diff --git a/apps/dashr-alignment-viewer/app.R b/apps/dashr-alignment-viewer/app.R index c4abf3c8b..08f7a4546 100644 --- a/apps/dashr-alignment-viewer/app.R +++ b/apps/dashr-alignment-viewer/app.R @@ -504,13 +504,13 @@ alignlayout <- htmlDiv(id="alignment-body", className="app-body",children=list( ###HEADER### header <- htmlDiv(children = list( htmlSpan(list(htmlA( - htmlImg(src='assets/index.png', - height = '50', - width = '50', - style = list('top' = '10', 'margin-left' = '10px')), + children = list( + htmlImg(src='assets/plotly-dash-bio-logo.png', height = '36', width = '180', + style = list('top' = '10', 'margin-left' = '10px', 'margin-top' = '20px', 'margin-right' = '20px')) + ), href='https://dash-bio.plotly.host/Portal/' ))), - "Dash Alignment Viewer", + "Alignment Viewer", htmlA(href="https://github.com/plotly/dash-sample-apps/blob/master/apps/dashr-alignment-viewer/app.R", style = list("color" = "white", diff --git a/apps/dashr-alignment-viewer/assets/general-app-page.css b/apps/dashr-alignment-viewer/assets/general-app-page.css index 697eaf7f1..b112110c9 100644 --- a/apps/dashr-alignment-viewer/assets/general-app-page.css +++ b/apps/dashr-alignment-viewer/assets/general-app-page.css @@ -1,4 +1,4 @@ -@import "assets/openSansFont.css"; +@import "openSansFont.css"; .dashbio-loading { display: inline-block; diff --git a/apps/dashr-alignment-viewer/assets/plotly-dash-bio-logo.png b/apps/dashr-alignment-viewer/assets/plotly-dash-bio-logo.png new file mode 100644 index 000000000..dc42cbaa1 Binary files /dev/null and b/apps/dashr-alignment-viewer/assets/plotly-dash-bio-logo.png differ diff --git a/apps/dashr-clustergram/README.MD b/apps/dashr-clustergram/README.MD index e965047ad..a6867bdca 100644 --- a/apps/dashr-clustergram/README.MD +++ b/apps/dashr-clustergram/README.MD @@ -1 +1,32 @@ -Hello +# DashR Clustergram + +## About this App: + +Clustergram is a combination of a heatmap and dendrograms that allows you to display hierarchical clustering data. Clusters on the dendrograms are highlighted in one color if they comprise data points that share some minimal level of correlation. + +In the "Data" tab, you can select a preloaded dataset to display or, alternatively, upload one of your own. A sample dataset is also available for download in the tab. + +In the "Graph" tab, you can choose the dimension(s) along which clustering will be performed (row or column). You can also change the threshold that determines the point at which clusters are highlighted for the row and column dendrograms, and choose which rows and columns are used to compute the clustering. + +In addition, you can highlight specific clusters by adding annotations to the clustergram, and choose whether to show or hide the labels for the rows and/or columns. + +Github Repo: [plotly/dash-sample-apps](https://github.com/plotly/dash-sample-apps/) + + +## How to Run the App: + +Clone the repository. + +Run `app.R` + +The app will load into your default browser window. If it does not, navigate to 127.0.0.1:8050. + +## Screenshots: + +![ClustergramMain.png](assets/ClustergramMain.png) + + +## More: + +Learn more about Plotly and Dash [here](https://plot.ly/dash). +# diff --git a/apps/dashr-clustergram/Rplot001.jpg b/apps/dashr-clustergram/Rplot001.jpg new file mode 100644 index 000000000..e69de29bb diff --git a/apps/dashr-clustergram/app.R b/apps/dashr-clustergram/app.R index 66bcec347..5130f0c9d 100644 --- a/apps/dashr-clustergram/app.R +++ b/apps/dashr-clustergram/app.R @@ -41,13 +41,12 @@ header <- htmlDiv( htmlA( id = "dashbio-logo", children = list( - htmlImg( - src = "assets/dashbio_logo_transparent.png" - ) + htmlImg(src='assets/plotly-dash-bio-logo.png', height = '36', width = '180', + style = list('top' = '10', 'margin-left' = '10px')) ), href = "/Portal" ), - htmlH2("Dash Clustergram"), + htmlH2("Clustergram"), htmlA( id = "gh-link", children = list("View on GitHub"), diff --git a/apps/dashr-clustergram/assets/ClustergramMain.png b/apps/dashr-clustergram/assets/ClustergramMain.png new file mode 100644 index 000000000..d1840bf87 Binary files /dev/null and b/apps/dashr-clustergram/assets/ClustergramMain.png differ diff --git a/apps/dashr-clustergram/assets/plotly-dash-bio-logo.png b/apps/dashr-clustergram/assets/plotly-dash-bio-logo.png new file mode 100644 index 000000000..dc42cbaa1 Binary files /dev/null and b/apps/dashr-clustergram/assets/plotly-dash-bio-logo.png differ diff --git a/apps/dashr-ideogram/app.R b/apps/dashr-ideogram/app.R index f35402f40..3c2d52de5 100644 --- a/apps/dashr-ideogram/app.R +++ b/apps/dashr-ideogram/app.R @@ -259,7 +259,7 @@ listOfOptions <- lapply(chromosomes, function(x) { dccDropdown( className = 'ideogram-dropdown', id = 'displayed-chromosomes', - options = listOfoptions, + options = listOfOptions, multi = TRUE, value = listofchromosomes ) @@ -274,14 +274,14 @@ listOfOptions <- lapply(chromosomes, function(x) { dccDropdown( className = 'ideogram-dropdown', id = 'chr-select-1', - options = listofOptions , value = '1' + options = listOfOptions , value = '1' ), dccDropdown( className = 'ideogram-dropdown', id = 'chr-select-2', value = '2', - options = listofOptions + options = listOfOptions ), chromosome_div( @@ -309,7 +309,7 @@ listOfOptions <- lapply(chromosomes, function(x) { dccDropdown( className = 'ideogram-dropdown', id = 'chr-brush', - options = listofOptions, value = 'X' + options = listOfOptions, value = 'X' ) )), @@ -547,11 +547,11 @@ listOfOptions <- lapply(chromosomes, function(x) { header <- htmlDiv(children = list( htmlSpan(list(htmlA( - htmlImg(src='assets/index.png', height = '50', width = '50', - style = list('top' = '10', 'margin-left' = '10px')), + htmlImg(src='assets/plotly-dash-bio-logo.png', height = '36', width = '180', + style = list('top' = '10', 'margin-left' = '10px', 'margin-right' = '15px')), href='https://dash-bio.plotly.host/Portal/'))), - " Dash Ideogram", + "Ideogram", htmlA(href="http://github.com/plotly/dash-bio/blob/master/tests/dashbio_demos/app_ideogram.py", @@ -1064,3 +1064,5 @@ if (appName != "") { app$run_server(showcase = TRUE) } + + \ No newline at end of file diff --git a/apps/dashr-ideogram/assets/general-app-page.css b/apps/dashr-ideogram/assets/general-app-page.css index 3b84dd10a..bfa038803 100644 --- a/apps/dashr-ideogram/assets/general-app-page.css +++ b/apps/dashr-ideogram/assets/general-app-page.css @@ -1,4 +1,4 @@ -@import "assets/openSansFont.css"; +@import "openSansFont.css"; .dashbio-loading { display: inline-block; diff --git a/apps/dashr-ideogram/assets/plotly-dash-bio-logo.png b/apps/dashr-ideogram/assets/plotly-dash-bio-logo.png new file mode 100644 index 000000000..dc42cbaa1 Binary files /dev/null and b/apps/dashr-ideogram/assets/plotly-dash-bio-logo.png differ diff --git a/apps/dashr-manhattan-plot/app.R b/apps/dashr-manhattan-plot/app.R index a152a79c6..36cc6163b 100644 --- a/apps/dashr-manhattan-plot/app.R +++ b/apps/dashr-manhattan-plot/app.R @@ -40,13 +40,12 @@ app$layout( htmlA( id = "dashbio-logo", children = list( - htmlImg( - src = "assets/dashbio_logo_transparent.png" - ) + htmlImg(src='assets/plotly-dash-bio-logo.png', height = '36', width = '190', + style = list('top' = '10', 'margin-left' = '10px')) ), href = "/Portal" ), - htmlH2("Dash Manhattan Plot"), + htmlH2("Manhattan Plot"), htmlA( id = "gh-link", children = list("View on GitHub"), diff --git a/apps/dashr-manhattan-plot/assets/plotly-dash-bio-logo.png b/apps/dashr-manhattan-plot/assets/plotly-dash-bio-logo.png new file mode 100644 index 000000000..dc42cbaa1 Binary files /dev/null and b/apps/dashr-manhattan-plot/assets/plotly-dash-bio-logo.png differ diff --git a/apps/dashr-molecule3d/app.R b/apps/dashr-molecule3d/app.R index af7cb95db..bca8f07d8 100644 --- a/apps/dashr-molecule3d/app.R +++ b/apps/dashr-molecule3d/app.R @@ -553,13 +553,12 @@ header <- htmlDiv( htmlA( id = "dashbio-logo", children = list( - htmlImg( - src = "assets/dashbio_logo_transparent.png" - ) + htmlImg(src='assets/plotly-dash-bio-logo.png', height = '36', width = '190', + style = list('top' = '10', 'margin-left' = '10px')) ), href = "/Portal" ), - htmlH2("Dash Molecule3D"), + htmlH2("Molecule3D"), htmlA( id = "gh-link", children = list("View on GitHub"), diff --git a/apps/dashr-molecule3d/assets/plotly-dash-bio-logo.png b/apps/dashr-molecule3d/assets/plotly-dash-bio-logo.png new file mode 100644 index 000000000..dc42cbaa1 Binary files /dev/null and b/apps/dashr-molecule3d/assets/plotly-dash-bio-logo.png differ diff --git a/apps/dashr-needleplot/app.R b/apps/dashr-needleplot/app.R index 67252e61c..9f077ff06 100644 --- a/apps/dashr-needleplot/app.R +++ b/apps/dashr-needleplot/app.R @@ -116,13 +116,12 @@ app$layout( htmlA( id = "dashbio-logo", children = list( - htmlImg( - src = "assets/dashbio_logo_transparent.png" - ) + htmlImg(src='assets/plotly-dash-bio-logo.png', height = '36', width = '190', + style = list('top' = '10', 'margin-left' = '10px')) ), href = "/Portal" ), - htmlH2("Dash Needle Plot"), + htmlH2("Needle Plot"), htmlA( id = "gh-link", children = list("View on GitHub"), diff --git a/apps/dashr-needleplot/assets/plotly-dash-bio-logo.png b/apps/dashr-needleplot/assets/plotly-dash-bio-logo.png new file mode 100644 index 000000000..dc42cbaa1 Binary files /dev/null and b/apps/dashr-needleplot/assets/plotly-dash-bio-logo.png differ diff --git a/apps/dashr-oncoprint/app.R b/apps/dashr-oncoprint/app.R index 4fc6c4587..fe388f2c4 100644 --- a/apps/dashr-oncoprint/app.R +++ b/apps/dashr-oncoprint/app.R @@ -101,13 +101,12 @@ app$layout( htmlA( id = "dashbio-logo", children = list( - htmlImg( - src = "assets/dashbio_logo_transparent.png" - ) + htmlImg(src='assets/plotly-dash-bio-logo.png', height = '36', width = '190', + style = list('top' = '10', 'margin-left' = '10px')) ), href = "/Portal" ), - htmlH2("Dash Onco Print"), + htmlH2("Onco Print"), htmlA( id = "gh-link", children = list("View on GitHub"), diff --git a/apps/dashr-oncoprint/assets/plotly-dash-bio-logo.png b/apps/dashr-oncoprint/assets/plotly-dash-bio-logo.png new file mode 100644 index 000000000..dc42cbaa1 Binary files /dev/null and b/apps/dashr-oncoprint/assets/plotly-dash-bio-logo.png differ diff --git a/apps/dashr-speck/app.R b/apps/dashr-speck/app.R index 7df8c68b1..461387349 100644 --- a/apps/dashr-speck/app.R +++ b/apps/dashr-speck/app.R @@ -304,13 +304,12 @@ header <- htmlDiv( htmlA( id = "dashbio-logo", children = list( - htmlImg( - src = "assets/dashbio_logo_transparent.png" - ) + htmlImg(src='assets/plotly-dash-bio-logo.png', height = '36', width = '190', + style = list('top' = '10', 'margin-left' = '10px')) ), href = "/Portal" ), - htmlH2("Dash Speck"), + htmlH2("Speck"), htmlA( id = "gh-link", children = list("View on GitHub"), diff --git a/apps/dashr-speck/assets/plotly-dash-bio-logo.png b/apps/dashr-speck/assets/plotly-dash-bio-logo.png new file mode 100644 index 000000000..dc42cbaa1 Binary files /dev/null and b/apps/dashr-speck/assets/plotly-dash-bio-logo.png differ diff --git a/apps/dashr-volcanoplot/app.R b/apps/dashr-volcanoplot/app.R index 459c47d50..d9dc99497 100644 --- a/apps/dashr-volcanoplot/app.R +++ b/apps/dashr-volcanoplot/app.R @@ -70,13 +70,12 @@ app$layout( htmlA( id = "dashbio-logo", children = list( - htmlImg( - src = "assets/dashbio_logo_transparent.png" - ) + htmlImg(src='assets/plotly-dash-bio-logo.png', height = '36', width = '190', + style = list('top' = '10', 'margin-left' = '10px')) ), href = "/Portal" ), - htmlH2("Dash Volcano Plot"), + htmlH2("Volcano Plot"), htmlA( id = "gh-link", children = list("View on GitHub"), diff --git a/apps/dashr-volcanoplot/assets/plotly-dash-bio-logo.png b/apps/dashr-volcanoplot/assets/plotly-dash-bio-logo.png new file mode 100644 index 000000000..dc42cbaa1 Binary files /dev/null and b/apps/dashr-volcanoplot/assets/plotly-dash-bio-logo.png differ