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Merge pull request #3850 from bgruening/phylocanvas

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Phylocanvas as a BioJS component for the Galaxy charts
This commit is contained in:
Aysam Guerler
2017-04-04 05:32:03 -04:00
committed by GitHub
parent 5169fbe917 339566bc03
commit 6f4e242b16
10 changed files with 563 additions and 59 deletions
Download Patch File Download Diff File Expand all files Collapse all files
config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
+258
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config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
+1
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config/plugins/visualizations/charts/static/repository/build/registry.js
+144 -56
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description : 'Renders a regular bar diagram using NVD3 hosted at http://www.nvd3.org.',
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return $.extend( true, {}, default_config, {
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description : 'Renders a horizontal bar diagram using NVD3 hosted at http://www.nvd3.org.',
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return $.extend( true, {}, nvd3_config, {
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description : 'Renders a stacked horizontal bar diagram using NVD3 hosted at http://www.nvd3.org.',
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title : 'Stacked',
description : 'Renders a stacked bar diagram using NVD3 hosted at http://www.nvd3.org.',
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return $.extend( true, {}, nvd3_config, {
title : 'Line chart',
description : 'Renders a line chart using NVD3 hosted at http://www.nvd3.org.',
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var __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [ __webpack_require__(7) ], __WEBPACK_AMD_DEFINE_RESULT__ = function( nvd3_config ) {
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return $.extend( true, {}, nvd3_config, {
title : 'Line with focus',
description : 'Renders a line chart with focus panel using NVD3 hosted at http://www.nvd3.org.',
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var __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [ __webpack_require__(7) ], __WEBPACK_AMD_DEFINE_RESULT__ = function( nvd3_config ) {
var __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [ __webpack_require__(4) ], __WEBPACK_AMD_DEFINE_RESULT__ = function( nvd3_config ) {
return $.extend( true, {}, nvd3_config, {
title : 'Scatter plot',
description : 'Renders a scatter plot using NVD3 hosted at http://www.nvd3.org.',
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var __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [ __webpack_require__(7) ], __WEBPACK_AMD_DEFINE_RESULT__ = function( nvd3_config ) {
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return $.extend( true, {}, nvd3_config, {
title : 'Stacked area',
zoomable : true,
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return $.extend( true, {}, nvd3_config, {
title : 'Expanded',
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return $.extend(true, {}, nvd3_config, {
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description : 'Renders a stream chart using NVD3 hosted at http://www.nvd3.org.',
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return $.extend( true, {}, plot_config, {
title : 'Bar diagram',
description : 'Renders a bar diagram using jqPlot hosted at http://www.jqplot.com.',
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library : 'jqPlot',
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library : 'jqPlot',
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return $.extend( true, {}, plot_config, {
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description : 'Renders a line chart using jqPlot hosted at http://www.jqplot.com.',
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value : '#00b050'
},
collapse_branch : {
label : 'Collapse the selected branch',
help : 'Select true to collapse the selected branch.',
type : 'select',
display : 'radio',
value : 'false',
data : [ { label : 'True', value : 'true' },
{ label : 'False', value : 'false' } ]
},
prune_branch : {
label : 'Prune the selected branch',
help : 'Select true to prune the selected branch.',
type : 'select',
display : 'radio',
value : 'false',
data : [ { label : 'True', value : 'true' },
{ label : 'False', value : 'false' } ]
},
show_labels: {
label : 'Show/Hide labels',
help : 'Select false to hide labels.',
type : 'select',
display : 'radio',
value : 'true',
data : [ { label : 'True', value : 'true' },
{ label : 'False', value : 'false' } ]
},
align_labels: {
label : 'Align labels',
help : 'Select to align the labels of tree. Supported with rectangular, circular, and hierarchical tree types.',
type : 'select',
display : 'radio',
value : 'true',
data : [ { label : 'True', value : 'true' },
{ label : 'False', value : 'false' } ]
},
node_shape : {
label : 'Node shapes for leaves',
help : 'Select a node shape for leaves.',
type : 'select',
display : 'radio',
value : 'circle',
data : [ { label : 'Circle', value : 'circle' },
{ label : 'Square', value: 'square' },
{ label : 'Star', value : 'star' },
{ label : 'Triangle', value : 'triangle' } ]
}
}
}
}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));
/***/ },
/* 27 */
/***/ function(module, exports, __webpack_require__) {
var __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function() {
@@ -737,10 +825,10 @@ define(function() { return /******/ (function(modules) { // webpackBootstrap
}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));
/***/ },
/* 30 */
/* 28 */
/***/ function(module, exports, __webpack_require__) {
var __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [ __webpack_require__(8) ], __WEBPACK_AMD_DEFINE_RESULT__ = function( default_config ) {
var __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [ __webpack_require__(5) ], __WEBPACK_AMD_DEFINE_RESULT__ = function( default_config ) {
return $.extend( true, {}, default_config, {
title : 'Heatmap',
description : 'Renders a heatmap from matrix data provided in 3-column format (x, y, observation).',
@@ -803,10 +891,10 @@ define(function() { return /******/ (function(modules) { // webpackBootstrap
}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));
/***/ },
/* 31 */
/* 29 */
/***/ function(module, exports, __webpack_require__) {
var __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [ __webpack_require__(30) ], __WEBPACK_AMD_DEFINE_RESULT__ = function( default_config ) {
var __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [ __webpack_require__(28) ], __WEBPACK_AMD_DEFINE_RESULT__ = function( default_config ) {
return $.extend( true, {}, default_config, {
title : 'Clustered Heatmap',
description : 'Applies hierarchical clustering to a matrix using R. The data has to be provided in 3-column format. The result is displayed as clustered heatmap.',
@@ -815,7 +903,7 @@ define(function() { return /******/ (function(modules) { // webpackBootstrap
}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));
/***/ },
/* 32 */
/* 30 */
/***/ function(module, exports, __webpack_require__) {
var __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function() {
@@ -908,7 +996,7 @@ define(function() { return /******/ (function(modules) { // webpackBootstrap
/***/ },
/* 33 */
/* 31 */
/***/ function(module, exports, __webpack_require__) {
var __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function() {
@@ -1016,7 +1104,7 @@ define(function() { return /******/ (function(modules) { // webpackBootstrap
}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));
/***/ },
/* 34 */
/* 32 */
/***/ function(module, exports, __webpack_require__) {
var __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function() {
@@ -1045,7 +1133,7 @@ define(function() { return /******/ (function(modules) { // webpackBootstrap
}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));
/***/ },
/* 35 */
/* 33 */
/***/ function(module, exports, __webpack_require__) {
var __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function() {
config/plugins/visualizations/charts/static/repository/build/registry.js.map
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config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
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define( [], function() { return {nvd3_bar:require( "visualizations/nvd3/bar/config" ), nvd3_bar_horizontal:require( "visualizations/nvd3/bar_horizontal/config" ), nvd3_bar_horizontal_stacked:require( "visualizations/nvd3/bar_horizontal_stacked/config" ), nvd3_bar_stacked:require( "visualizations/nvd3/bar_stacked/config" ), nvd3_line:require( "visualizations/nvd3/line/config" ), nvd3_line_focus:require( "visualizations/nvd3/line_focus/config" ), nvd3_scatter:require( "visualizations/nvd3/scatter/config" ), nvd3_stackedarea:require( "visualizations/nvd3/stackedarea/config" ), nvd3_stackedarea_full:require( "visualizations/nvd3/stackedarea_full/config" ), nvd3_stackedarea_stream:require( "visualizations/nvd3/stackedarea_stream/config" ), nvd3_pie:require( "visualizations/nvd3/pie/config" ), nvd3_histogram:require( "visualizations/nvd3/histogram/config" ), nvd3_histogram_discrete:require( "visualizations/nvd3/histogram_discrete/config" ), jqplot_bar:require( "visualizations/jqplot/bar/config" ), jqplot_boxplot:require( "visualizations/jqplot/boxplot/config" ), jqplot_histogram_discrete:require( "visualizations/jqplot/histogram_discrete/config" ), jqplot_line:require( "visualizations/jqplot/line/config" ), jqplot_scatter:require( "visualizations/jqplot/scatter/config" ), biojs_msa:require( "visualizations/biojs/msa/config" ), biojs_drawrnajs:require( "visualizations/biojs/drawrnajs/config" ), others_example:require( "visualizations/others/example/config" ), others_heatmap:require( "visualizations/others/heatmap/config" ), others_heatmap_cluster:require( "visualizations/others/heatmap_cluster/config" ), cytoscape_viewer:require( "visualizations/cytoscape/viewer/config" ), pv_viewer:require( "visualizations/pv/viewer/config" ), benfred_venn:require( "visualizations/benfred/venn/config" ), ngl_viewer:require( "visualizations/ngl/viewer/config" ),} } );
define( [], function() { return {nvd3_bar:require( "visualizations/nvd3/bar/config" ), nvd3_bar_horizontal:require( "visualizations/nvd3/bar_horizontal/config" ), nvd3_bar_horizontal_stacked:require( "visualizations/nvd3/bar_horizontal_stacked/config" ), nvd3_bar_stacked:require( "visualizations/nvd3/bar_stacked/config" ), nvd3_line:require( "visualizations/nvd3/line/config" ), nvd3_line_focus:require( "visualizations/nvd3/line_focus/config" ), nvd3_scatter:require( "visualizations/nvd3/scatter/config" ), nvd3_stackedarea:require( "visualizations/nvd3/stackedarea/config" ), nvd3_stackedarea_full:require( "visualizations/nvd3/stackedarea_full/config" ), nvd3_stackedarea_stream:require( "visualizations/nvd3/stackedarea_stream/config" ), nvd3_pie:require( "visualizations/nvd3/pie/config" ), nvd3_histogram:require( "visualizations/nvd3/histogram/config" ), nvd3_histogram_discrete:require( "visualizations/nvd3/histogram_discrete/config" ), jqplot_bar:require( "visualizations/jqplot/bar/config" ), jqplot_boxplot:require( "visualizations/jqplot/boxplot/config" ), jqplot_histogram_discrete:require( "visualizations/jqplot/histogram_discrete/config" ), jqplot_line:require( "visualizations/jqplot/line/config" ), jqplot_scatter:require( "visualizations/jqplot/scatter/config" ), biojs_msa:require( "visualizations/biojs/msa/config" ), biojs_drawrnajs:require( "visualizations/biojs/drawrnajs/config" ), biojs_phylocanvas:require( "visualizations/biojs/phylocanvas/config" ), others_example:require( "visualizations/others/example/config" ), others_heatmap:require( "visualizations/others/heatmap/config" ), others_heatmap_cluster:require( "visualizations/others/heatmap_cluster/config" ), cytoscape_viewer:require( "visualizations/cytoscape/viewer/config" ), pv_viewer:require( "visualizations/pv/viewer/config" ), benfred_venn:require( "visualizations/benfred/venn/config" ), ngl_viewer:require( "visualizations/ngl/viewer/config" ),} } );
config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js
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config/plugins/visualizations/charts/static/repository/registry.json
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{
"nvd3" : [ "bar", "bar_horizontal", "bar_horizontal_stacked", "bar_stacked", "line", "line_focus", "scatter", "stackedarea", "stackedarea_full", "stackedarea_stream", "pie", "histogram", "histogram_discrete" ],
"jqplot" : [ "bar", "boxplot", "histogram_discrete", "line", "scatter" ],
"biojs" : [ "msa", "drawrnajs" ],
"biojs" : [ "msa", "drawrnajs", "phylocanvas" ],
"others" : [ "example", "heatmap", "heatmap_cluster" ],
"cytoscape" : [ "viewer" ],
"pv" : [ "viewer" ],
config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
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define( [], function() {
return {
title : 'Phylogenetic Tree Visualization',
library : 'BioJS',
datatypes : [ 'nhx' ],
keywords : 'biojs phylogenetic tree',
description : 'A performant, reusable, and extensible tree visualisation library for the web hosted at: http://biojs.io/d/phylocanvas',
settings : {
tree_type : {
label : 'Tree types',
help : 'Select a tree type.',
type : 'select',
display : 'radio',
value : 'rectangular',
data : [ { label : 'Circular', value : 'circular' },
{ label : 'Diagonal', value: 'diagonal' },
{ label : 'Hierarchial', value : 'hierarchical' },
{ label : 'Radial', value : 'radial' },
{ label : 'Rectangular', value : 'rectangular' } ]
},
edge_color : {
label : 'Select a color for the tree',
type : 'color',
value : '#548DB8'
},
highlighted_color: {
label : 'Select a color for the highlighted branch of tree',
type : 'color',
value : '#548DB8'
},
selected_color: {
label : 'Select a color for the selected branch of tree',
type : 'color',
value : '#00b050'
},
collapse_branch : {
label : 'Collapse the selected branch',
help : 'Select true to collapse the selected branch.',
type : 'select',
display : 'radio',
value : 'false',
data : [ { label : 'True', value : 'true' },
{ label : 'False', value : 'false' } ]
},
prune_branch : {
label : 'Prune the selected branch',
help : 'Select true to prune the selected branch.',
type : 'select',
display : 'radio',
value : 'false',
data : [ { label : 'True', value : 'true' },
{ label : 'False', value : 'false' } ]
},
show_labels: {
label : 'Show/Hide labels',
help : 'Select false to hide labels.',
type : 'select',
display : 'radio',
value : 'true',
data : [ { label : 'True', value : 'true' },
{ label : 'False', value : 'false' } ]
},
align_labels: {
label : 'Align labels',
help : 'Select to align the labels of tree. Supported with rectangular, circular, and hierarchical tree types.',
type : 'select',
display : 'radio',
value : 'true',
data : [ { label : 'True', value : 'true' },
{ label : 'False', value : 'false' } ]
},
node_shape : {
label : 'Node shapes for leaves',
help : 'Select a node shape for leaves.',
type : 'select',
display : 'radio',
value : 'circle',
data : [ { label : 'Circle', value : 'circle' },
{ label : 'Square', value: 'square' },
{ label : 'Star', value : 'star' },
{ label : 'Triangle', value : 'triangle' } ]
}
}
}
});
config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png
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config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
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define( [ 'utilities/utils', 'plugins/biojs/phylocanvas/phylocanvas' ], function( Utils, Phylocanvas ) {
return Backbone.Model.extend({
initialize: function( options ) {
var chart = options.chart,
dataset = options.dataset,
settings = options.chart.settings;
Utils.get( {
url : dataset.download_url,
success : function( content ) {
try {
var tree = Phylocanvas.default.createTree( options.targets[ 0 ] ),
node_size = 20,
text_size = 20,
line_width = 2;
// Set different properties of the tree
tree.setTreeType( settings.get( 'tree_type' ) );
// Set properties related to labels
tree.showLabels = settings.get( 'show_labels' ) === "true" ? true : false;
tree.alignLabels = settings.get( 'align_labels' ) === "true" ? true : false;
// Set properties related to colors
tree.branchColour = settings.get( 'edge_color' );
tree.highlightColour = settings.get( 'highlighted_color' );
tree.selectedColour = settings.get( 'selected_color' );
// Set properties related to size
tree.setNodeSize( node_size );
tree.setTextSize( text_size );
tree.lineWidth = line_width;
// Register click event on tree
tree.on( 'click', function ( e ) {
var node = tree.getNodeAtMousePosition( e );
// Here collapse action is taking preference.
// Whenver collapse and prune both are selected true,
// collapse action will be performed
// Collapse the selected branch
if( settings.get( 'collapse_branch' ) === "true" ) {
tree.branches[ node.id ].collapsed = true;
tree.draw();
}// Prune the selected branch
else if( settings.get( 'prune_branch' ) === "true" ) {
tree.branches[ node.id ].pruned = true;
tree.draw();
}
});
// Draw the phylogenetic tree
tree.load( content );
// Set node shape
for(var j = 0, length = tree.leaves.length; j < length; j++) {
tree.leaves[ j ].nodeShape = settings.get( 'node_shape' );
}
tree.draw();
chart.state( 'ok', 'Done.' );
options.process.resolve();
// Adjust the size of tree on window resize
$( window ).resize( function() {
tree.fitInPanel( tree.leaves ); tree.draw();
} );
} catch( err ) {
chart.state( 'failed', err );
}
},
error: function() {
chart.state( 'failed', 'Failed to access dataset.' );
options.process.resolve();
}
});
}
});
});