Add dashCytoscape v0.3.0 for R

.Rbuildignore

@@ -7,6 +7,11 @@ lib/
 .builderrc
 .eslintrc
 .npmignore
+.editorconfig
+.eslintignore
+.prettierrc
+.circleci
+.github
 
 # demo folder has special meaning in R
 # this should hopefully make it still
@@ -15,7 +20,7 @@ demo/.*\.js
 demo/.*\.html
 demo/.*\.css
 
-# ignore python files/folders
+# ignore Python files/folders
 setup.py
 usage.py
 setup.py

CHANGELOG.md

@@ -4,7 +4,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## [0.3.0] - 2021-05-19 
+
+### Added
+* Contributed initial build of Julia package.
+* R package now includes an example application for `cytoCytoscape`.
 
 ### Changed
 * Dash has been upgraded to 1.* in requirements.txt and tests/requirements.txt (#123)
@@ -15,7 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 * Various security fixes
 
-## [0.2.0] - 20120-07-09
+## [0.2.0] - 2020-07-09
 
 ### Added
 * Contributed initial build of R package.

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: dashCytoscape
-Title: A Component Library for Dash aimed at facilitating network visualization in R, wrapped around Cytoscape.js
-Version: 0.1.1
-Description: A Component Library for Dash aimed at facilitating network visualization in R, wrapped around Cytoscape.js
+Title: A Component Library for 'Dash' aimed at facilitating network visualization in R, wrapped around Cytoscape.js.
+Version: 0.3.0
+Description: A Component Library for 'Dash' aimed at facilitating network visualization in R, wrapped around Cytoscape.js.
 Depends: R (>= 3.0.2)
 Imports: 
 Suggests: 
+Authors@R: c(person("Chris", "Parmer", email = "chris@plotly.com", role = c("aut")), person("Xing Han", "Lu", email = "xinghan@plotly.com", role = c("cre")), person(family = "Plotly Technologies, Inc.", role = "cph"))
 License: MIT + file LICENSE
+Copyright: Plotly Technologies, Inc.
 URL: https://github.com/plotly/dash-cytoscape
 BugReports: https://github.com/plotly/dash-cytoscape/issues
 Encoding: UTF-8
 LazyData: true
 KeepSource: true
-Author: The Plotly Team [aut]
-Maintainer: The Plotly Team <cytoscape@plotly.com>

R/cytoCytoscape.R

@@ -1,16 +1,16 @@
 # AUTO GENERATED FILE - DO NOT EDIT
 
-cytoCytoscape <- function(id=NULL, className=NULL, style=NULL, elements=NULL, stylesheet=NULL, layout=NULL, pan=NULL, zoom=NULL, panningEnabled=NULL, userPanningEnabled=NULL, minZoom=NULL, maxZoom=NULL, zoomingEnabled=NULL, userZoomingEnabled=NULL, boxSelectionEnabled=NULL, autoungrabify=NULL, autolock=NULL, autounselectify=NULL, autoRefreshLayout=NULL, tapNode=NULL, tapNodeData=NULL, tapEdge=NULL, tapEdgeData=NULL, mouseoverNodeData=NULL, mouseoverEdgeData=NULL, selectedNodeData=NULL, selectedEdgeData=NULL) {
+cytoCytoscape <- function(id=NULL, autoRefreshLayout=NULL, autolock=NULL, autoungrabify=NULL, autounselectify=NULL, boxSelectionEnabled=NULL, className=NULL, elements=NULL, generateImage=NULL, imageData=NULL, layout=NULL, maxZoom=NULL, minZoom=NULL, mouseoverEdgeData=NULL, mouseoverNodeData=NULL, pan=NULL, panningEnabled=NULL, responsive=NULL, selectedEdgeData=NULL, selectedNodeData=NULL, style=NULL, stylesheet=NULL, tapEdge=NULL, tapEdgeData=NULL, tapNode=NULL, tapNodeData=NULL, userPanningEnabled=NULL, userZoomingEnabled=NULL, zoom=NULL, zoomingEnabled=NULL) {
 
-    props <- list(id=id, className=className, style=style, elements=elements, stylesheet=stylesheet, layout=layout, pan=pan, zoom=zoom, panningEnabled=panningEnabled, userPanningEnabled=userPanningEnabled, minZoom=minZoom, maxZoom=maxZoom, zoomingEnabled=zoomingEnabled, userZoomingEnabled=userZoomingEnabled, boxSelectionEnabled=boxSelectionEnabled, autoungrabify=autoungrabify, autolock=autolock, autounselectify=autounselectify, autoRefreshLayout=autoRefreshLayout, tapNode=tapNode, tapNodeData=tapNodeData, tapEdge=tapEdge, tapEdgeData=tapEdgeData, mouseoverNodeData=mouseoverNodeData, mouseoverEdgeData=mouseoverEdgeData, selectedNodeData=selectedNodeData, selectedEdgeData=selectedEdgeData)
+    props <- list(id=id, autoRefreshLayout=autoRefreshLayout, autolock=autolock, autoungrabify=autoungrabify, autounselectify=autounselectify, boxSelectionEnabled=boxSelectionEnabled, className=className, elements=elements, generateImage=generateImage, imageData=imageData, layout=layout, maxZoom=maxZoom, minZoom=minZoom, mouseoverEdgeData=mouseoverEdgeData, mouseoverNodeData=mouseoverNodeData, pan=pan, panningEnabled=panningEnabled, responsive=responsive, selectedEdgeData=selectedEdgeData, selectedNodeData=selectedNodeData, style=style, stylesheet=stylesheet, tapEdge=tapEdge, tapEdgeData=tapEdgeData, tapNode=tapNode, tapNodeData=tapNodeData, userPanningEnabled=userPanningEnabled, userZoomingEnabled=userZoomingEnabled, zoom=zoom, zoomingEnabled=zoomingEnabled)
     if (length(props) > 0) {
         props <- props[!vapply(props, is.null, logical(1))]
     }
     component <- list(
         props = props,
         type = 'Cytoscape',
         namespace = 'dash_cytoscape',
-        propNames = c('id', 'className', 'style', 'elements', 'stylesheet', 'layout', 'pan', 'zoom', 'panningEnabled', 'userPanningEnabled', 'minZoom', 'maxZoom', 'zoomingEnabled', 'userZoomingEnabled', 'boxSelectionEnabled', 'autoungrabify', 'autolock', 'autounselectify', 'autoRefreshLayout', 'tapNode', 'tapNodeData', 'tapEdge', 'tapEdgeData', 'mouseoverNodeData', 'mouseoverEdgeData', 'selectedNodeData', 'selectedEdgeData'),
+        propNames = c('id', 'autoRefreshLayout', 'autolock', 'autoungrabify', 'autounselectify', 'boxSelectionEnabled', 'className', 'elements', 'generateImage', 'imageData', 'layout', 'maxZoom', 'minZoom', 'mouseoverEdgeData', 'mouseoverNodeData', 'pan', 'panningEnabled', 'responsive', 'selectedEdgeData', 'selectedNodeData', 'style', 'stylesheet', 'tapEdge', 'tapEdgeData', 'tapNode', 'tapNodeData', 'userPanningEnabled', 'userZoomingEnabled', 'zoom', 'zoomingEnabled'),
         package = 'dashCytoscape'
         )
 

R/internal.R

@@ -1,6 +1,6 @@
 .dashCytoscape_js_metadata <- function() {
 deps_metadata <- list(`dash_cytoscape` = structure(list(name = "dash_cytoscape",
-version = "0.1.1", src = list(href = NULL,
+version = "0.3.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
 script = 'dash_cytoscape.min.js',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashCytoscape",

dash-info.yaml

@@ -1,4 +1,62 @@
 pkg_help_description: >-
-    A Component Library for Dash aimed at facilitating network visualization in R, wrapped around Cytoscape.js
+    A Component Library for 'Dash' aimed at facilitating network visualization in R, wrapped around Cytoscape.js.
 pkg_help_title: >-
-    A Component Library for Dash aimed at facilitating network visualization in R, wrapped around Cytoscape.js
+    A Component Library for 'Dash' aimed at facilitating network visualization in R, wrapped around Cytoscape.js.
+pkg_authors: >-
+    c(person("Chris", "Parmer", email = "chris@plotly.com", role = c("aut")), person("Xing Han", "Lu", email = "xinghan@plotly.com", role = c("cre")), person(family = "Plotly Technologies, Inc.", role = "cph"))
+pkg_copyright: >-
+    Plotly Technologies, Inc.
+r_examples:
+    - name: cytoCytoscape
+      dontrun: FALSE
+      code: |
+            if (interactive()) {
+              library(dash)
+              library(dashCytoscape)
+
+              app <- Dash$new()
+
+              app$layout(
+                cytoCytoscape(
+                id='cytoscape-elements-boolean',
+                layout = list(name = 'preset'),
+                style = list(width = '100\%', height = '400px'),
+                elements=list(
+                  list(
+                    data = list(id = 'one', label = 'Locked'),
+                    position = list(x = 75, y = 75),
+                    locked = TRUE
+                  ),
+                  list(
+                    data = list(id = 'two', label = 'Selected'),
+                    position = list(x = 75, y = 200),
+                    selected = TRUE
+                  ),
+                  list(
+                    data = list(id = 'three', label = 'Not Selectable'),
+                    position = list(x = 200, y = 75),
+                    selectable = FALSE
+                  ),
+                  list(
+                    data = list(id = 'four', label = 'Not Grabbable'),
+                    position = list(x = 200, y = 200),
+                    grabbable = FALSE
+                  ),
+                  list(
+                    data = list(source = 'one', target = 'two')
+                  ),
+                  list(
+                    data = list(source = 'two', target = 'three')
+                  ),
+                  list(
+                    data = list(source = 'three', target = 'four')
+                  ),
+                  list(
+                    data = list(source = 'two', target = 'four')
+                  )
+                )
+               )
+              )
+
+              app$run_server()
+            }

demosR/usage-animated-bfs.R

@@ -0,0 +1,71 @@
+# 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(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)

demosR/usage-breadthfirst-layout.R

@@ -0,0 +1,128 @@
+# original demo: http://js.cytoscape.org/demos/images-breadthfirst-layout/
+#
+# note: click animation is not implemented
+
+library(dash)
+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)