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morpheus.js
Commit eb2cc358 authored by Joshua Gould's avatar Joshua Gould
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specify https protocol to enable running locally without server

parent dc0545ce
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js/morpheus-latest.min.js
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src/sample_datasets.js
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morpheus.SampleDatasets = function(options) { morpheus.SampleDatasets = function (options) {
if (!options.openText) { if (!options.openText) {
options.openText = 'Open'; options.openText = 'Open';
} }
...@@ -10,34 +10,34 @@ morpheus.SampleDatasets = function(options) { ...@@ -10,34 +10,34 @@ morpheus.SampleDatasets = function(options) {
exampleHtml.push('<table class="table table-condensed">'); exampleHtml.push('<table class="table table-condensed">');
exampleHtml exampleHtml
.push('<td>Cancer Cell Line Encyclopedia (CCLE), Project Achilles</td>'); .push('<td>Cancer Cell Line Encyclopedia (CCLE), Project Achilles</td>');
exampleHtml exampleHtml
.push('<td><input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="mrna"> Gene Expression</td>'); .push('<td><input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="mrna"> Gene Expression</td>');
exampleHtml exampleHtml
.push('<td><input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="cn"> Copy Number By Gene</td>'); .push('<td><input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="cn"> Copy Number By Gene</td>');
exampleHtml exampleHtml
.push('<td><input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="sig_genes"> Mutations</td>'); .push('<td><input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="sig_genes"> Mutations</td>');
exampleHtml exampleHtml
.push('<td><input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="ach"> Gene essentiality</td>'); .push('<td><input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="ach"> Gene essentiality</td>');
exampleHtml exampleHtml
.push('<td><button disabled type="button" class="btn btn-default" name="ccle">' .push('<td><button disabled type="button" class="btn btn-default" name="ccle">'
+ options.openText + '</button></td>'); + options.openText + '</button></td>');
exampleHtml.push('</tr></table>'); exampleHtml.push('</tr></table>');
exampleHtml exampleHtml
.push('<div class="text-muted">TCGA data version 1/11/2015</div><span class="text-muted">Please adhere to <a target="_blank" href="http://cancergenome.nih.gov/abouttcga/policies/publicationguidelines"> the TCGA publication guidelines</a></u> when using TCGA data in your publications.</span>'); .push('<div class="text-muted">TCGA data version 1/11/2015</div><span class="text-muted">Please adhere to <a target="_blank" href="http://cancergenome.nih.gov/abouttcga/policies/publicationguidelines"> the TCGA publication guidelines</a></u> when using TCGA data in your publications.</span>');
exampleHtml.push('<div name="tcga"></div>'); exampleHtml.push('<div name="tcga"></div>');
$(exampleHtml.join('')).appendTo($el); $(exampleHtml.join('')).appendTo($el);
$el.find('[name=ccle]').on('click', function(e) { $el.find('[name=ccle]').on('click', function (e) {
e.preventDefault(); e.preventDefault();
var $this = $(this); var $this = $(this);
var obj = {}; var obj = {};
$this.parents('tr').find('input:checked').each(function(i, c) { $this.parents('tr').find('input:checked').each(function (i, c) {
obj[$(c).data('type')] = true; obj[$(c).data('type')] = true;
}); });
...@@ -45,12 +45,12 @@ morpheus.SampleDatasets = function(options) { ...@@ -45,12 +45,12 @@ morpheus.SampleDatasets = function(options) {
}); });
$el.on('click', '[name=tcgaLink]', function(e) { $el.on('click', '[name=tcgaLink]', function (e) {
e.preventDefault(); e.preventDefault();
var $this = $(this); var $this = $(this);
var type = $this.data('disease-type'); var type = $this.data('disease-type');
var obj = {}; var obj = {};
$this.parents('tr').find('input:checked').each(function(i, c) { $this.parents('tr').find('input:checked').each(function (i, c) {
obj[$(c).data('type')] = true; obj[$(c).data('type')] = true;
}); });
var options; var options;
...@@ -65,143 +65,143 @@ morpheus.SampleDatasets = function(options) { ...@@ -65,143 +65,143 @@ morpheus.SampleDatasets = function(options) {
_this.openTcga(obj); _this.openTcga(obj);
}); });
$el $el
.on( .on(
'click', 'click',
'[data-toggle=dataTypeToggle]', '[data-toggle=dataTypeToggle]',
function(e) { function (e) {
var $this = $(this); var $this = $(this);
var $button = $this.parents('tr').find('button'); var $button = $this.parents('tr').find('button');
var isDisabled = $this.parents('tr').find( var isDisabled = $this.parents('tr').find(
'input:checked').length === 0; 'input:checked').length === 0;
$button.prop('disabled', isDisabled); $button.prop('disabled', isDisabled);
if (!isDisabled) { if (!isDisabled) {
$button $button
.removeClass('animated flash') .removeClass('animated flash')
.addClass('animated flash') .addClass('animated flash')
.one( .one(
'webkitAnimationEnd mozAnimationEnd MSAnimationEnd oanimationend animationend', 'webkitAnimationEnd mozAnimationEnd MSAnimationEnd oanimationend animationend',
function() { function () {
$(this).removeClass( $(this).removeClass(
'animated flash'); 'animated flash');
});
}
}); });
}
});
$ $
.ajax( .ajax(
'//s3.amazonaws.com/data.clue.io/morpheus/tcga/tcga_index.txt') 'https://s3.amazonaws.com/data.clue.io/morpheus/tcga/tcga_index.txt')
.done( .done(
function(text) { function (text) {
var lines = text.split('\n'); var lines = text.split('\n');
var diseases = []; var diseases = [];
for (var i = 0; i < lines.length; i++) { for (var i = 0; i < lines.length; i++) {
var line = lines[i]; var line = lines[i];
if (line === '') { if (line === '') {
continue; continue;
} }
var tokens = line.split('\t'); var tokens = line.split('\t');
var type = tokens[0]; var type = tokens[0];
var dataTypes = tokens[1].split(','); var dataTypes = tokens[1].split(',');
var name = morpheus.TcgaUtil.DISEASE_STUDIES[type]; var name = morpheus.TcgaUtil.DISEASE_STUDIES[type];
var disease = { var disease = {
mrna : dataTypes mrna: dataTypes
.indexOf('mRNAseq_RSEM_normalized_log2.txt') !== -1, .indexOf('mRNAseq_RSEM_normalized_log2.txt') !== -1,
sig_genes : dataTypes.indexOf('sig_genes.txt') !== -1, sig_genes: dataTypes.indexOf('sig_genes.txt') !== -1,
gistic : dataTypes gistic: dataTypes
.indexOf('all_lesions.conf_99.txt') !== -1, .indexOf('all_lesions.conf_99.txt') !== -1,
sample_info : dataTypes.indexOf('All_CDEs.txt') !== -1, sample_info: dataTypes.indexOf('All_CDEs.txt') !== -1,
mutation : dataTypes mutation: dataTypes
.indexOf('mutations_merged.maf.txt') !== -1, .indexOf('mutations_merged.maf.txt') !== -1,
rppa : dataTypes.indexOf('rppa.txt') !== -1, rppa: dataTypes.indexOf('rppa.txt') !== -1,
methylation : dataTypes methylation: dataTypes
.indexOf('meth.by_mean.data.txt') !== -1, .indexOf('meth.by_mean.data.txt') !== -1,
name : name, name: name,
type : type, type: type,
dataTypes : dataTypes dataTypes: dataTypes
}; };
if (disease.mrna || disease.gistic if (disease.mrna || disease.gistic
|| disease.sig_genes || disease.rppa || disease.sig_genes || disease.rppa
|| disease.methylation) { || disease.methylation) {
diseases.push(disease); diseases.push(disease);
} }
} }
diseases.sort(function(a, b) { diseases.sort(function (a, b) {
a = a.name.toLowerCase(); a = a.name.toLowerCase();
b = b.name.toLowerCase(); b = b.name.toLowerCase();
return (a === b ? 0 : (a < b ? -1 : 1)); return (a === b ? 0 : (a < b ? -1 : 1));
}); });
var tcga = []; var tcga = [];
_this.diseases = diseases; _this.diseases = diseases;
tcga.push('<table class="table table-condensed">'); tcga.push('<table class="table table-condensed">');
// ><tr><th>Disease</th><th>Gene Expression</th><th>Copy // ><tr><th>Disease</th><th>Gene Expression</th><th>Copy
// Number</th><th>Copy Number By // Number</th><th>Copy Number By
// Gene</th><th>Mutations</th><th>Proteomics</th><th>Methylation</th></tr> // Gene</th><th>Mutations</th><th>Proteomics</th><th>Methylation</th></tr>
for (var i = 0; i < diseases.length; i++) { for (var i = 0; i < diseases.length; i++) {
var disease = diseases[i]; var disease = diseases[i];
tcga.push('<tr>'); tcga.push('<tr>');
tcga.push('<td>' + disease.name + '</td>'); tcga.push('<td>' + disease.name + '</td>');
tcga.push('<td>'); tcga.push('<td>');
if (disease.mrna) { if (disease.mrna) {
tcga tcga
.push('<input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="mrna"> Gene Expression'); .push('<input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="mrna"> Gene Expression');
} }
tcga.push('</td>'); tcga.push('</td>');
tcga.push('<td>'); tcga.push('<td>');
if (disease.gistic) { if (disease.gistic) {
tcga tcga
.push('<input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="gistic"> GISTIC Copy Number'); .push('<input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="gistic"> GISTIC Copy Number');
} }
tcga.push('</td>'); tcga.push('</td>');
tcga.push('<td>'); tcga.push('<td>');
if (disease.gistic) { if (disease.gistic) {
tcga tcga
.push('<input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="gisticGene"> Copy Number By Gene'); .push('<input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="gisticGene"> Copy Number By Gene');
} }
tcga.push('</td>'); tcga.push('</td>');
tcga.push('<td>'); tcga.push('<td>');
if (disease.sig_genes) { if (disease.sig_genes) {
tcga tcga
.push('<input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="sig_genes"> Mutations'); .push('<input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="sig_genes"> Mutations');
} }
tcga.push('</td>'); tcga.push('</td>');
tcga.push('<td>'); tcga.push('<td>');
if (disease.rppa) { if (disease.rppa) {
tcga tcga
.push('<input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="rppa"> Proteomics'); .push('<input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="rppa"> Proteomics');
} }
tcga.push('</td>'); tcga.push('</td>');
tcga.push('<td>'); tcga.push('<td>');
if (disease.methylation) { if (disease.methylation) {
tcga tcga
.push('<input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="methylation"> Methylation'); .push('<input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle" data-type="methylation"> Methylation');
} }
tcga.push('</td>'); tcga.push('</td>');
tcga.push('<td>'); tcga.push('<td>');
tcga tcga
.push('<td><button disabled type="button" class="btn btn-default" name="tcgaLink" data-disease-type="' .push('<td><button disabled type="button" class="btn btn-default" name="tcgaLink" data-disease-type="'
+ disease.type + disease.type
+ '">' + '">'
+ options.openText + options.openText
+ '</button></td>'); + '</button></td>');
tcga.push('</td>'); tcga.push('</td>');
tcga.push('</tr>'); tcga.push('</tr>');
} }
tcga.push('</table>'); tcga.push('</table>');
$(tcga.join('')).appendTo($el.find('[name=tcga]')); $(tcga.join('')).appendTo($el.find('[name=tcga]'));
}); });
}; };
morpheus.SampleDatasets.getTcgaDataset = function(options) { morpheus.SampleDatasets.getTcgaDataset = function (options) {
var baseUrl = '//s3.amazonaws.com/data.clue.io/morpheus/tcga/' var baseUrl = 'https://s3.amazonaws.com/data.clue.io/morpheus/tcga/'
+ options.type + '/'; + options.type + '/';
var datasetOptions = {}; var datasetOptions = {};
if (options.mrna) { if (options.mrna) {
datasetOptions.mrna = baseUrl + 'mRNAseq_RSEM_normalized_log2.txt'; datasetOptions.mrna = baseUrl + 'mRNAseq_RSEM_normalized_log2.txt';
...@@ -227,21 +227,21 @@ morpheus.SampleDatasets.getTcgaDataset = function(options) { ...@@ -227,21 +227,21 @@ morpheus.SampleDatasets.getTcgaDataset = function(options) {
datasetOptions.mrnaClust = baseUrl + 'bestclus.txt'; datasetOptions.mrnaClust = baseUrl + 'bestclus.txt';
datasetOptions.columnAnnotations = [ { datasetOptions.columnAnnotations = [{
file : baseUrl + 'All_CDEs.txt', file: baseUrl + 'All_CDEs.txt',
datasetField : 'participant_id', datasetField: 'participant_id',
fileField : 'patient_id' fileField: 'patient_id'
} ]; }];
return morpheus.TcgaUtil.getDataset(datasetOptions); return morpheus.TcgaUtil.getDataset(datasetOptions);
}; };
morpheus.SampleDatasets.getCCLEDataset = function(options) { morpheus.SampleDatasets.getCCLEDataset = function (options) {
var datasets = []; var datasets = [];
if (options.sig_genes) { if (options.sig_genes) {
datasets datasets
.push({ .push({
dataset : '//s3.amazonaws.com/data.clue.io/morpheus/CCLE_hybrid_capture1650_hg19_NoCommonSNPs_NoNeutralVariants_CDS_2012.05.07.maf.txt' dataset: 'https://s3.amazonaws.com/data.clue.io/morpheus/CCLE_hybrid_capture1650_hg19_NoCommonSNPs_NoNeutralVariants_CDS_2012.05.07.maf.txt'
}); });
// datasets // datasets
// .push({ // .push({
// dataset : // dataset :
...@@ -250,65 +250,65 @@ morpheus.SampleDatasets.getCCLEDataset = function(options) { ...@@ -250,65 +250,65 @@ morpheus.SampleDatasets.getCCLEDataset = function(options) {
} }
if (options.cn) { if (options.cn) {
datasets datasets
.push({ .push({
dataset : '//s3.amazonaws.com/data.clue.io/morpheus/CCLE_copynumber_byGene_2013-12-03.gct' dataset: 'https://s3.amazonaws.com/data.clue.io/morpheus/CCLE_copynumber_byGene_2013-12-03.gct'
}); });
} }
if (options.mrna) { if (options.mrna) {
datasets datasets
.push({ .push({
dataset : '//s3.amazonaws.com/data.clue.io/morpheus/CCLE_Expression_Entrez_2012-09-29.txt' dataset: 'https://s3.amazonaws.com/data.clue.io/morpheus/CCLE_Expression_Entrez_2012-09-29.txt'
}); });
} }
if (options.ach) { if (options.ach) {
datasets datasets
.push({ .push({
dataset : '//s3.amazonaws.com/data.clue.io/morpheus/Achilles_QC_v2.4.3.rnai.Gs.gct' dataset: 'https://s3.amazonaws.com/data.clue.io/morpheus/Achilles_QC_v2.4.3.rnai.Gs.gct'
}); });
} }
var columnAnnotations = [ { var columnAnnotations = [{
file : '//s3.amazonaws.com/data.clue.io/morpheus/CCLE_Sample_Info.txt', file: 'https://s3.amazonaws.com/data.clue.io/morpheus/CCLE_Sample_Info.txt',
datasetField : 'id', datasetField: 'id',
fileField : 'id' fileField: 'id'
} ]; }];
if (options.ach) { if (options.ach) {
// there are several cell lines that are in Achilles but not CCLE // there are several cell lines that are in Achilles but not CCLE
columnAnnotations columnAnnotations
.push({ .push({
file : '//s3.amazonaws.com/data.clue.io/morpheus/Achilles_v2.4_SampleInfo_small.txt', file: 'https://s3.amazonaws.com/data.clue.io/morpheus/Achilles_v2.4_SampleInfo_small.txt',
datasetField : 'id', datasetField: 'id',
fileField : 'id' fileField: 'id'
}); });
} }
var returnDeferred = $.Deferred(); var returnDeferred = $.Deferred();
var datasetDef = morpheus.DatasetUtil.readDatasetArray({ var datasetDef = morpheus.DatasetUtil.readDatasetArray({
dataset : datasets dataset: datasets
}); });
var annotationDef = morpheus.DatasetUtil.annotate({ var annotationDef = morpheus.DatasetUtil.annotate({
annotations : columnAnnotations, annotations: columnAnnotations,
isColumns : true isColumns: true
}); });
var datasetToReturn; var datasetToReturn;
datasetDef.done(function(d) { datasetDef.done(function (d) {
datasetToReturn = d; datasetToReturn = d;
}); });
datasetDef.fail(function(message) { datasetDef.fail(function (message) {
returnDeferred.reject(message); returnDeferred.reject(message);
}); });
var annotationCallbacks; var annotationCallbacks;
annotationDef.done(function(callbacks) { annotationDef.done(function (callbacks) {
annotationCallbacks = callbacks; annotationCallbacks = callbacks;
}); });
annotationDef.fail(function(message) { annotationDef.fail(function (message) {
returnDeferred.reject(message); returnDeferred.reject(message);
}); });
$.when.apply($, [ datasetDef, annotationDef ]).then(function() { $.when.apply($, [datasetDef, annotationDef]).then(function () {
annotationCallbacks.forEach(function(f) { annotationCallbacks.forEach(function (f) {
f(datasetToReturn); f(datasetToReturn);
}); });
returnDeferred.resolve(datasetToReturn); returnDeferred.resolve(datasetToReturn);
...@@ -318,82 +318,82 @@ morpheus.SampleDatasets.getCCLEDataset = function(options) { ...@@ -318,82 +318,82 @@ morpheus.SampleDatasets.getCCLEDataset = function(options) {
}; };
morpheus.SampleDatasets.prototype = { morpheus.SampleDatasets.prototype = {
openTcga : function(options) { openTcga: function (options) {
this this
.callback({ .callback({
name : options.name, name: options.name,
renderReady : function(heatMap) { renderReady: function (heatMap) {
var whitelist = [ var whitelist = [
'age_at_initial_pathologic_diagnosis', 'age_at_initial_pathologic_diagnosis',
'breast_carcinoma_estrogen_receptor_status', 'breast_carcinoma_estrogen_receptor_status',
'breast_carcinoma_progesterone_receptor_status', 'breast_carcinoma_progesterone_receptor_status',
'lab_proc_her2_neu_immunohistochemistry_receptor_status', 'lab_proc_her2_neu_immunohistochemistry_receptor_status',
'days_to_death', 'ethnicity', 'gender', 'days_to_death', 'ethnicity', 'gender',
'histological_type', 'pathologic_stage' ]; 'histological_type', 'pathologic_stage'];
var columnMetadata = heatMap.getProject() var columnMetadata = heatMap.getProject()
.getFullDataset().getColumnMetadata(); .getFullDataset().getColumnMetadata();
for (var i = 0; i < whitelist.length; i++) { for (var i = 0; i < whitelist.length; i++) {
if (columnMetadata.getByName(whitelist[i])) { if (columnMetadata.getByName(whitelist[i])) {
heatMap.addTrack(whitelist[i], true, 'color'); heatMap.addTrack(whitelist[i], true, 'color');
} }
} }
// view in space of mutation sample ids only // view in space of mutation sample ids only
if (options.sig_genes) { if (options.sig_genes) {
if (heatMap.getTrackIndex('q_value', false) === -1) { if (heatMap.getTrackIndex('q_value', false) === -1) {
heatMap.addTrack('q_value', false, 'text'); heatMap.addTrack('q_value', false, 'text');
} }
} }
}, },
columns : [ { columns: [{
field : 'participant_id', field: 'participant_id',
display : 'text' display: 'text'
}, { }, {
field : 'sample_type', field: 'sample_type',
display : 'color' display: 'color'
}, { }, {
field : 'mutation_summary', field: 'mutation_summary',
display : 'stacked_bar' display: 'stacked_bar'
}, { }, {
field : 'mRNAseq_cluster', field: 'mRNAseq_cluster',
display : 'color, highlight' display: 'color, highlight'
} ], }],
dataset : morpheus.SampleDatasets.getTcgaDataset(options) dataset: morpheus.SampleDatasets.getTcgaDataset(options)
}); });
}, },
openCCLE : function(options) { openCCLE: function (options) {
this.callback({ this.callback({
name : 'CCLE', name: 'CCLE',
rows : [ { rows: [{
field : 'id', field: 'id',
display : 'text,tooltip' display: 'text,tooltip'
}, { }, {
field : 'mutation_summary', field: 'mutation_summary',
display : 'stacked_bar' display: 'stacked_bar'
}, { }, {
field : 'Source', field: 'Source',
display : 'color' display: 'color'
} ], }],
columns : [ { columns: [{
field : 'id', field: 'id',
display : 'text' display: 'text'
}, { }, {
field : 'mutation_summary', field: 'mutation_summary',
display : 'stacked_bar' display: 'stacked_bar'
}, { }, {
field : 'gender', field: 'gender',
display : 'color, highlight' display: 'color, highlight'
}, { }, {
field : 'histology', field: 'histology',
display : 'color, highlight' display: 'color, highlight'
}, { }, {
field : 'histology subtype', field: 'histology subtype',
display : 'color, highlight' display: 'color, highlight'
}, { }, {
field : 'primary_site', field: 'primary_site',
display : 'color, highlight' display: 'color, highlight'
} ], }],
dataset : morpheus.SampleDatasets.getCCLEDataset(options) dataset: morpheus.SampleDatasets.getCCLEDataset(options)
}); });
} }
}; };
src/ui/heat_map_key_listener.js
View file @ eb2cc358
morpheus.HeatMapKeyListener = function(controller) { morpheus.HeatMapKeyListener = function(controller) {
var keydown = function(e) { var keydown = function(e) {
// if ((e.isImmediatePropagationStopped && e
// .isImmediatePropagationStopped())
// || (e.isDefaultPrevented && e.isDefaultPrevented())) {
// return;
// }
var tagName = e.target.tagName; var tagName = e.target.tagName;
if (tagName == 'INPUT' || tagName == 'SELECT' || tagName == 'TEXTAREA') { if (tagName == 'INPUT' || tagName == 'SELECT' || tagName == 'TEXTAREA') {
return; return;
...@@ -189,4 +182,4 @@ morpheus.HeatMapKeyListener = function(controller) { ...@@ -189,4 +182,4 @@ morpheus.HeatMapKeyListener = function(controller) {
e.preventDefault(); e.preventDefault();
e.stopPropagation(); e.stopPropagation();
}); });
}; };
\ No newline at end of file
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