rc1c0c0c0c0', target = 'rc1c0c0c0c0s1', sourceCladeId = 'rc1c0c0c0c0')), + list(data = list(source = 'rc1c0c0c0c0s1', target = 'rc1c0c0c0c0c1', length = 0.21648, sourceCladeId = 'rc1c0c0c0c0')), + list(data = list(source = 'rc1c0c0c0', target = 'rc1c0c0c0s1', sourceCladeId = 'rc1c0c0c0')), + list(data = list(source = 'rc1c0c0c0s1', target = 'rc1c0c0c0c1', length = 0.09305, sourceCladeId = 'rc1c0c0c0')), + list(data = list(source = 'rc1c0c0c0c1', target = 'rc1c0c0c0c1s0', sourceCladeId = 'rc1c0c0c0c1')), + list(data = list(source = 'rc1c0c0c0c1s0', target = 'rc1c0c0c0c1c0', length = 0.28437, sourceCladeId = 'rc1c0c0c0c1')), + list(data = list(source = 'rc1c0c0c0c1', target = 'rc1c0c0c0c1s1', sourceCladeId = 'rc1c0c0c0c1')), + list(data = list(source = 'rc1c0c0c0c1s1', target = 'rc1c0c0c0c1c1', length = 0.28437, sourceCladeId = 'rc1c0c0c0c1')), + list(data = list(source = 'rc1c0c0', target = 'rc1c0c0s1', sourceCladeId = 'rc1c0c0')), + list(data = list(source = 'rc1c0c0s1', target = 'rc1c0c0c1', length = 0.54836, sourceCladeId = 'rc1c0c0')), + list(data = list(source = 'rc1c0', target = 'rc1c0s1', sourceCladeId = 'rc1c0')), + list(data = list(source = 'rc1c0s1', target = 'rc1c0c1', length = 0.15891, sourceCladeId = 'rc1c0')), + list(data = list(source = 'rc1c0c1', target = 'rc1c0c1s0', sourceCladeId = 'rc1c0c1')), + list(data = list(source = 'rc1c0c1s0', target = 'rc1c0c1c0', length = 0.34914, sourceCladeId = 'rc1c0c1')), + list(data = list(source = 'rc1c0c1c0', target = 'rc1c0c1c0s0', sourceCladeId = 'rc1c0c1c0')), + list(data = list(source = 'rc1c0c1c0s0', target = 'rc1c0c1c0c0', length = 0.22189, sourceCladeId = 'rc1c0c1c0')), + list(data = list(source = 'rc1c0c1c0', target = 'rc1c0c1c0s1', sourceCladeId = 'rc1c0c1c0')), + list(data = list(source = 'rc1c0c1c0s1', target = 'rc1c0c1c0c1', length = 0.22189, sourceCladeId = 'rc1c0c1c0')), + list(data = list(source = 'rc1c0c1', target = 'rc1c0c1s1', sourceCladeId = 'rc1c0c1')), + list(data = list(source = 'rc1c0c1s1', target = 'rc1c0c1c1', length = 0.34914, sourceCladeId = 'rc1c0c1')), + list(data = list(source = 'rc1', target = 'rc1s1', sourceCladeId = 'rc1')), + list(data = list(source = 'rc1s1', target = 'rc1c1', length = 0.18105, sourceCladeId = 'rc1')), + list(data = list(source = 'rc1c1', target = 'rc1c1s0', sourceCladeId = 'rc1c1')), + list(data = list(source = 'rc1c1s0', target = 'rc1c1c0', length = 0.43438, sourceCladeId = 'rc1c1')), + list(data = list(source = 'rc1c1c0', target = 'rc1c1c0s0', sourceCladeId = 'rc1c1c0')), + list(data = list(source = 'rc1c1c0s0', target = 'rc1c1c0c0', length = 0.92214, sourceCladeId = 'rc1c1c0')), + list(data = list(source = 'rc1c1c0', target = 'rc1c1c0s1', sourceCladeId = 'rc1c1c0')), + list(data = list(source = 'rc1c1c0s1', target = 'rc1c1c0c1', length = 0.92214, sourceCladeId = 'rc1c1c0')), + list(data = list(source = 'rc1c1', target = 'rc1c1s1', sourceCladeId = 'rc1c1')), + list(data = list(source = 'rc1c1s1', target = 'rc1c1c1', length = 0.43438, sourceCladeId = 'rc1c1')) +) + +dummyElements <- c(dummyNodes, dummyEdges) \ No newline at end of file diff --git a/demosR/phylogeny/treePy.txt b/demosR/phylogeny/treePy.txt new file mode 100644 index 00000000..05e24dd7 --- /dev/null +++ b/demosR/phylogeny/treePy.txt @@ -0,0 +1,140 @@ +Phylogeny(rooted=True) + Clade() + Clade(branch_length=0.18105) + Confidence(type='unknown', value=89.0) + Clade(branch_length=0.07466) + Confidence(type='unknown', value=32.0) + Clade(branch_length=0.26168) + Confidence(type='unknown', value=100.0) + Clade(branch_length=0.22058) + Confidence(type='unknown', value=89.0) + Clade(branch_length=0.28901) + Confidence(type='unknown', value=100.0) + Clade(branch_length=0.06584) + Confidence(type='unknown', value=100.0) + Clade(branch_length=0.02309) + Confidence(type='unknown', value=43.0) + Clade(branch_length=0.0746) + Confidence(type='unknown', value=100.0) + Clade(branch_length=0.02365) + Confidence(type='unknown', value=88.0) + Clade(branch_length=0.05998, name='22_MOUSE') + MOUSE + Sequence() + DomainArchitecture(length=1249) + ProteinDomain(confidence=7e-26, end=90, start=5, value='CARD') + ProteinDomain(confidence=7.2e-117, end=414, start=108, value='NB-ARC') + ProteinDomain(confidence=2.4e-06, end=643, start=604, value='WD40') + ProteinDomain(confidence=1.1e-12, end=685, start=646, value='WD40') + ProteinDomain(confidence=2.4e-07, end=729, start=688, value='WD40') + ProteinDomain(confidence=4.7e-14, end=771, start=732, value='WD40') + ProteinDomain(confidence=2.5e-08, end=910, start=871, value='WD40') + ProteinDomain(confidence=4.6e-06, end=1031, start=992, value='WD40') + ProteinDomain(confidence=6.3e-07, end=1113, start=1074, value='WD40') + ProteinDomain(confidence=1.4e-07, end=1155, start=1116, value='WD40') + ProteinDomain(confidence=0.3, end=1204, start=1167, value='WD40') + Clade(branch_length=0.01825, name='Apaf-1_HUMAN') + HUMAN + Sequence() + DomainArchitecture(length=1248) + ProteinDomain(confidence=1.1e-25, end=90, start=5, value='CARD') + ProteinDomain(confidence=3e-134, end=414, start=108, value='NB-ARC') + ProteinDomain(confidence=8.5e-06, end=643, start=604, value='WD40') + ProteinDomain(confidence=2.5e-11, end=685, start=646, value='WD40') + ProteinDomain(confidence=2.4e-08, end=729, start=688, value='WD40') + ProteinDomain(confidence=3.6e-14, end=771, start=732, value='WD40') + ProteinDomain(confidence=3.8e-08, end=910, start=871, value='WD40') + ProteinDomain(confidence=4e-07, end=1113, start=1074, value='WD40') + ProteinDomain(confidence=5.9e-08, end=1155, start=1116, value='WD40') + Clade(branch_length=0.04683, name='12_CANFA') + CANFA + Sequence() + DomainArchitecture(length=1153) + ProteinDomain(confidence=4.5e-22, end=90, start=5, value='CARD') + ProteinDomain(confidence=4e-119, end=415, start=109, value='NB-ARC') + ProteinDomain(confidence=3.9e-05, end=635, start=596, value='WD40') + ProteinDomain(confidence=2.5e-11, end=677, start=638, value='WD40') + ProteinDomain(confidence=1.8e-07, end=721, start=680, value='WD40') + ProteinDomain(confidence=9.4e-13, end=763, start=724, value='WD40') + ProteinDomain(confidence=1.1e-06, end=927, start=888, value='WD40') + ProteinDomain(confidence=1.7e-07, end=1009, start=970, value='WD40') + ProteinDomain(confidence=1.9e-07, end=1051, start=1012, value='WD40') + Clade(branch_length=0.15226, name='11_CHICK') + CHICK + Sequence() + DomainArchitecture(length=1207) + ProteinDomain(confidence=3.6e-21, end=90, start=5, value='CARD') + ProteinDomain(confidence=3.6e-109, end=414, start=108, value='NB-ARC') + ProteinDomain(confidence=0.00016, end=641, start=602, value='WD40') + ProteinDomain(confidence=8.2e-11, end=683, start=644, value='WD40') + ProteinDomain(confidence=6.2e-10, end=727, start=686, value='WD40') + ProteinDomain(confidence=1.8e-11, end=769, start=730, value='WD40') + ProteinDomain(confidence=1.8, end=866, start=827, value='WD40') + ProteinDomain(confidence=0.00029, end=1030, start=992, value='WD40') + ProteinDomain(confidence=1.7e-08, end=1072, start=1033, value='WD40') + ProteinDomain(confidence=7.5e-09, end=1114, start=1075, value='WD40') + ProteinDomain(confidence=0.044, end=1163, start=1126, value='WD40') + Clade(branch_length=0.4409, name='16_XENLA') + XENLA + Sequence() + DomainArchitecture(length=1362) + ProteinDomain(confidence=4e-20, end=90, start=5, value='CARD') + ProteinDomain(confidence=3.1e-56, end=410, start=108, value='NB-ARC') + ProteinDomain(confidence=0.8, end=298, start=147, value='NACHT') + ProteinDomain(confidence=7e-06, end=767, start=728, value='WD40') + ProteinDomain(confidence=2.3e-11, end=809, start=770, value='WD40') + ProteinDomain(confidence=1.1e-08, end=853, start=812, value='WD40') + ProteinDomain(confidence=1.1e-10, end=895, start=856, value='WD40') + ProteinDomain(confidence=8.4e-09, end=1030, start=991, value='WD40') + ProteinDomain(confidence=7.3e-11, end=1154, start=1115, value='WD40') + ProteinDomain(confidence=1.6e-08, end=1196, start=1157, value='WD40') + ProteinDomain(confidence=1.2e-07, end=1238, start=1199, value='WD40') + Clade(branch_length=0.17031) + Confidence(type='unknown', value=100.0) + Clade(branch_length=0.10929) + Confidence(type='unknown', value=100.0) + Clade(branch_length=0.02255, name='14_FUGRU') + FUGRU + Sequence() + DomainArchitecture(length=1258) + ProteinDomain(confidence=4.6e-24, end=92, start=7, value='CARD') + ProteinDomain(confidence=7e-74, end=418, start=110, value='NB-ARC') + ProteinDomain(confidence=0.00028, end=647, start=608, value='WD40') + ProteinDomain(confidence=2.3e-12, end=689, start=650, value='WD40') + ProteinDomain(confidence=1.8e-06, end=778, start=739, value='WD40') + ProteinDomain(confidence=1.6e-09, end=912, start=873, value='WD40') + ProteinDomain(confidence=9.8e-13, end=1036, start=997, value='WD40') + ProteinDomain(confidence=0.00016, end=1080, start=1039, value='WD40') + ProteinDomain(confidence=1.5e-09, end=1122, start=1083, value='WD40') + ProteinDomain(confidence=6.2e-09, end=1164, start=1125, value='WD40') + Clade(branch_length=0.09478, name='15_TETNG') + TETNG + Sequence() + DomainArchitecture(length=621) + ProteinDomain(confidence=2.5e-24, end=92, start=7, value='CARD') + ProteinDomain(confidence=9.8e-11, end=308, start=103, value='NB-ARC') + ProteinDomain(confidence=1.2e-12, end=404, start=365, value='WD40') + ProteinDomain(confidence=1e-10, end=493, start=454, value='WD40') + ProteinDomain(confidence=4.1e-10, end=575, start=536, value='WD40') + Clade(branch_length=0.1811, name='17_BRARE') + BRARE + Sequence() + DomainArchitecture(length=1260) + ProteinDomain(confidence=3.9e-23, end=90, start=5, value='CARD') + ProteinDomain(confidence=1.7e-72, end=444, start=136, value='NB-ARC') + ProteinDomain(confidence=1.6, end=673, start=634, value='WD40') + ProteinDomain(confidence=5.3e-12, end=732, start=693, value='WD40') + ProteinDomain(confidence=2e-08, end=821, start=782, value='WD40') + ProteinDomain(confidence=2.4e-08, end=1078, start=1039, value='WD40') + ProteinDomain(confidence=0.00066, end=1121, start=1080, value='WD40') + ProteinDomain(confidence=5.1e-08, end=1163, start=1124, value='WD40') + ProteinDomain(confidence=1.3e-07, end=1205, start=1166, value='WD40') + Clade(branch_length=0.01594) + Confidence(type='unknown', value=53.0) + Clade(branch_length=0.10709) + Confidence(type='unknown', value=68.0) + Clade(branch_length=0.26131, name='1_BRAFL') + BRAFL + Sequence() + DomainArchitecture(length=1238) + ... \ No newline at end of file diff --git a/demosR/phylogeny/treeR.txt b/demosR/phylogeny/treeR.txt new file mode 100644 index 00000000..760cfc13 --- /dev/null +++ b/demosR/phylogeny/treeR.txt @@ -0,0 +1,2881 @@ +$clade +$clade$clade +$clade$clade$branch_length +[1] "0.18105" + +$clade$clade$confidence +$clade$clade$confidence$text +[1] "89.0" + +$clade$clade$confidence$.attrs + type +"unknown" + + +$clade$clade$clade +$clade$clade$clade$branch_length +[1] "0.07466" + +$clade$clade$clade$confidence +$clade$clade$clade$confidence$text +[1] "32.0" + +$clade$clade$clade$confidence$.attrs + type +"unknown" + + +$clade$clade$clade$clade +$clade$clade$clade$clade$branch_length +[1] "0.26168" + +$clade$clade$clade$clade$confidence +$clade$clade$clade$clade$confidence$text +[1] "100.0" + +$clade$clade$clade$clade$confidence$.attrs + type +"unknown" + + +$clade$clade$clade$clade$clade +$clade$clade$clade$clade$clade$branch_length +[1] "0.22058" + +$clade$clade$clade$clade$clade$confidence +$clade$clade$clade$clade$clade$confidence$text +[1] "89.0" + +$clade$clade$clade$clade$clade$confidence$.attrs + type +"unknown" + + +$clade$clade$clade$clade$clade$clade +$clade$clade$clade$clade$clade$clade$branch_length +[1] "0.28901" + +$clade$clade$clade$clade$clade$clade$confidence +$clade$clade$clade$clade$clade$clade$confidence$text +[1] "100.0" + +$clade$clade$clade$clade$clade$clade$confidence$.attrs + type +"unknown" + + +$clade$clade$clade$clade$clade$clade$clade +$clade$clade$clade$clade$clade$clade$clade$branch_length +[1] "0.06584" + +$clade$clade$clade$clade$clade$clade$clade$confidence +$clade$clade$clade$clade$clade$clade$clade$confidence$text +[1] "100.0" + +$clade$clade$clade$clade$clade$clade$clade$confidence$.attrs + type +"unknown" + + +$clade$clade$clade$clade$clade$clade$clade$clade +$clade$clade$clade$clade$clade$clade$clade$clade$branch_length +[1] "0.02309" + +$clade$clade$clade$clade$clade$clade$clade$clade$confidence +$clade$clade$clade$clade$clade$clade$clade$clade$confidence$text +[1] "43.0" + +$clade$clade$clade$clade$clade$clade$clade$clade$confidence$.attrs + type +"unknown" + + +$clade$clade$clade$clade$clade$clade$clade$clade$clade 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+$clade$clade$clade$clade$confidence$.attrs + type +"unknown" + + +$clade$clade$clade$clade$clade +$clade$clade$clade$clade$clade$name +[1] "37_BRAFL" + +$clade$clade$clade$clade$clade$branch_length +[1] "0.21133" + +$clade$clade$clade$clade$clade$taxonomy +$clade$clade$clade$clade$clade$taxonomy$code +[1] "BRAFL" + + +$clade$clade$clade$clade$clade$sequence +$clade$clade$clade$clade$clade$sequence$domain_architecture +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text +[1] "CARD" + +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs + from to confidence + "6" "89" "9.6E-13" + + +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text +[1] "CARD" + +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs + from to confidence + "118" "202" "4.5E-9" + + +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text +[1] "NB-ARC" + +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs + from to confidence + "206" "491" "0.0011" + + +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text +[1] "NACHT" + +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs + from to confidence + "238" "388" "0.0043" + + +$clade$clade$clade$clade$clade$sequence$domain_architecture$.attrs +length +"1793" + + + + +$clade$clade$clade$clade$clade +$clade$clade$clade$clade$clade$name +[1] "36_BRAFL" + +$clade$clade$clade$clade$clade$branch_length +[1] "0.16225" + +$clade$clade$clade$clade$clade$taxonomy +$clade$clade$clade$clade$clade$taxonomy$code +[1] "BRAFL" + + +$clade$clade$clade$clade$clade$sequence +$clade$clade$clade$clade$clade$sequence$domain_architecture +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text +[1] "CARD" + +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs + from to confidence + "9" "93" "1.6E-9" + + +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text +[1] "NB-ARC" + +$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs + from to confidence + "98" "403" "0.0019" + + +$clade$clade$clade$clade$clade$sequence$domain_architecture$.attrs +length + "918" + + + + + +$clade$clade$clade$clade +$clade$clade$clade$clade$name +[1] "33_BRAFL" + +$clade$clade$clade$clade$branch_length +[1] "0.8363" + +$clade$clade$clade$clade$taxonomy +$clade$clade$clade$clade$taxonomy$code +[1] "BRAFL" + + +$clade$clade$clade$clade$sequence +$clade$clade$clade$clade$sequence$domain_architecture +$clade$clade$clade$clade$sequence$domain_architecture$domain +$clade$clade$clade$clade$sequence$domain_architecture$domain$text +[1] "Death" + +$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs + from to confidence + "5" "87" "4.7E-12" + + +$clade$clade$clade$clade$sequence$domain_architecture$domain +$clade$clade$clade$clade$sequence$domain_architecture$domain$text +[1] "NB-ARC" + +$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs + from to confidence + "154" "465" "2.0E-6" + + +$clade$clade$clade$clade$sequence$domain_architecture$.attrs +length +"1212" + + + + + + + +$.attrs +rooted +"true" + diff --git a/demosR/usage-phylogeny.R b/demosR/usage-phylogeny.R index 09bd13c9..78effb77 100644 --- a/demosR/usage-phylogeny.R +++ b/demosR/usage-phylogeny.R @@ -2,12 +2,13 @@ library(dash) library(dashHtmlComponents) library(dashCytoscape) library(XML) -source("demosR/dummyData.R") + +# TODO: remove once "elements" defined +source("demosR/phylogeny/dummyData.R") app <- Dash$new() tree <- xmlToList(xmlParse(file = "demos/data/apaf.xml"))$phylogeny -capture.output(tree, file = "demosR/treeR.txt", append = FALSE) generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, i=list(), n=1) { # there are 31 "terminal" nodes with their respective 31 "support" nodes From 5a636ffa704ba4d91dad47a639574bf18f776109 Mon Sep 17 00:00:00 2001 From: ohaanika Date: Sun, 11 Aug 2019 09:48:59 -0400 Subject: [PATCH 18/22] update usage-phylogeny.R --- demosR/usage-phylogeny.R | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/demosR/usage-phylogeny.R b/demosR/usage-phylogeny.R index 78effb77..e8c5c3e9 100644 --- a/demosR/usage-phylogeny.R +++ b/demosR/usage-phylogeny.R @@ -37,7 +37,7 @@ generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, i=list(), support_id <- paste0(child_id, "s", i[[length(i)]]) child_id <- paste0(child_id, "c", i[[length(i)]]) n <<- n+2 - # support node and edge + # support node and preceding edge nodes[[n-1]] <<- list( data = list(id = support_id), # TODO: edit (x,y) according to branch_length = child$branch_length @@ -52,7 +52,7 @@ generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, i=list(), sourceCladeId = clade_id ) ) - # terminal node and edge + # terminal node and preceding edge nodes[[n]] <<- list( data = list(id = child_id, name = child$name), # TODO: edit (x,y) according to branch_length = child$branch_length @@ -75,7 +75,7 @@ generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, i=list(), support_id <- paste0(child_id, "s", i[[length(i)]]) child_id <- paste0(child_id, "c", i[[length(i)]]) n <<- n+2 - # support node and edge + # support node and preceding edge nodes[[n-1]] <<- list( data = list(id = support_id), # TODO: edit (x,y) according to branch_length = child$branch_length @@ -90,7 +90,7 @@ generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, i=list(), sourceCladeId = clade_id ) ) - # nonterminal node and edge + # nonterminal node and preceding edge nodes[[n]] <<- list( data = list(id = child_id, confidence = child$confidence$text), # TODO: edit (x,y) according to branch_length = child$branch_length From 6df310c1d4f0f7a686b87cc287f2df210ee2f706 Mon Sep 17 00:00:00 2001 From: Ryan Patrick Kyle Date: Thu, 20 May 2021 16:25:11 -0400 Subject: [PATCH 19/22] chore: :hocho: deprecated :package:, remove unfinished ex --- demosR/usage-animated-bfs.R | 1 - demosR/usage-breadthfirst-layout.R | 1 - demosR/usage-circle-layout.R | 1 - demosR/usage-compound-nodes.R | 1 - demosR/usage-events.R | 6 +- demosR/usage-grid-layout.R | 1 - demosR/usage-multiple-instances.R | 1 - demosR/usage-phylogeny.R | 252 ----------------------------- demosR/usage-pie-style.R | 1 - demosR/usage-visual-style.R | 1 - 10 files changed, 2 insertions(+), 264 deletions(-) delete mode 100644 demosR/usage-phylogeny.R diff --git a/demosR/usage-animated-bfs.R b/demosR/usage-animated-bfs.R index 2ea1f5d1..f3a47219 100644 --- a/demosR/usage-animated-bfs.R +++ b/demosR/usage-animated-bfs.R @@ -4,7 +4,6 @@ # note: animation not implemented yet, please refer to code. library(dash) -library(dashHtmlComponents) library(dashCytoscape) library(jsonlite) diff --git a/demosR/usage-breadthfirst-layout.R b/demosR/usage-breadthfirst-layout.R index f9bae1d9..73977b44 100644 --- a/demosR/usage-breadthfirst-layout.R +++ b/demosR/usage-breadthfirst-layout.R @@ -3,7 +3,6 @@ # note: click animation is not implemented library(dash) -library(dashHtmlComponents) library(dashCytoscape) library(jsonlite) diff --git a/demosR/usage-circle-layout.R b/demosR/usage-circle-layout.R index cc642b0b..576d28ac 100644 --- a/demosR/usage-circle-layout.R +++ b/demosR/usage-circle-layout.R @@ -1,7 +1,6 @@ # original demo: http://js.cytoscape.org/demos/circle-layout/ library(dash) -library(dashHtmlComponents) library(dashCytoscape) library(jsonlite) diff --git a/demosR/usage-compound-nodes.R b/demosR/usage-compound-nodes.R index 935ea831..64671ed0 100644 --- a/demosR/usage-compound-nodes.R +++ b/demosR/usage-compound-nodes.R @@ -3,7 +3,6 @@ # note: the Dash version is also uncentered, and otherwise it works library(dash) -library(dashHtmlComponents) library(dashCytoscape) app <- Dash$new() diff --git a/demosR/usage-events.R b/demosR/usage-events.R index 9e43962a..a4efff0c 100644 --- a/demosR/usage-events.R +++ b/demosR/usage-events.R @@ -1,13 +1,11 @@ library(dash) -library(dashHtmlComponents) -library(dashCoreComponents) library(dashCytoscape) library(jsonlite) app <- Dash$new() # define elements -basic_elements = list( +basic_elements <- list( list( 'data' = list('id' = 'one', 'label' = 'Node 1'), 'position' = list('x' = 50, 'y' = 50) @@ -98,7 +96,7 @@ basic_elements = list( ) ) -styles = list( +styles <- list( 'json-output' = list( 'overflow-y' = 'scroll', 'height' = 'calc(50% - 25px)', diff --git a/demosR/usage-grid-layout.R b/demosR/usage-grid-layout.R index f55f4445..bb640ed8 100644 --- a/demosR/usage-grid-layout.R +++ b/demosR/usage-grid-layout.R @@ -1,7 +1,6 @@ # original demo: http://js.cytoscape.org/demos/grid-layout/ library(dash) -library(dashHtmlComponents) library(dashCytoscape) library(jsonlite) diff --git a/demosR/usage-multiple-instances.R b/demosR/usage-multiple-instances.R index 6c6d6126..7dd63c9c 100644 --- a/demosR/usage-multiple-instances.R +++ b/demosR/usage-multiple-instances.R @@ -1,7 +1,6 @@ # original demo: http://js.cytoscape.org/demos/multiple-instances/ library(dash) -library(dashHtmlComponents) library(dashCytoscape) library(jsonlite) diff --git a/demosR/usage-phylogeny.R b/demosR/usage-phylogeny.R deleted file mode 100644 index e8c5c3e9..00000000 --- a/demosR/usage-phylogeny.R +++ /dev/null @@ -1,252 +0,0 @@ -library(dash) -library(dashHtmlComponents) -library(dashCytoscape) -library(XML) - -# TODO: remove once "elements" defined -source("demosR/phylogeny/dummyData.R") - -app <- Dash$new() - -tree <- xmlToList(xmlParse(file = "demos/data/apaf.xml"))$phylogeny - -generate_elements <- function(tree, xlen=30, ylen=30, grabbable=FALSE, i=list(), n=1) { - # there are 31 "terminal" nodes with their respective 31 "support" nodes - # and 30 "nonterminal" nodes with their respective 29 "support" nodes - # since the root node does not require a preceding "support" node; - # each "support" node has the same x position as the parent clade, - # and the same y position as the child clade; it is used to create - # the 90 degree angle between the parent and the children; - # edge config: parent -> support -> child - nodes <- list() - edges <- list() - - # append root element - nodes[[n]] <- list( - data = list(id = "r"), - position = list(x = 30, y = 1200), - classes = "nonterminal", - grabbable = FALSE - ) - - # append all child nodes/edges and respective support nodes/edges - explore_child <- function(child, child_id, branch_length) { - if (class(child) == "list") { - if (!is.null(child$name)) { - clade_id <- child_id - support_id <- paste0(child_id, "s", i[[length(i)]]) - child_id <- paste0(child_id, "c", i[[length(i)]]) - n <<- n+2 - # support node and preceding edge - nodes[[n-1]] <<- list( - data = list(id = support_id), - # TODO: edit (x,y) according to branch_length = child$branch_length - # position = list(x = 0, y = 0), - classes = "support", - grabbable = FALSE - ) - edges[[n-2]] <<- list( - data = list( - source = clade_id, - target = support_id, - sourceCladeId = clade_id - ) - ) - # terminal node and preceding edge - nodes[[n]] <<- list( - data = list(id = child_id, name = child$name), - # TODO: edit (x,y) according to branch_length = child$branch_length - # position = list(x = 0, y = 0), - classes = "terminal", - grabbable = FALSE - ) - edges[[n-1]] <<- list( - data = list( - source = support_id, - target = child_id, - length = branch_length, - sourceCladeId = clade_id - ) - ) - i[[length(i)]] <<- i[[length(i)]]+1 - } else { - if (!is.null(child$confidence$text)) { - clade_id <- child_id - support_id <- paste0(child_id, "s", i[[length(i)]]) - child_id <- paste0(child_id, "c", i[[length(i)]]) - n <<- n+2 - # support node and preceding edge - nodes[[n-1]] <<- list( - data = list(id = support_id), - # TODO: edit (x,y) according to branch_length = child$branch_length - # position = list(x = 0, y = 0), - classes = "support", - grabbable = FALSE - ) - edges[[n-2]] <<- list( - data = list( - source = clade_id, - target = support_id, - sourceCladeId = clade_id - ) - ) - # nonterminal node and preceding edge - nodes[[n]] <<- list( - data = list(id = child_id, confidence = child$confidence$text), - # TODO: edit (x,y) according to branch_length = child$branch_length - # position = list(x = 0, y = 0), - classes = "nonterminal", - grabbable = FALSE - ) - edges[[n-1]] <<- list( - data = list( - source = support_id, - target = child_id, - length = branch_length, - sourceCladeId = clade_id - ) - ) - i[[length(i)]] <<- i[[length(i)]]+1 - } - i[[length(i)+1]] <<- 0 - lapply(child, explore_child, child_id=child_id, branch_length=child$branch_length) - i <<- i[-length(i)] - } - } - } - lapply(tree, explore_child, child_id="r", branch_length=0) - - # TODO: remove these draft functions and respective outputs - # get_terminals <- function(tree, terminals=list()) { - # get_name <- function(child) { - # if (class(child) == "list") { - # if (!is.null(child$name)) { - # terminals[[length(terminals)+1]] <<- list( - # name = child$name, - # branch_length = child$branch_length - # ) - # } else { - # lapply(child, get_name) - # } - # } - # } - # lapply(tree, get_name) - # return(terminals) - # } - # - # get_col_positions <- function(tree, taxa, column_width=80) { - # # note constants for drawing calculations - # max_label_width <- max(unlist(lapply(taxa, function(taxon) return(nchar(taxon$name))))) - # drawing_width <- column_width - max_label_width - 1 - # - # return(list()) - # } - # - # get_row_positions <- function(tree, taxa) { - # positions <- lapply(1:length(taxa), function(id) return(2*(id-1))) - # names(positions) <- lapply(taxa, function(taxon) return(taxon$name)) - # - # return(list()) - # } - # - # taxa <- get_terminals(tree) - # col_positions <- get_col_positions(tree, taxa) - # row_positions <- get_row_positions(tree, taxa) - - # TODO: delete test print statements - # print("NODES") - # str(nodes) - # print(paste("SIZE", length(nodes))) - # print("EDGES") - # str(edges) - # print(paste("SIZE", length(edges))) - - # TODO: add remaining attributes for nodes (i.e. position) in function the explore_child - elements <- c(nodes, edges) - - return(elements) -} - -elements <- generate_elements(tree) - -# TODO: delete test print statements -# print("ELEMENTS") -# str(elements) -# print(paste("SIZE", length(elements))) - -stylesheet <- list( - list( - "selector" = "edge", - "style" = list( - "source-endpoint" = "inside-to-node", - "target-endpoint" = "inside-to-node" - ) - ), - list( - "selector" = ".support", - "style" = list( - "background-opacity" = 0 - ) - ), - list( - "selector" = ".nonterminal", - "style" = list( - "label" = "data(confidence)", - "text-valign" = "top", - "text-halign" = "left", - "background-opacity" = 0 - ) - ), - list( - "selector" = ".terminal", - "style" = list( - "label" = "data(name)", - "text-valign" = "center", - "text-halign" = "right", - "width" = 10, - "height" = 10, - "background-color" = "#222222" - ) - ) -) - -app$layout( - htmlDiv( - list( - cytoCytoscape( - id = "cytoscape", - elements = dummyElements, # TODO: change to "elements" once defined - stylesheet = stylesheet, - layout = list( - "name" = "preset" - ), - style = list( - "height" = "95vh", - "width" = "100%" - ) - ) - ) - ) -) - -app$callback( - output = list(id = "cytoscape", property = "stylesheet"), - params = list(input(id = "cytoscape", property = "mouseoverEdgeData")), - function(edgeData) { - if (is.null(edgeData)) { - return(stylesheet) - } - val <- ifelse(grepl("s", edgeData$source), strsplit(edgeData$source, "s")[[1]], edgeData$source) - children_style = list( - list( - selector = sprintf("edge[source *= '%s']", val), - style = list( - 'line-color' = 'blue' - ) - ) - ) - return(c(stylesheet, children_style)) - } -) - -app$run_server(port = "8080", debug = TRUE) diff --git a/demosR/usage-pie-style.R b/demosR/usage-pie-style.R index eee5ab04..2851bcda 100644 --- a/demosR/usage-pie-style.R +++ b/demosR/usage-pie-style.R @@ -1,7 +1,6 @@ # original demo: http://js.cytoscape.org/demos/pie-style/ library(dash) -library(dashHtmlComponents) library(dashCytoscape) library(jsonlite) diff --git a/demosR/usage-visual-style.R b/demosR/usage-visual-style.R index 1f3d00d1..6a5cf4f7 100644 --- a/demosR/usage-visual-style.R +++ b/demosR/usage-visual-style.R @@ -1,7 +1,6 @@ # original demo: http://js.cytoscape.org/demos/visual-style/ library(dash) -library(dashHtmlComponents) library(dashCytoscape) app <- Dash$new() From df6f9f03bd12e4431d0478bd59f97120472ca32a Mon Sep 17 00:00:00 2001 From: Ryan Patrick Kyle Date: Fri, 21 May 2021 13:03:30 -0400 Subject: [PATCH 20/22] :hocho: line Co-authored-by: HammadTheOne <30986043+HammadTheOne@users.noreply.github.com> --- demosR/usage-compound-nodes.R | 1 - 1 file changed, 1 deletion(-) diff --git a/demosR/usage-compound-nodes.R b/demosR/usage-compound-nodes.R index 64671ed0..cb20df65 100644 --- a/demosR/usage-compound-nodes.R +++ b/demosR/usage-compound-nodes.R @@ -1,6 +1,5 @@ # original demo: http://js.cytoscape.org/demos/compound-nodes/ # -# note: the Dash version is also uncentered, and otherwise it works library(dash) library(dashCytoscape) From fb097a69840a270b8b1b542e481cba00773b1802 Mon Sep 17 00:00:00 2001 From: Ryan Patrick Kyle Date: Fri, 21 May 2021 13:03:53 -0400 Subject: [PATCH 21/22] :pencil2: add note Co-authored-by: HammadTheOne <30986043+HammadTheOne@users.noreply.github.com> --- demosR/usage-visual-style.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/demosR/usage-visual-style.R b/demosR/usage-visual-style.R index 6a5cf4f7..8045befb 100644 --- a/demosR/usage-visual-style.R +++ b/demosR/usage-visual-style.R @@ -1,5 +1,6 @@ # original demo: http://js.cytoscape.org/demos/visual-style/ - +# +# note: animation has not been implemented yet, please refer to code. library(dash) library(dashCytoscape) From abd0a9141a8769c79d76c37c4030a7400f2e0991 Mon Sep 17 00:00:00 2001 From: Ryan Patrick Kyle Date: Mon, 24 May 2021 23:31:36 -0400 Subject: [PATCH 22/22] chore: remove phylogeny directory --- demosR/phylogeny/dummyData.R | 248 --- demosR/phylogeny/elementsPy.txt | 254 --- demosR/phylogeny/elementsR.txt | 248 --- demosR/phylogeny/treePy.txt | 140 -- demosR/phylogeny/treeR.txt | 2881 ------------------------------- 5 files changed, 3771 deletions(-) delete mode 100644 demosR/phylogeny/dummyData.R delete mode 100644 demosR/phylogeny/elementsPy.txt delete mode 100644 demosR/phylogeny/elementsR.txt delete mode 100644 demosR/phylogeny/treePy.txt delete mode 100644 demosR/phylogeny/treeR.txt diff --git a/demosR/phylogeny/dummyData.R b/demosR/phylogeny/dummyData.R deleted file mode 100644 index 88dd34aa..00000000 --- a/demosR/phylogeny/dummyData.R +++ /dev/null @@ -1,248 +0,0 @@ -dummyNodes <- list( - list(data = list(id = 'r'), position = list('x' = 30, 'y' = 1200), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rs0'), position = list('x' = 30, 'y' = 840), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0', confidence = 89.0), position = list('x' = 180, 'y' = 840), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0s0'), position = list('x' = 180, 'y' = 660), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0', confidence = 32.0), position = list('x' = 240, 'y' = 660), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0s0'), position = list('x' = 240, 'y' = 540), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0', confidence = 100.0), position = list('x' = 450, 'y' = 540), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0s0'), position = list('x' = 450, 'y' = 390), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0', confidence = 89.0), position = list('x' = 630, 'y' = 390), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0s0'), position = list('x' = 630, 'y' = 270), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0', confidence = 100.0), position = list('x' = 870, 'y' = 270), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0s0'), position = list('x' = 870, 'y' = 180), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0', confidence = 100.0), position = list('x' = 930, 'y' = 180), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0s0'), position = list('x' = 930, 'y' = 120), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0', confidence = 43.0), position = list('x' = 960, 'y' = 120), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0s0'), position = list('x' = 960, 'y' = 60), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0', confidence = 100.0), position = list('x' = 1020, 'y' = 60), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0s0'), position = list('x' = 1020, 'y' = 30), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0c0', confidence = 88.0), position = list('x' = 1020, 'y' = 30), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0c0s0'), position = list('x' = 1020, 'y' = 0), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0c0c0', name = '22_MOUSE'), position = list('x' = 1080, 'y' = 0), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0c0s1'), position = list('x' = 1020, 'y' = 60), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0c0c1', name = 'Apaf-1_HUMAN'), position = list('x' = 1050, 'y' = 60), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0s1'), position = list('x' = 1020, 'y' = 120), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0c1', name = '12_CANFA'), position = list('x' = 1050, 'y' = 120), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0s1'), position = list('x' = 960, 'y' = 180), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c1', name = '11_CHICK'), position = list('x' = 1080, 'y' = 180), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0s1'), position = list('x' = 930, 'y' = 240), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c1', name = '16_XENLA'), position = list('x' = 1290, 'y' = 240), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0s1'), position = list('x' = 870, 'y' = 360), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1', confidence = 100.0), position = list('x' = 1020, 'y' = 360), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1s0'), position = list('x' = 1020, 'y' = 330), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1c0', confidence = 100.0), position = list('x' = 1110, 'y' = 330), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1c0s0'), position = list('x' = 1110, 'y' = 300), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1c0c0', name = '14_FUGRU'), position = list('x' = 1140, 'y' = 300), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1c0s1'), position = list('x' = 1110, 'y' = 360), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1c0c1', name = '15_TETNG'), position = list('x' = 1200, 'y' = 360), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1s1'), position = list('x' = 1020, 'y' = 420), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1c1', name = '17_BRARE'), position = list('x' = 1170, 'y' = 420), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0s1'), position = list('x' = 630, 'y' = 540), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1', confidence = 53.0), position = list('x' = 660, 'y' = 540), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1s0'), position = list('x' = 660, 'y' = 510), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1c0', confidence = 68.0), position = list('x' = 750, 'y' = 510), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1c0s0'), position = list('x' = 750, 'y' = 480), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1c0c0', name = '1_BRAFL'), position = list('x' = 960, 'y' = 480), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1c0s1'), position = list('x' = 750, 'y' = 540), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1c0c1', name = '18_NEMVE'), position = list('x' = 1050, 'y' = 540), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1s1'), position = list('x' = 660, 'y' = 600), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1c1', name = '23_STRPU'), position = list('x' = 1050, 'y' = 600), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0s1'), position = list('x' = 450, 'y' = 690), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c1', confidence = 100.0), position = list('x' = 750, 'y' = 690), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c1s0'), position = list('x' = 750, 'y' = 660), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c1c0', name = '26_STRPU'), position = list('x' = 1050, 'y' = 660), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c1s1'), position = list('x' = 750, 'y' = 720), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c1c1', name = '25_STRPU'), position = list('x' = 1020, 'y' = 720), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0s1'), position = list('x' = 240, 'y' = 810), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c1', confidence = 100.0), position = list('x' = 1320, 'y' = 810), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c1s0'), position = list('x' = 1320, 'y' = 780), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c1c0', name = 'CED4_CAEEL'), position = list('x' = 1440, 'y' = 780), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c1s1'), position = list('x' = 1320, 'y' = 840), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c1c1', name = '31_CAEBR'), position = list('x' = 1380, 'y' = 840), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0s1'), position = list('x' = 180, 'y' = 1020), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c1', confidence = 45.0), position = list('x' = 270, 'y' = 1020), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c1s0'), position = list('x' = 270, 'y' = 960), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c1c0', confidence = 95.0), position = list('x' = 480, 'y' = 960), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c1c0s0'), position = list('x' = 480, 'y' = 930), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c1c0c0', confidence = 100.0), position = list('x' = 1140, 'y' = 930), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c1c0c0s0'), position = list('x' = 1140, 'y' = 900), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c1c0c0c0', name = '28_DROPS'), position = list('x' = 1260, 'y' = 900), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c1c0c0s1'), position = list('x' = 1140, 'y' = 960), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c1c0c0c1', name = 'Dark_DROME'), position = list('x' = 1290, 'y' = 960), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c1c0s1'), position = list('x' = 480, 'y' = 1020), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c1c0c1', name = '29_AEDAE'), position = list('x' = 1200, 'y' = 1020), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c1s1'), position = list('x' = 270, 'y' = 1080), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c1c1', name = '30_TRICA'), position = list('x' = 1080, 'y' = 1080), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rs1'), position = list('x' = 30, 'y' = 1590), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1', confidence = 89.0), position = list('x' = 180, 'y' = 1590), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1s0'), position = list('x' = 180, 'y' = 1440), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0', confidence = 64.0), position = list('x' = 300, 'y' = 1440), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c0s0'), position = list('x' = 300, 'y' = 1350), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0', confidence = 100.0), position = list('x' = 750, 'y' = 1350), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0s0'), position = list('x' = 750, 'y' = 1260), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0', confidence = 46.0), position = list('x' = 840, 'y' = 1260), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0s0'), position = list('x' = 840, 'y' = 1200), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0', confidence = 61.0), position = list('x' = 1020, 'y' = 1200), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0s0'), position = list('x' = 1020, 'y' = 1170), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0c0', confidence = 100.0), position = list('x' = 1800, 'y' = 1170), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0c0s0'), position = list('x' = 1800, 'y' = 1140), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0c0c0', name = '34_BRAFL'), position = list('x' = 1860, 'y' = 1140), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0c0s1'), position = list('x' = 1800, 'y' = 1200), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0c0c1', name = '35_BRAFL'), position = list('x' = 1860, 'y' = 1200), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0s1'), position = list('x' = 1020, 'y' = 1260), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0c1', name = '8_BRAFL'), position = list('x' = 1500, 'y' = 1260), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0s1'), position = list('x' = 840, 'y' = 1350), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c1', confidence = 84.0), position = list('x' = 1080, 'y' = 1350), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c1s0'), position = list('x' = 1080, 'y' = 1320), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c1c0', name = '20_NEMVE'), position = list('x' = 1680, 'y' = 1320), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c1s1'), position = list('x' = 1080, 'y' = 1380), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c1c1', name = '21_NEMVE'), position = list('x' = 1890, 'y' = 1380), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0s1'), position = list('x' = 750, 'y' = 1440), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c1', name = '9_BRAFL'), position = list('x' = 1680, 'y' = 1440), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c0s1'), position = list('x' = 300, 'y' = 1560), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c1', confidence = 98.0), position = list('x' = 600, 'y' = 1560), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c1s0'), position = list('x' = 600, 'y' = 1530), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c1c0', confidence = 95.0), position = list('x' = 780, 'y' = 1530), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c1c0s0'), position = list('x' = 780, 'y' = 1500), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c1c0c0', name = '3_BRAFL'), position = list('x' = 1200, 'y' = 1500), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c1c0s1'), position = list('x' = 780, 'y' = 1560), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c1c0c1', name = '2_BRAFL'), position = list('x' = 1320, 'y' = 1560), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c1s1'), position = list('x' = 600, 'y' = 1620), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c1c1', name = '19_NEMVE'), position = list('x' = 1080, 'y' = 1620), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1s1'), position = list('x' = 180, 'y' = 1740), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c1', confidence = 92.0), position = list('x' = 540, 'y' = 1740), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c1s0'), position = list('x' = 540, 'y' = 1710), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c1c0', confidence = 100.0), position = list('x' = 1290, 'y' = 1710), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c1c0s0'), position = list('x' = 1290, 'y' = 1680), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c1c0c0', name = '37_BRAFL'), position = list('x' = 1470, 'y' = 1680), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c1c0s1'), position = list('x' = 1290, 'y' = 1740), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c1c0c1', name = '36_BRAFL'), position = list('x' = 1440, 'y' = 1740), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c1s1'), position = list('x' = 540, 'y' = 1800), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c1c1', name = '33_BRAFL'), position = list('x' = 1230, 'y' = 1800), classes = 'terminal', grabbable = FALSE) -) - -dummyEdges <- list( - list(data = list(source = 'r', target = 'rs0', sourceCladeId = 'r')), - list(data = list(source = 'rs0', target = 'rc0', length = 0, sourceCladeId = 'r')), - list(data = list(source = 'rc0', target = 'rc0s0', sourceCladeId = 'rc0')), - list(data = list(source = 'rc0s0', target = 'rc0c0', length = 0.18105, sourceCladeId = 'rc0')), - list(data = list(source = 'rc0c0', target = 'rc0c0s0', sourceCladeId = 'rc0c0')), - list(data = list(source = 'rc0c0s0', target = 'rc0c0c0', length = 0.07466, sourceCladeId = 'rc0c0')), - list(data = list(source = 'rc0c0c0', target = 'rc0c0c0s0', sourceCladeId = 'rc0c0c0')), - list(data = list(source = 'rc0c0c0s0', target = 'rc0c0c0c0', length = 0.26168, sourceCladeId = 'rc0c0c0')), - list(data = list(source = 'rc0c0c0c0', target = 'rc0c0c0c0s0', sourceCladeId = 'rc0c0c0c0')), - list(data = list(source = 'rc0c0c0c0s0', target = 'rc0c0c0c0c0', length = 0.22058, sourceCladeId = 'rc0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0', target = 'rc0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0s0', target = 'rc0c0c0c0c0c0', length = 0.28901, sourceCladeId = 'rc0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0', target = 'rc0c0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0s0', target = 'rc0c0c0c0c0c0c0', length = 0.06584, sourceCladeId = 'rc0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0s0', target = 'rc0c0c0c0c0c0c0c0', length = 0.02309, sourceCladeId = 'rc0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0c0s0', target = 'rc0c0c0c0c0c0c0c0c0', length = 0.0746, sourceCladeId = 'rc0c0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0c0c0s0', target = 'rc0c0c0c0c0c0c0c0c0c0', length = 0.02365, sourceCladeId = 'rc0c0c0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0c0c0s1', target = 'rc0c0c0c0c0c0c0c0c0c1', length = 0.02365, sourceCladeId = 'rc0c0c0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0c0s1', target = 'rc0c0c0c0c0c0c0c0c1', length = 0.0746, sourceCladeId = 'rc0c0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0s1', target = 'rc0c0c0c0c0c0c0c1', length = 0.02309, sourceCladeId = 'rc0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0', target = 'rc0c0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0s1', target = 'rc0c0c0c0c0c0c1', length = 0.06584, sourceCladeId = 'rc0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0', target = 'rc0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0s1', target = 'rc0c0c0c0c0c1', length = 0.28901, sourceCladeId = 'rc0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c1', target = 'rc0c0c0c0c0c1s0', sourceCladeId = 'rc0c0c0c0c0c1')), - list(data = list(source = 'rc0c0c0c0c0c1s0', target = 'rc0c0c0c0c0c1c0', length = 0.17031, sourceCladeId = 'rc0c0c0c0c0c1')), - list(data = list(source = 'rc0c0c0c0c0c1c0', target = 'rc0c0c0c0c0c1c0s0', sourceCladeId = 'rc0c0c0c0c0c1c0')), - list(data = list(source = 'rc0c0c0c0c0c1c0s0', target = 'rc0c0c0c0c0c1c0c0', length = 0.10929, sourceCladeId = 'rc0c0c0c0c0c1c0')), - list(data = list(source = 'rc0c0c0c0c0c1c0', target = 'rc0c0c0c0c0c1c0s1', sourceCladeId = 'rc0c0c0c0c0c1c0')), - list(data = list(source = 'rc0c0c0c0c0c1c0s1', target = 'rc0c0c0c0c0c1c0c1', length = 0.10929, sourceCladeId = 'rc0c0c0c0c0c1c0')), - list(data = list(source = 'rc0c0c0c0c0c1', target = 'rc0c0c0c0c0c1s1', sourceCladeId = 'rc0c0c0c0c0c1')), - list(data = list(source = 'rc0c0c0c0c0c1s1', target = 'rc0c0c0c0c0c1c1', length = 0.17031, sourceCladeId = 'rc0c0c0c0c0c1')), - list(data = list(source = 'rc0c0c0c0', target = 'rc0c0c0c0s1', sourceCladeId = 'rc0c0c0c0')), - list(data = list(source = 'rc0c0c0c0s1', target = 'rc0c0c0c0c1', length = 0.22058, sourceCladeId = 'rc0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c1', target = 'rc0c0c0c0c1s0', sourceCladeId = 'rc0c0c0c0c1')), - list(data = list(source = 'rc0c0c0c0c1s0', target = 'rc0c0c0c0c1c0', length = 0.01594, sourceCladeId = 'rc0c0c0c0c1')), - list(data = list(source = 'rc0c0c0c0c1c0', target = 'rc0c0c0c0c1c0s0', sourceCladeId = 'rc0c0c0c0c1c0')), - list(data = list(source = 'rc0c0c0c0c1c0s0', target = 'rc0c0c0c0c1c0c0', length = 0.10709, sourceCladeId = 'rc0c0c0c0c1c0')), - list(data = list(source = 'rc0c0c0c0c1c0', target = 'rc0c0c0c0c1c0s1', sourceCladeId = 'rc0c0c0c0c1c0')), - list(data = list(source = 'rc0c0c0c0c1c0s1', target = 'rc0c0c0c0c1c0c1', length = 0.10709, sourceCladeId = 'rc0c0c0c0c1c0')), - list(data = list(source = 'rc0c0c0c0c1', target = 'rc0c0c0c0c1s1', sourceCladeId = 'rc0c0c0c0c1')), - list(data = list(source = 'rc0c0c0c0c1s1', target = 'rc0c0c0c0c1c1', length = 0.01594, sourceCladeId = 'rc0c0c0c0c1')), - list(data = list(source = 'rc0c0c0', target = 'rc0c0c0s1', sourceCladeId = 'rc0c0c0')), - list(data = list(source = 'rc0c0c0s1', target = 'rc0c0c0c1', length = 0.26168, sourceCladeId = 'rc0c0c0')), - list(data = list(source = 'rc0c0c0c1', target = 'rc0c0c0c1s0', sourceCladeId = 'rc0c0c0c1')), - list(data = list(source = 'rc0c0c0c1s0', target = 'rc0c0c0c1c0', length = 0.34475, sourceCladeId = 'rc0c0c0c1')), - list(data = list(source = 'rc0c0c0c1', target = 'rc0c0c0c1s1', sourceCladeId = 'rc0c0c0c1')), - list(data = list(source = 'rc0c0c0c1s1', target = 'rc0c0c0c1c1', length = 0.34475, sourceCladeId = 'rc0c0c0c1')), - list(data = list(source = 'rc0c0', target = 'rc0c0s1', sourceCladeId = 'rc0c0')), - list(data = list(source = 'rc0c0s1', target = 'rc0c0c1', length = 0.07466, sourceCladeId = 'rc0c0')), - list(data = list(source = 'rc0c0c1', target = 'rc0c0c1s0', sourceCladeId = 'rc0c0c1')), - list(data = list(source = 'rc0c0c1s0', target = 'rc0c0c1c0', length = 1.31498, sourceCladeId = 'rc0c0c1')), - list(data = list(source = 'rc0c0c1', target = 'rc0c0c1s1', sourceCladeId = 'rc0c0c1')), - list(data = list(source = 'rc0c0c1s1', target = 'rc0c0c1c1', length = 1.31498, sourceCladeId = 'rc0c0c1')), - list(data = list(source = 'rc0', target = 'rc0s1', sourceCladeId = 'rc0')), - list(data = list(source = 'rc0s1', target = 'rc0c1', length = 0.18105, sourceCladeId = 'rc0')), - list(data = list(source = 'rc0c1', target = 'rc0c1s0', sourceCladeId = 'rc0c1')), - list(data = list(source = 'rc0c1s0', target = 'rc0c1c0', length = 0.13172, sourceCladeId = 'rc0c1')), - list(data = list(source = 'rc0c1c0', target = 'rc0c1c0s0', sourceCladeId = 'rc0c1c0')), - list(data = list(source = 'rc0c1c0s0', target = 'rc0c1c0c0', length = 0.24915, sourceCladeId = 'rc0c1c0')), - list(data = list(source = 'rc0c1c0c0', target = 'rc0c1c0c0s0', sourceCladeId = 'rc0c1c0c0')), - list(data = list(source = 'rc0c1c0c0s0', target = 'rc0c1c0c0c0', length = 0.76898, sourceCladeId = 'rc0c1c0c0')), - list(data = list(source = 'rc0c1c0c0', target = 'rc0c1c0c0s1', sourceCladeId = 'rc0c1c0c0')), - list(data = list(source = 'rc0c1c0c0s1', target = 'rc0c1c0c0c1', length = 0.76898, sourceCladeId = 'rc0c1c0c0')), - list(data = list(source = 'rc0c1c0', target = 'rc0c1c0s1', sourceCladeId = 'rc0c1c0')), - list(data = list(source = 'rc0c1c0s1', target = 'rc0c1c0c1', length = 0.24915, sourceCladeId = 'rc0c1c0')), - list(data = list(source = 'rc0c1', target = 'rc0c1s1', sourceCladeId = 'rc0c1')), - list(data = list(source = 'rc0c1s1', target = 'rc0c1c1', length = 0.13172, sourceCladeId = 'rc0c1')), - list(data = list(source = 'r', target = 'rs1', sourceCladeId = 'r')), - list(data = list(source = 'rs1', target = 'rc1', length = 0, sourceCladeId = 'r')), - list(data = list(source = 'rc1', target = 'rc1s0', sourceCladeId = 'rc1')), - list(data = list(source = 'rc1s0', target = 'rc1c0', length = 0.18105, sourceCladeId = 'rc1')), - list(data = list(source = 'rc1c0', target = 'rc1c0s0', sourceCladeId = 'rc1c0')), - list(data = list(source = 'rc1c0s0', target = 'rc1c0c0', length = 0.15891, sourceCladeId = 'rc1c0')), - list(data = list(source = 'rc1c0c0', target = 'rc1c0c0s0', sourceCladeId = 'rc1c0c0')), - list(data = list(source = 'rc1c0c0s0', target = 'rc1c0c0c0', length = 0.54836, sourceCladeId = 'rc1c0c0')), - list(data = list(source = 'rc1c0c0c0', target = 'rc1c0c0c0s0', sourceCladeId = 'rc1c0c0c0')), - list(data = list(source = 'rc1c0c0c0s0', target = 'rc1c0c0c0c0', length = 0.09305, sourceCladeId = 'rc1c0c0c0')), - list(data = list(source = 'rc1c0c0c0c0', target = 'rc1c0c0c0c0s0', sourceCladeId = 'rc1c0c0c0c0')), - list(data = list(source = 'rc1c0c0c0c0s0', target = 'rc1c0c0c0c0c0', length = 0.21648, sourceCladeId = 'rc1c0c0c0c0')), - list(data = list(source = 'rc1c0c0c0c0c0', target = 'rc1c0c0c0c0c0s0', sourceCladeId = 'rc1c0c0c0c0c0')), - list(data = list(source = 'rc1c0c0c0c0c0s0', target = 'rc1c0c0c0c0c0c0', length = 0.93134, sourceCladeId = 'rc1c0c0c0c0c0')), - list(data = list(source = 'rc1c0c0c0c0c0', target = 'rc1c0c0c0c0c0s1', sourceCladeId = 'rc1c0c0c0c0c0')), - list(data = list(source = 'rc1c0c0c0c0c0s1', target = 'rc1c0c0c0c0c0c1', length = 0.93134, sourceCladeId = 'rc1c0c0c0c0c0')), - list(data = list(source = 'rc1c0c0c0c0', target = 'rc1c0c0c0c0s1', sourceCladeId = 'rc1c0c0c0c0')), - list(data = list(source = 'rc1c0c0c0c0s1', target = 'rc1c0c0c0c0c1', length = 0.21648, sourceCladeId = 'rc1c0c0c0c0')), - list(data = list(source = 'rc1c0c0c0', target = 'rc1c0c0c0s1', sourceCladeId = 'rc1c0c0c0')), - list(data = list(source = 'rc1c0c0c0s1', target = 'rc1c0c0c0c1', length = 0.09305, sourceCladeId = 'rc1c0c0c0')), - list(data = list(source = 'rc1c0c0c0c1', target = 'rc1c0c0c0c1s0', sourceCladeId = 'rc1c0c0c0c1')), - list(data = list(source = 'rc1c0c0c0c1s0', target = 'rc1c0c0c0c1c0', length = 0.28437, sourceCladeId = 'rc1c0c0c0c1')), - list(data = list(source = 'rc1c0c0c0c1', target = 'rc1c0c0c0c1s1', sourceCladeId = 'rc1c0c0c0c1')), - list(data = list(source = 'rc1c0c0c0c1s1', target = 'rc1c0c0c0c1c1', length = 0.28437, sourceCladeId = 'rc1c0c0c0c1')), - list(data = list(source = 'rc1c0c0', target = 'rc1c0c0s1', sourceCladeId = 'rc1c0c0')), - list(data = list(source = 'rc1c0c0s1', target = 'rc1c0c0c1', length = 0.54836, sourceCladeId = 'rc1c0c0')), - list(data = list(source = 'rc1c0', target = 'rc1c0s1', sourceCladeId = 'rc1c0')), - list(data = list(source = 'rc1c0s1', target = 'rc1c0c1', length = 0.15891, sourceCladeId = 'rc1c0')), - list(data = list(source = 'rc1c0c1', target = 'rc1c0c1s0', sourceCladeId = 'rc1c0c1')), - list(data = list(source = 'rc1c0c1s0', target = 'rc1c0c1c0', length = 0.34914, sourceCladeId = 'rc1c0c1')), - list(data = list(source = 'rc1c0c1c0', target = 'rc1c0c1c0s0', sourceCladeId = 'rc1c0c1c0')), - list(data = list(source = 'rc1c0c1c0s0', target = 'rc1c0c1c0c0', length = 0.22189, sourceCladeId = 'rc1c0c1c0')), - list(data = list(source = 'rc1c0c1c0', target = 'rc1c0c1c0s1', sourceCladeId = 'rc1c0c1c0')), - list(data = list(source = 'rc1c0c1c0s1', target = 'rc1c0c1c0c1', length = 0.22189, sourceCladeId = 'rc1c0c1c0')), - list(data = list(source = 'rc1c0c1', target = 'rc1c0c1s1', sourceCladeId = 'rc1c0c1')), - list(data = list(source = 'rc1c0c1s1', target = 'rc1c0c1c1', length = 0.34914, sourceCladeId = 'rc1c0c1')), - list(data = list(source = 'rc1', target = 'rc1s1', sourceCladeId = 'rc1')), - list(data = list(source = 'rc1s1', target = 'rc1c1', length = 0.18105, sourceCladeId = 'rc1')), - list(data = list(source = 'rc1c1', target = 'rc1c1s0', sourceCladeId = 'rc1c1')), - list(data = list(source = 'rc1c1s0', target = 'rc1c1c0', length = 0.43438, sourceCladeId = 'rc1c1')), - list(data = list(source = 'rc1c1c0', target = 'rc1c1c0s0', sourceCladeId = 'rc1c1c0')), - list(data = list(source = 'rc1c1c0s0', target = 'rc1c1c0c0', length = 0.92214, sourceCladeId = 'rc1c1c0')), - list(data = list(source = 'rc1c1c0', target = 'rc1c1c0s1', sourceCladeId = 'rc1c1c0')), - list(data = list(source = 'rc1c1c0s1', target = 'rc1c1c0c1', length = 0.92214, sourceCladeId = 'rc1c1c0')), - list(data = list(source = 'rc1c1', target = 'rc1c1s1', sourceCladeId = 'rc1c1')), - list(data = list(source = 'rc1c1s1', target = 'rc1c1c1', length = 0.43438, sourceCladeId = 'rc1c1')) -) - -dummyElements <- c(dummyNodes, dummyEdges) diff --git a/demosR/phylogeny/elementsPy.txt b/demosR/phylogeny/elementsPy.txt deleted file mode 100644 index 7dc27e18..00000000 --- a/demosR/phylogeny/elementsPy.txt +++ /dev/null @@ -1,254 +0,0 @@ -[ - -# NODES -{'data': {'id': 'r'}, 'position': {'x': 30, 'y': 1200}, 'classes': 'nonterminal', 'grabbable': False}, -{'data': {'id': 'rs0'}, 'position': {'x': 30, 'y': 840}, 'grabbable': False, 'classes': 'support'}, -{'data': {'id': 'rc0', 'confidence': 89.0}, 'position': {'x': 180, 'y': 840}, 'classes': 'nonterminal', 'grabbable': False}, -{'data': {'id': 'rc0s0'}, 'position': {'x': 180, 'y': 660}, 'grabbable': False, 'classes': 'support'}, -{'data': {'id': 'rc0c0', 'confidence': 32.0}, 'position': {'x': 240, 'y': 660}, 'classes': 'nonterminal', 'grabbable': False}, -{'data': {'id': 'rc0c0s0'}, 'position': {'x': 240, 'y': 540}, 'grabbable': False, 'classes': 'support'}, -{'data': {'id': 'rc0c0c0', 'confidence': 100.0}, 'position': {'x': 450, 'y': 540}, 'classes': 'nonterminal', 'grabbable': False}, -{'data': {'id': 'rc0c0c0s0'}, 'position': {'x': 450, 'y': 390}, 'grabbable': False, 'classes': 'support'}, -{'data': {'id': 'rc0c0c0c0', 'confidence': 89.0}, 'position': {'x': 630, 'y': 390}, 'classes': 'nonterminal', 'grabbable': False}, -{'data': {'id': 'rc0c0c0c0s0'}, 'position': {'x': 630, 'y': 270}, 'grabbable': False, 'classes': 'support'}, -{'data': {'id': 'rc0c0c0c0c0', 'confidence': 100.0}, 'position': {'x': 870, 'y': 270}, 'classes': 'nonterminal', 'grabbable': False}, -{'data': {'id': 'rc0c0c0c0c0s0'}, 'position': {'x': 870, 'y': 180}, 'grabbable': False, 'classes': 'support'}, -{'data': {'id': 'rc0c0c0c0c0c0', 'confidence': 100.0}, 'position': {'x': 930, 'y': 180}, 'classes': 'nonterminal', 'grabbable': False}, -{'data': {'id': 'rc0c0c0c0c0c0s0'}, 'position': {'x': 930, 'y': 120}, 'grabbable': False, 'classes': 'support'}, -{'data': {'id': 'rc0c0c0c0c0c0c0', 'confidence': 43.0}, 'position': {'x': 960, 'y': 120}, 'classes': 'nonterminal', 'grabbable': False}, -{'data': {'id': 'rc0c0c0c0c0c0c0s0'}, 'position': {'x': 960, 'y': 60}, 'grabbable': False, 'classes': 'support'}, -{'data': {'id': 'rc0c0c0c0c0c0c0c0', 'confidence': 100.0}, 'position': {'x': 1020, 'y': 60}, 'classes': 'nonterminal', 'grabbable': False}, -{'data': {'id': 'rc0c0c0c0c0c0c0c0s0'}, 'position': {'x': 1020, 'y': 30}, 'grabbable': False, 'classes': 'support'}, -{'data': {'id': 'rc0c0c0c0c0c0c0c0c0', 'confidence': 88.0}, 'position': {'x': 1020, 'y': 30}, 'classes': 'nonterminal', 'grabbable': False}, -{'data': {'id': 'rc0c0c0c0c0c0c0c0c0s0'}, 'position': {'x': 1020, 'y': 0}, 'grabbable': False, 'classes': 'support'}, -{'data': {'id': 'rc0c0c0c0c0c0c0c0c0c0', 'name': '22_MOUSE'}, 'position': {'x': 1080, 'y': 0}, 'classes': 'terminal', 'grabbable': False}, -{'data': 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-{'data': {'source': 'rc0c0c0c1', 'target': 'rc0c0c0c1s1', 'sourceCladeId': 'rc0c0c0c1'}}, -{'data': {'source': 'rc0c0c0c1s1', 'target': 'rc0c0c0c1c1', 'length': 0.34475, 'sourceCladeId': 'rc0c0c0c1'}}, -{'data': {'source': 'rc0c0', 'target': 'rc0c0s1', 'sourceCladeId': 'rc0c0'}}, -{'data': {'source': 'rc0c0s1', 'target': 'rc0c0c1', 'length': 0.07466, 'sourceCladeId': 'rc0c0'}}, -{'data': {'source': 'rc0c0c1', 'target': 'rc0c0c1s0', 'sourceCladeId': 'rc0c0c1'}}, -{'data': {'source': 'rc0c0c1s0', 'target': 'rc0c0c1c0', 'length': 1.31498, 'sourceCladeId': 'rc0c0c1'}}, -{'data': {'source': 'rc0c0c1', 'target': 'rc0c0c1s1', 'sourceCladeId': 'rc0c0c1'}}, -{'data': {'source': 'rc0c0c1s1', 'target': 'rc0c0c1c1', 'length': 1.31498, 'sourceCladeId': 'rc0c0c1'}}, -{'data': {'source': 'rc0', 'target': 'rc0s1', 'sourceCladeId': 'rc0'}}, -{'data': {'source': 'rc0s1', 'target': 'rc0c1', 'length': 0.18105, 'sourceCladeId': 'rc0'}}, -{'data': {'source': 'rc0c1', 'target': 'rc0c1s0', 'sourceCladeId': 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'rc1c1'}}, -{'data': {'source': 'rc1c1c0', 'target': 'rc1c1c0s0', 'sourceCladeId': 'rc1c1c0'}}, -{'data': {'source': 'rc1c1c0s0', 'target': 'rc1c1c0c0', 'length': 0.92214, 'sourceCladeId': 'rc1c1c0'}}, -{'data': {'source': 'rc1c1c0', 'target': 'rc1c1c0s1', 'sourceCladeId': 'rc1c1c0'}}, -{'data': {'source': 'rc1c1c0s1', 'target': 'rc1c1c0c1', 'length': 0.92214, 'sourceCladeId': 'rc1c1c0'}}, -{'data': {'source': 'rc1c1', 'target': 'rc1c1s1', 'sourceCladeId': 'rc1c1'}}, -{'data': {'source': 'rc1c1s1', 'target': 'rc1c1c1', 'length': 0.43438, 'sourceCladeId': 'rc1c1'}} - -] - - - - - - diff --git a/demosR/phylogeny/elementsR.txt b/demosR/phylogeny/elementsR.txt deleted file mode 100644 index 6f180a78..00000000 --- a/demosR/phylogeny/elementsR.txt +++ /dev/null @@ -1,248 +0,0 @@ -dummyNodes <- list( - list(data = list(id = 'r'), position = list('x' = 30, 'y' = 1200), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rs0'), position = list('x' = 30, 'y' = 840), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0', confidence = 89.0), position = list('x' = 180, 'y' = 840), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0s0'), position = list('x' = 180, 'y' = 660), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0', confidence = 32.0), position = list('x' = 240, 'y' = 660), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0s0'), position = list('x' = 240, 'y' = 540), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0', confidence = 100.0), position = list('x' = 450, 'y' = 540), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0s0'), position = list('x' = 450, 'y' = 390), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0', confidence = 89.0), position = list('x' = 630, 'y' = 390), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0s0'), position = list('x' = 630, 'y' = 270), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0', confidence = 100.0), position = list('x' = 870, 'y' = 270), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0s0'), position = list('x' = 870, 'y' = 180), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0', confidence = 100.0), position = list('x' = 930, 'y' = 180), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0s0'), position = list('x' = 930, 'y' = 120), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0', confidence = 43.0), position = list('x' = 960, 'y' = 120), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0s0'), position = list('x' = 960, 'y' = 60), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0', confidence = 100.0), position = list('x' = 1020, 'y' = 60), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0s0'), position = list('x' = 1020, 'y' = 30), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0c0', confidence = 88.0), position = list('x' = 1020, 'y' = 30), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0c0s0'), position = list('x' = 1020, 'y' = 0), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0c0c0', name = '22_MOUSE'), position = list('x' = 1080, 'y' = 0), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0c0s1'), position = list('x' = 1020, 'y' = 60), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0c0c1', name = 'Apaf-1_HUMAN'), position = list('x' = 1050, 'y' = 60), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0s1'), position = list('x' = 1020, 'y' = 120), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c0c1', name = '12_CANFA'), position = list('x' = 1050, 'y' = 120), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0s1'), position = list('x' = 960, 'y' = 180), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c0c1', name = '11_CHICK'), position = list('x' = 1080, 'y' = 180), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0s1'), position = list('x' = 930, 'y' = 240), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c0c1', name = '16_XENLA'), position = list('x' = 1290, 'y' = 240), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0s1'), position = list('x' = 870, 'y' = 360), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1', confidence = 100.0), position = list('x' = 1020, 'y' = 360), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1s0'), position = list('x' = 1020, 'y' = 330), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1c0', confidence = 100.0), position = list('x' = 1110, 'y' = 330), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1c0s0'), position = list('x' = 1110, 'y' = 300), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1c0c0', name = '14_FUGRU'), position = list('x' = 1140, 'y' = 300), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1c0s1'), position = list('x' = 1110, 'y' = 360), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1c0c1', name = '15_TETNG'), position = list('x' = 1200, 'y' = 360), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1s1'), position = list('x' = 1020, 'y' = 420), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c0c1c1', name = '17_BRARE'), position = list('x' = 1170, 'y' = 420), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0s1'), position = list('x' = 630, 'y' = 540), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1', confidence = 53.0), position = list('x' = 660, 'y' = 540), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1s0'), position = list('x' = 660, 'y' = 510), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1c0', confidence = 68.0), position = list('x' = 750, 'y' = 510), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1c0s0'), position = list('x' = 750, 'y' = 480), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1c0c0', name = '1_BRAFL'), position = list('x' = 960, 'y' = 480), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1c0s1'), position = list('x' = 750, 'y' = 540), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1c0c1', name = '18_NEMVE'), position = list('x' = 1050, 'y' = 540), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1s1'), position = list('x' = 660, 'y' = 600), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c0c1c1', name = '23_STRPU'), position = list('x' = 1050, 'y' = 600), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0s1'), position = list('x' = 450, 'y' = 690), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c1', confidence = 100.0), position = list('x' = 750, 'y' = 690), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c1s0'), position = list('x' = 750, 'y' = 660), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c1c0', name = '26_STRPU'), position = list('x' = 1050, 'y' = 660), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c1s1'), position = list('x' = 750, 'y' = 720), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c0c1c1', name = '25_STRPU'), position = list('x' = 1020, 'y' = 720), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0s1'), position = list('x' = 240, 'y' = 810), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c1', confidence = 100.0), position = list('x' = 1320, 'y' = 810), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c1s0'), position = list('x' = 1320, 'y' = 780), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c1c0', name = 'CED4_CAEEL'), position = list('x' = 1440, 'y' = 780), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c0c1s1'), position = list('x' = 1320, 'y' = 840), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c0c1c1', name = '31_CAEBR'), position = list('x' = 1380, 'y' = 840), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0s1'), position = list('x' = 180, 'y' = 1020), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c1', confidence = 45.0), position = list('x' = 270, 'y' = 1020), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c1s0'), position = list('x' = 270, 'y' = 960), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c1c0', confidence = 95.0), position = list('x' = 480, 'y' = 960), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c1c0s0'), position = list('x' = 480, 'y' = 930), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c1c0c0', confidence = 100.0), position = list('x' = 1140, 'y' = 930), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc0c1c0c0s0'), position = list('x' = 1140, 'y' = 900), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c1c0c0c0', name = '28_DROPS'), position = list('x' = 1260, 'y' = 900), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c1c0c0s1'), position = list('x' = 1140, 'y' = 960), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c1c0c0c1', name = 'Dark_DROME'), position = list('x' = 1290, 'y' = 960), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c1c0s1'), position = list('x' = 480, 'y' = 1020), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c1c0c1', name = '29_AEDAE'), position = list('x' = 1200, 'y' = 1020), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc0c1s1'), position = list('x' = 270, 'y' = 1080), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc0c1c1', name = '30_TRICA'), position = list('x' = 1080, 'y' = 1080), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rs1'), position = list('x' = 30, 'y' = 1590), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1', confidence = 89.0), position = list('x' = 180, 'y' = 1590), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1s0'), position = list('x' = 180, 'y' = 1440), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0', confidence = 64.0), position = list('x' = 300, 'y' = 1440), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c0s0'), position = list('x' = 300, 'y' = 1350), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0', confidence = 100.0), position = list('x' = 750, 'y' = 1350), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0s0'), position = list('x' = 750, 'y' = 1260), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0', confidence = 46.0), position = list('x' = 840, 'y' = 1260), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0s0'), position = list('x' = 840, 'y' = 1200), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0', confidence = 61.0), position = list('x' = 1020, 'y' = 1200), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0s0'), position = list('x' = 1020, 'y' = 1170), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0c0', confidence = 100.0), position = list('x' = 1800, 'y' = 1170), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0c0s0'), position = list('x' = 1800, 'y' = 1140), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0c0c0', name = '34_BRAFL'), position = list('x' = 1860, 'y' = 1140), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0c0s1'), position = list('x' = 1800, 'y' = 1200), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0c0c1', name = '35_BRAFL'), position = list('x' = 1860, 'y' = 1200), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0s1'), position = list('x' = 1020, 'y' = 1260), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c0c1', name = '8_BRAFL'), position = list('x' = 1500, 'y' = 1260), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0s1'), position = list('x' = 840, 'y' = 1350), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c1', confidence = 84.0), position = list('x' = 1080, 'y' = 1350), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c1s0'), position = list('x' = 1080, 'y' = 1320), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c1c0', name = '20_NEMVE'), position = list('x' = 1680, 'y' = 1320), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c1s1'), position = list('x' = 1080, 'y' = 1380), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c0c1c1', name = '21_NEMVE'), position = list('x' = 1890, 'y' = 1380), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c0s1'), position = list('x' = 750, 'y' = 1440), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c0c1', name = '9_BRAFL'), position = list('x' = 1680, 'y' = 1440), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c0s1'), position = list('x' = 300, 'y' = 1560), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c1', confidence = 98.0), position = list('x' = 600, 'y' = 1560), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c1s0'), position = list('x' = 600, 'y' = 1530), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c1c0', confidence = 95.0), position = list('x' = 780, 'y' = 1530), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c1c0s0'), position = list('x' = 780, 'y' = 1500), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c1c0c0', name = '3_BRAFL'), position = list('x' = 1200, 'y' = 1500), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c1c0s1'), position = list('x' = 780, 'y' = 1560), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c1c0c1', name = '2_BRAFL'), position = list('x' = 1320, 'y' = 1560), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c0c1s1'), position = list('x' = 600, 'y' = 1620), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c0c1c1', name = '19_NEMVE'), position = list('x' = 1080, 'y' = 1620), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1s1'), position = list('x' = 180, 'y' = 1740), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c1', confidence = 92.0), position = list('x' = 540, 'y' = 1740), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c1s0'), position = list('x' = 540, 'y' = 1710), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c1c0', confidence = 100.0), position = list('x' = 1290, 'y' = 1710), classes = 'nonterminal', grabbable = FALSE), - list(data = list(id = 'rc1c1c0s0'), position = list('x' = 1290, 'y' = 1680), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c1c0c0', name = '37_BRAFL'), position = list('x' = 1470, 'y' = 1680), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c1c0s1'), position = list('x' = 1290, 'y' = 1740), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c1c0c1', name = '36_BRAFL'), position = list('x' = 1440, 'y' = 1740), classes = 'terminal', grabbable = FALSE), - list(data = list(id = 'rc1c1s1'), position = list('x' = 540, 'y' = 1800), classes = 'support', grabbable = FALSE), - list(data = list(id = 'rc1c1c1', name = '33_BRAFL'), position = list('x' = 1230, 'y' = 1800), classes = 'terminal', grabbable = FALSE) -) - -dummyEdges <- list( - list(data = list(source = 'r', target = 'rs0', sourceCladeId = 'r')), - list(data = list(source = 'rs0', target = 'rc0', length = 0, sourceCladeId = 'r')), - list(data = list(source = 'rc0', target = 'rc0s0', sourceCladeId = 'rc0')), - list(data = list(source = 'rc0s0', target = 'rc0c0', length = 0.18105, sourceCladeId = 'rc0')), - list(data = list(source = 'rc0c0', target = 'rc0c0s0', sourceCladeId = 'rc0c0')), - list(data = list(source = 'rc0c0s0', target = 'rc0c0c0', length = 0.07466, sourceCladeId = 'rc0c0')), - list(data = list(source = 'rc0c0c0', target = 'rc0c0c0s0', sourceCladeId = 'rc0c0c0')), - list(data = list(source = 'rc0c0c0s0', target = 'rc0c0c0c0', length = 0.26168, sourceCladeId = 'rc0c0c0')), - list(data = list(source = 'rc0c0c0c0', target = 'rc0c0c0c0s0', sourceCladeId = 'rc0c0c0c0')), - list(data = list(source = 'rc0c0c0c0s0', target = 'rc0c0c0c0c0', length = 0.22058, sourceCladeId = 'rc0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0', target = 'rc0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0s0', target = 'rc0c0c0c0c0c0', length = 0.28901, sourceCladeId = 'rc0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0', target = 'rc0c0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0s0', target = 'rc0c0c0c0c0c0c0', length = 0.06584, sourceCladeId = 'rc0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0s0', target = 'rc0c0c0c0c0c0c0c0', length = 0.02309, sourceCladeId = 'rc0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0c0s0', target = 'rc0c0c0c0c0c0c0c0c0', length = 0.0746, sourceCladeId = 'rc0c0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0c0c0s0', sourceCladeId = 'rc0c0c0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0c0c0s0', target = 'rc0c0c0c0c0c0c0c0c0c0', length = 0.02365, sourceCladeId = 'rc0c0c0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0c0c0s1', target = 'rc0c0c0c0c0c0c0c0c0c1', length = 0.02365, sourceCladeId = 'rc0c0c0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0c0s1', target = 'rc0c0c0c0c0c0c0c0c1', length = 0.0746, sourceCladeId = 'rc0c0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0', target = 'rc0c0c0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0c0s1', target = 'rc0c0c0c0c0c0c0c1', length = 0.02309, sourceCladeId = 'rc0c0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0', target = 'rc0c0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c0s1', target = 'rc0c0c0c0c0c0c1', length = 0.06584, sourceCladeId = 'rc0c0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0', target = 'rc0c0c0c0c0s1', sourceCladeId = 'rc0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0s1', target = 'rc0c0c0c0c0c1', length = 0.28901, sourceCladeId = 'rc0c0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c0c1', target = 'rc0c0c0c0c0c1s0', sourceCladeId = 'rc0c0c0c0c0c1')), - list(data = list(source = 'rc0c0c0c0c0c1s0', target = 'rc0c0c0c0c0c1c0', length = 0.17031, sourceCladeId = 'rc0c0c0c0c0c1')), - list(data = list(source = 'rc0c0c0c0c0c1c0', target = 'rc0c0c0c0c0c1c0s0', sourceCladeId = 'rc0c0c0c0c0c1c0')), - list(data = list(source = 'rc0c0c0c0c0c1c0s0', target = 'rc0c0c0c0c0c1c0c0', length = 0.10929, sourceCladeId = 'rc0c0c0c0c0c1c0')), - list(data = list(source = 'rc0c0c0c0c0c1c0', target = 'rc0c0c0c0c0c1c0s1', sourceCladeId = 'rc0c0c0c0c0c1c0')), - list(data = list(source = 'rc0c0c0c0c0c1c0s1', target = 'rc0c0c0c0c0c1c0c1', length = 0.10929, sourceCladeId = 'rc0c0c0c0c0c1c0')), - list(data = list(source = 'rc0c0c0c0c0c1', target = 'rc0c0c0c0c0c1s1', sourceCladeId = 'rc0c0c0c0c0c1')), - list(data = list(source = 'rc0c0c0c0c0c1s1', target = 'rc0c0c0c0c0c1c1', length = 0.17031, sourceCladeId = 'rc0c0c0c0c0c1')), - list(data = list(source = 'rc0c0c0c0', target = 'rc0c0c0c0s1', sourceCladeId = 'rc0c0c0c0')), - list(data = list(source = 'rc0c0c0c0s1', target = 'rc0c0c0c0c1', length = 0.22058, sourceCladeId = 'rc0c0c0c0')), - list(data = list(source = 'rc0c0c0c0c1', target = 'rc0c0c0c0c1s0', sourceCladeId = 'rc0c0c0c0c1')), - list(data = list(source = 'rc0c0c0c0c1s0', target = 'rc0c0c0c0c1c0', length = 0.01594, sourceCladeId = 'rc0c0c0c0c1')), - list(data = list(source = 'rc0c0c0c0c1c0', target = 'rc0c0c0c0c1c0s0', sourceCladeId = 'rc0c0c0c0c1c0')), - list(data = list(source = 'rc0c0c0c0c1c0s0', target = 'rc0c0c0c0c1c0c0', length = 0.10709, sourceCladeId = 'rc0c0c0c0c1c0')), - list(data = list(source = 'rc0c0c0c0c1c0', target = 'rc0c0c0c0c1c0s1', sourceCladeId = 'rc0c0c0c0c1c0')), - list(data = list(source = 'rc0c0c0c0c1c0s1', target = 'rc0c0c0c0c1c0c1', length = 0.10709, sourceCladeId = 'rc0c0c0c0c1c0')), - list(data = list(source = 'rc0c0c0c0c1', target = 'rc0c0c0c0c1s1', sourceCladeId = 'rc0c0c0c0c1')), - list(data = list(source = 'rc0c0c0c0c1s1', target = 'rc0c0c0c0c1c1', length = 0.01594, sourceCladeId = 'rc0c0c0c0c1')), - list(data = list(source = 'rc0c0c0', target = 'rc0c0c0s1', sourceCladeId = 'rc0c0c0')), - list(data = list(source = 'rc0c0c0s1', target = 'rc0c0c0c1', length = 0.26168, sourceCladeId = 'rc0c0c0')), - list(data = list(source = 'rc0c0c0c1', target = 'rc0c0c0c1s0', sourceCladeId = 'rc0c0c0c1')), - list(data = list(source = 'rc0c0c0c1s0', target = 'rc0c0c0c1c0', length = 0.34475, sourceCladeId = 'rc0c0c0c1')), - list(data = list(source = 'rc0c0c0c1', target = 'rc0c0c0c1s1', sourceCladeId = 'rc0c0c0c1')), - list(data = list(source = 'rc0c0c0c1s1', target = 'rc0c0c0c1c1', length = 0.34475, sourceCladeId = 'rc0c0c0c1')), - list(data = list(source = 'rc0c0', target = 'rc0c0s1', sourceCladeId = 'rc0c0')), - list(data = list(source = 'rc0c0s1', target = 'rc0c0c1', length = 0.07466, sourceCladeId = 'rc0c0')), - list(data = list(source = 'rc0c0c1', target = 'rc0c0c1s0', sourceCladeId = 'rc0c0c1')), - list(data = list(source = 'rc0c0c1s0', target = 'rc0c0c1c0', length = 1.31498, sourceCladeId = 'rc0c0c1')), - list(data = list(source = 'rc0c0c1', target = 'rc0c0c1s1', sourceCladeId = 'rc0c0c1')), - list(data = list(source = 'rc0c0c1s1', target = 'rc0c0c1c1', length = 1.31498, sourceCladeId = 'rc0c0c1')), - list(data = list(source = 'rc0', target = 'rc0s1', sourceCladeId = 'rc0')), - list(data = list(source = 'rc0s1', target = 'rc0c1', length = 0.18105, sourceCladeId = 'rc0')), - list(data = list(source = 'rc0c1', target = 'rc0c1s0', sourceCladeId = 'rc0c1')), - list(data = list(source = 'rc0c1s0', target = 'rc0c1c0', length = 0.13172, sourceCladeId = 'rc0c1')), - list(data = list(source = 'rc0c1c0', target = 'rc0c1c0s0', sourceCladeId = 'rc0c1c0')), - list(data = list(source = 'rc0c1c0s0', target = 'rc0c1c0c0', length = 0.24915, sourceCladeId = 'rc0c1c0')), - list(data = list(source = 'rc0c1c0c0', target = 'rc0c1c0c0s0', sourceCladeId = 'rc0c1c0c0')), - list(data = list(source = 'rc0c1c0c0s0', target = 'rc0c1c0c0c0', length = 0.76898, sourceCladeId = 'rc0c1c0c0')), - list(data = list(source = 'rc0c1c0c0', target = 'rc0c1c0c0s1', sourceCladeId = 'rc0c1c0c0')), - list(data = list(source = 'rc0c1c0c0s1', target = 'rc0c1c0c0c1', length = 0.76898, sourceCladeId = 'rc0c1c0c0')), - list(data = list(source = 'rc0c1c0', target = 'rc0c1c0s1', sourceCladeId = 'rc0c1c0')), - list(data = list(source = 'rc0c1c0s1', target = 'rc0c1c0c1', length = 0.24915, sourceCladeId = 'rc0c1c0')), - list(data = list(source = 'rc0c1', target = 'rc0c1s1', sourceCladeId = 'rc0c1')), - list(data = list(source = 'rc0c1s1', target = 'rc0c1c1', length = 0.13172, sourceCladeId = 'rc0c1')), - list(data = list(source = 'r', target = 'rs1', sourceCladeId = 'r')), - list(data = list(source = 'rs1', target = 'rc1', length = 0, sourceCladeId = 'r')), - list(data = list(source = 'rc1', target = 'rc1s0', sourceCladeId = 'rc1')), - list(data = list(source = 'rc1s0', target = 'rc1c0', length = 0.18105, sourceCladeId = 'rc1')), - list(data = list(source = 'rc1c0', target = 'rc1c0s0', sourceCladeId = 'rc1c0')), - list(data = list(source = 'rc1c0s0', target = 'rc1c0c0', length = 0.15891, sourceCladeId = 'rc1c0')), - list(data = list(source = 'rc1c0c0', target = 'rc1c0c0s0', sourceCladeId = 'rc1c0c0')), - list(data = list(source = 'rc1c0c0s0', target = 'rc1c0c0c0', length = 0.54836, sourceCladeId = 'rc1c0c0')), - list(data = list(source = 'rc1c0c0c0', target = 'rc1c0c0c0s0', sourceCladeId = 'rc1c0c0c0')), - list(data = list(source = 'rc1c0c0c0s0', target = 'rc1c0c0c0c0', length = 0.09305, sourceCladeId = 'rc1c0c0c0')), - list(data = list(source = 'rc1c0c0c0c0', target = 'rc1c0c0c0c0s0', sourceCladeId = 'rc1c0c0c0c0')), - list(data = list(source = 'rc1c0c0c0c0s0', target = 'rc1c0c0c0c0c0', length = 0.21648, sourceCladeId = 'rc1c0c0c0c0')), - list(data = list(source = 'rc1c0c0c0c0c0', target = 'rc1c0c0c0c0c0s0', sourceCladeId = 'rc1c0c0c0c0c0')), - list(data = list(source = 'rc1c0c0c0c0c0s0', target = 'rc1c0c0c0c0c0c0', length = 0.93134, sourceCladeId = 'rc1c0c0c0c0c0')), - list(data = list(source = 'rc1c0c0c0c0c0', target = 'rc1c0c0c0c0c0s1', sourceCladeId = 'rc1c0c0c0c0c0')), - list(data = list(source = 'rc1c0c0c0c0c0s1', target = 'rc1c0c0c0c0c0c1', length = 0.93134, sourceCladeId = 'rc1c0c0c0c0c0')), - list(data = list(source = 'rc1c0c0c0c0', target = 'rc1c0c0c0c0s1', sourceCladeId = 'rc1c0c0c0c0')), - list(data = list(source = 'rc1c0c0c0c0s1', target = 'rc1c0c0c0c0c1', length = 0.21648, sourceCladeId = 'rc1c0c0c0c0')), - list(data = list(source = 'rc1c0c0c0', target = 'rc1c0c0c0s1', sourceCladeId = 'rc1c0c0c0')), - list(data = list(source = 'rc1c0c0c0s1', target = 'rc1c0c0c0c1', length = 0.09305, sourceCladeId = 'rc1c0c0c0')), - list(data = list(source = 'rc1c0c0c0c1', target = 'rc1c0c0c0c1s0', sourceCladeId = 'rc1c0c0c0c1')), - list(data = list(source = 'rc1c0c0c0c1s0', target = 'rc1c0c0c0c1c0', length = 0.28437, sourceCladeId = 'rc1c0c0c0c1')), - list(data = list(source = 'rc1c0c0c0c1', target = 'rc1c0c0c0c1s1', sourceCladeId = 'rc1c0c0c0c1')), - list(data = list(source = 'rc1c0c0c0c1s1', target = 'rc1c0c0c0c1c1', length = 0.28437, sourceCladeId = 'rc1c0c0c0c1')), - list(data = list(source = 'rc1c0c0', target = 'rc1c0c0s1', sourceCladeId = 'rc1c0c0')), - list(data = list(source = 'rc1c0c0s1', target = 'rc1c0c0c1', length = 0.54836, sourceCladeId = 'rc1c0c0')), - list(data = list(source = 'rc1c0', target = 'rc1c0s1', sourceCladeId = 'rc1c0')), - list(data = list(source = 'rc1c0s1', target = 'rc1c0c1', length = 0.15891, sourceCladeId = 'rc1c0')), - list(data = list(source = 'rc1c0c1', target = 'rc1c0c1s0', sourceCladeId = 'rc1c0c1')), - list(data = list(source = 'rc1c0c1s0', target = 'rc1c0c1c0', length = 0.34914, sourceCladeId = 'rc1c0c1')), - list(data = list(source = 'rc1c0c1c0', target = 'rc1c0c1c0s0', sourceCladeId = 'rc1c0c1c0')), - list(data = list(source = 'rc1c0c1c0s0', target = 'rc1c0c1c0c0', length = 0.22189, sourceCladeId = 'rc1c0c1c0')), - list(data = list(source = 'rc1c0c1c0', target = 'rc1c0c1c0s1', sourceCladeId = 'rc1c0c1c0')), - list(data = list(source = 'rc1c0c1c0s1', target = 'rc1c0c1c0c1', length = 0.22189, sourceCladeId = 'rc1c0c1c0')), - list(data = list(source = 'rc1c0c1', target = 'rc1c0c1s1', sourceCladeId = 'rc1c0c1')), - list(data = list(source = 'rc1c0c1s1', target = 'rc1c0c1c1', length = 0.34914, sourceCladeId = 'rc1c0c1')), - list(data = list(source = 'rc1', target = 'rc1s1', sourceCladeId = 'rc1')), - list(data = list(source = 'rc1s1', target = 'rc1c1', length = 0.18105, sourceCladeId = 'rc1')), - list(data = list(source = 'rc1c1', target = 'rc1c1s0', sourceCladeId = 'rc1c1')), - list(data = list(source = 'rc1c1s0', target = 'rc1c1c0', length = 0.43438, sourceCladeId = 'rc1c1')), - list(data = list(source = 'rc1c1c0', target = 'rc1c1c0s0', sourceCladeId = 'rc1c1c0')), - list(data = list(source = 'rc1c1c0s0', target = 'rc1c1c0c0', length = 0.92214, sourceCladeId = 'rc1c1c0')), - list(data = list(source = 'rc1c1c0', target = 'rc1c1c0s1', sourceCladeId = 'rc1c1c0')), - list(data = list(source = 'rc1c1c0s1', target = 'rc1c1c0c1', length = 0.92214, sourceCladeId = 'rc1c1c0')), - list(data = list(source = 'rc1c1', target = 'rc1c1s1', sourceCladeId = 'rc1c1')), - list(data = list(source = 'rc1c1s1', target = 'rc1c1c1', length = 0.43438, sourceCladeId = 'rc1c1')) -) - -dummyElements <- c(dummyNodes, dummyEdges) \ No newline at end of file diff --git a/demosR/phylogeny/treePy.txt b/demosR/phylogeny/treePy.txt deleted file mode 100644 index 05e24dd7..00000000 --- a/demosR/phylogeny/treePy.txt +++ /dev/null @@ -1,140 +0,0 @@ -Phylogeny(rooted=True) - Clade() - Clade(branch_length=0.18105) - Confidence(type='unknown', value=89.0) - Clade(branch_length=0.07466) - Confidence(type='unknown', value=32.0) - Clade(branch_length=0.26168) - Confidence(type='unknown', value=100.0) - Clade(branch_length=0.22058) - Confidence(type='unknown', value=89.0) - Clade(branch_length=0.28901) - Confidence(type='unknown', value=100.0) - Clade(branch_length=0.06584) - Confidence(type='unknown', value=100.0) - Clade(branch_length=0.02309) - Confidence(type='unknown', value=43.0) - Clade(branch_length=0.0746) - Confidence(type='unknown', value=100.0) - Clade(branch_length=0.02365) - Confidence(type='unknown', value=88.0) - Clade(branch_length=0.05998, name='22_MOUSE') - MOUSE - Sequence() - DomainArchitecture(length=1249) - ProteinDomain(confidence=7e-26, end=90, start=5, value='CARD') - ProteinDomain(confidence=7.2e-117, end=414, start=108, value='NB-ARC') - ProteinDomain(confidence=2.4e-06, end=643, start=604, value='WD40') - ProteinDomain(confidence=1.1e-12, end=685, start=646, value='WD40') - ProteinDomain(confidence=2.4e-07, end=729, start=688, value='WD40') - ProteinDomain(confidence=4.7e-14, end=771, start=732, value='WD40') - ProteinDomain(confidence=2.5e-08, end=910, start=871, value='WD40') - ProteinDomain(confidence=4.6e-06, end=1031, start=992, value='WD40') - ProteinDomain(confidence=6.3e-07, end=1113, start=1074, value='WD40') - ProteinDomain(confidence=1.4e-07, end=1155, start=1116, value='WD40') - ProteinDomain(confidence=0.3, end=1204, start=1167, value='WD40') - Clade(branch_length=0.01825, name='Apaf-1_HUMAN') - HUMAN - Sequence() - DomainArchitecture(length=1248) - ProteinDomain(confidence=1.1e-25, end=90, start=5, value='CARD') - ProteinDomain(confidence=3e-134, end=414, start=108, value='NB-ARC') - ProteinDomain(confidence=8.5e-06, end=643, start=604, value='WD40') - ProteinDomain(confidence=2.5e-11, end=685, start=646, value='WD40') - ProteinDomain(confidence=2.4e-08, end=729, start=688, value='WD40') - ProteinDomain(confidence=3.6e-14, end=771, start=732, value='WD40') - ProteinDomain(confidence=3.8e-08, end=910, start=871, value='WD40') - ProteinDomain(confidence=4e-07, end=1113, start=1074, value='WD40') - ProteinDomain(confidence=5.9e-08, end=1155, start=1116, value='WD40') - Clade(branch_length=0.04683, name='12_CANFA') - CANFA - Sequence() - DomainArchitecture(length=1153) - ProteinDomain(confidence=4.5e-22, end=90, start=5, value='CARD') - ProteinDomain(confidence=4e-119, end=415, start=109, value='NB-ARC') - ProteinDomain(confidence=3.9e-05, end=635, start=596, value='WD40') - ProteinDomain(confidence=2.5e-11, end=677, start=638, value='WD40') - ProteinDomain(confidence=1.8e-07, end=721, start=680, value='WD40') - ProteinDomain(confidence=9.4e-13, end=763, start=724, value='WD40') - ProteinDomain(confidence=1.1e-06, end=927, start=888, value='WD40') - ProteinDomain(confidence=1.7e-07, end=1009, start=970, value='WD40') - ProteinDomain(confidence=1.9e-07, end=1051, start=1012, value='WD40') - Clade(branch_length=0.15226, name='11_CHICK') - CHICK - Sequence() - DomainArchitecture(length=1207) - ProteinDomain(confidence=3.6e-21, end=90, start=5, value='CARD') - ProteinDomain(confidence=3.6e-109, end=414, start=108, value='NB-ARC') - ProteinDomain(confidence=0.00016, end=641, start=602, value='WD40') - ProteinDomain(confidence=8.2e-11, end=683, start=644, value='WD40') - ProteinDomain(confidence=6.2e-10, end=727, start=686, value='WD40') - ProteinDomain(confidence=1.8e-11, end=769, start=730, value='WD40') - ProteinDomain(confidence=1.8, end=866, start=827, value='WD40') - ProteinDomain(confidence=0.00029, end=1030, start=992, value='WD40') - ProteinDomain(confidence=1.7e-08, end=1072, start=1033, value='WD40') - ProteinDomain(confidence=7.5e-09, end=1114, start=1075, value='WD40') - ProteinDomain(confidence=0.044, end=1163, start=1126, value='WD40') - Clade(branch_length=0.4409, name='16_XENLA') - XENLA - Sequence() - DomainArchitecture(length=1362) - ProteinDomain(confidence=4e-20, end=90, start=5, value='CARD') - ProteinDomain(confidence=3.1e-56, end=410, start=108, value='NB-ARC') - ProteinDomain(confidence=0.8, end=298, start=147, value='NACHT') - ProteinDomain(confidence=7e-06, end=767, start=728, value='WD40') - ProteinDomain(confidence=2.3e-11, end=809, start=770, value='WD40') - ProteinDomain(confidence=1.1e-08, end=853, start=812, value='WD40') - ProteinDomain(confidence=1.1e-10, end=895, start=856, value='WD40') - ProteinDomain(confidence=8.4e-09, end=1030, start=991, value='WD40') - ProteinDomain(confidence=7.3e-11, end=1154, start=1115, value='WD40') - ProteinDomain(confidence=1.6e-08, end=1196, start=1157, value='WD40') - ProteinDomain(confidence=1.2e-07, end=1238, start=1199, value='WD40') - Clade(branch_length=0.17031) - Confidence(type='unknown', value=100.0) - Clade(branch_length=0.10929) - Confidence(type='unknown', value=100.0) - Clade(branch_length=0.02255, name='14_FUGRU') - FUGRU - Sequence() - DomainArchitecture(length=1258) - ProteinDomain(confidence=4.6e-24, end=92, start=7, value='CARD') - ProteinDomain(confidence=7e-74, end=418, start=110, value='NB-ARC') - ProteinDomain(confidence=0.00028, end=647, start=608, value='WD40') - ProteinDomain(confidence=2.3e-12, end=689, start=650, value='WD40') - ProteinDomain(confidence=1.8e-06, end=778, start=739, value='WD40') - ProteinDomain(confidence=1.6e-09, end=912, start=873, value='WD40') - ProteinDomain(confidence=9.8e-13, end=1036, start=997, value='WD40') - ProteinDomain(confidence=0.00016, end=1080, start=1039, value='WD40') - ProteinDomain(confidence=1.5e-09, end=1122, start=1083, value='WD40') - ProteinDomain(confidence=6.2e-09, end=1164, start=1125, value='WD40') - Clade(branch_length=0.09478, name='15_TETNG') - TETNG - Sequence() - DomainArchitecture(length=621) - ProteinDomain(confidence=2.5e-24, end=92, start=7, value='CARD') - ProteinDomain(confidence=9.8e-11, end=308, start=103, value='NB-ARC') - ProteinDomain(confidence=1.2e-12, end=404, start=365, value='WD40') - ProteinDomain(confidence=1e-10, end=493, start=454, value='WD40') - ProteinDomain(confidence=4.1e-10, end=575, start=536, value='WD40') - Clade(branch_length=0.1811, name='17_BRARE') - BRARE - Sequence() - DomainArchitecture(length=1260) - ProteinDomain(confidence=3.9e-23, end=90, start=5, value='CARD') - ProteinDomain(confidence=1.7e-72, end=444, start=136, value='NB-ARC') - ProteinDomain(confidence=1.6, end=673, start=634, value='WD40') - ProteinDomain(confidence=5.3e-12, end=732, start=693, value='WD40') - ProteinDomain(confidence=2e-08, end=821, start=782, value='WD40') - ProteinDomain(confidence=2.4e-08, end=1078, start=1039, value='WD40') - ProteinDomain(confidence=0.00066, end=1121, start=1080, value='WD40') - ProteinDomain(confidence=5.1e-08, end=1163, start=1124, value='WD40') - ProteinDomain(confidence=1.3e-07, end=1205, start=1166, value='WD40') - Clade(branch_length=0.01594) - Confidence(type='unknown', value=53.0) - Clade(branch_length=0.10709) - Confidence(type='unknown', value=68.0) - Clade(branch_length=0.26131, name='1_BRAFL') - BRAFL - Sequence() - DomainArchitecture(length=1238) - ... \ No newline at end of file diff --git a/demosR/phylogeny/treeR.txt b/demosR/phylogeny/treeR.txt deleted file mode 100644 index 760cfc13..00000000 --- a/demosR/phylogeny/treeR.txt +++ /dev/null @@ -1,2881 +0,0 @@ -$clade -$clade$clade -$clade$clade$branch_length -[1] "0.18105" - -$clade$clade$confidence -$clade$clade$confidence$text -[1] "89.0" - -$clade$clade$confidence$.attrs - type -"unknown" - - -$clade$clade$clade -$clade$clade$clade$branch_length -[1] "0.07466" - -$clade$clade$clade$confidence -$clade$clade$clade$confidence$text -[1] "32.0" - -$clade$clade$clade$confidence$.attrs - type -"unknown" - - -$clade$clade$clade$clade -$clade$clade$clade$clade$branch_length -[1] "0.26168" - -$clade$clade$clade$clade$confidence -$clade$clade$clade$clade$confidence$text -[1] "100.0" - -$clade$clade$clade$clade$confidence$.attrs - type -"unknown" - - -$clade$clade$clade$clade$clade -$clade$clade$clade$clade$clade$branch_length -[1] "0.22058" - -$clade$clade$clade$clade$clade$confidence -$clade$clade$clade$clade$clade$confidence$text -[1] "89.0" - -$clade$clade$clade$clade$clade$confidence$.attrs - type -"unknown" - - -$clade$clade$clade$clade$clade$clade -$clade$clade$clade$clade$clade$clade$branch_length -[1] "0.28901" - -$clade$clade$clade$clade$clade$clade$confidence -$clade$clade$clade$clade$clade$clade$confidence$text -[1] "100.0" - -$clade$clade$clade$clade$clade$clade$confidence$.attrs - type -"unknown" - - -$clade$clade$clade$clade$clade$clade$clade -$clade$clade$clade$clade$clade$clade$clade$branch_length -[1] "0.06584" - -$clade$clade$clade$clade$clade$clade$clade$confidence -$clade$clade$clade$clade$clade$clade$clade$confidence$text -[1] "100.0" - -$clade$clade$clade$clade$clade$clade$clade$confidence$.attrs - type -"unknown" - - -$clade$clade$clade$clade$clade$clade$clade$clade -$clade$clade$clade$clade$clade$clade$clade$clade$branch_length -[1] "0.02309" - -$clade$clade$clade$clade$clade$clade$clade$clade$confidence -$clade$clade$clade$clade$clade$clade$clade$clade$confidence$text -[1] "43.0" - -$clade$clade$clade$clade$clade$clade$clade$clade$confidence$.attrs - type -"unknown" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade -$clade$clade$clade$clade$clade$clade$clade$clade$clade$branch_length -[1] "0.0746" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$confidence -$clade$clade$clade$clade$clade$clade$clade$clade$clade$confidence$text -[1] "100.0" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$confidence$.attrs - type -"unknown" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$branch_length -[1] "0.02365" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$confidence -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$confidence$text -[1] "88.0" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$confidence$.attrs - type -"unknown" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$name -[1] "22_MOUSE" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$branch_length -[1] "0.05998" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$taxonomy -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$taxonomy$code -[1] "MOUSE" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "CARD" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "6" "90" "7.0E-26" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "NB-ARC" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "109" "414" "7.2E-117" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "605" "643" "2.4E-6" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "647" "685" "1.1E-12" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "689" "729" "2.4E-7" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "733" "771" "4.7E-14" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "872" "910" "2.5E-8" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "993" "1031" "4.6E-6" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "1075" "1113" "6.3E-7" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "1117" "1155" "1.4E-7" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "1168" "1204" "0.3" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$.attrs -length -"1249" - - - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$name -[1] "Apaf-1_HUMAN" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$branch_length -[1] "0.01825" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$taxonomy -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$taxonomy$code -[1] "HUMAN" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "CARD" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "6" "90" "1.1E-25" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "NB-ARC" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "109" "414" "3.0E-134" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "605" "643" "8.5E-6" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "647" "685" "2.5E-11" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "689" "729" "2.4E-8" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "733" "771" "3.6E-14" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "872" "910" "3.8E-8" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "1075" "1113" "4.0E-7" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "1117" "1155" "5.9E-8" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$.attrs -length -"1248" - - - - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$name -[1] "12_CANFA" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$branch_length -[1] "0.04683" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$taxonomy -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$taxonomy$code -[1] "CANFA" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "CARD" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "6" "90" "4.5E-22" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "NB-ARC" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "110" "415" "4.0E-119" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "597" "635" "3.9E-5" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "639" "677" "2.5E-11" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "681" "721" "1.8E-7" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "725" "763" "9.4E-13" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "889" "927" "1.1E-6" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "971" "1009" "1.7E-7" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "WD40" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "1013" "1051" "1.9E-7" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$.attrs -length -"1153" - - - - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade -$clade$clade$clade$clade$clade$clade$clade$clade$clade$name -[1] "11_CHICK" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$branch_length -[1] "0.15226" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$taxonomy -$clade$clade$clade$clade$clade$clade$clade$clade$clade$taxonomy$code -[1] "CHICK" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence -$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture -$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain -$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$text -[1] "CARD" - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain$.attrs - from to confidence - "6" "90" "3.6E-21" - - -$clade$clade$clade$clade$clade$clade$clade$clade$clade$sequence$domain_architecture$domain 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