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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

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