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morpheus.js
Commit bc8c2428 authored by Joshua Gould's avatar Joshua Gould
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js/morpheus-latest.min.js
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src/matrix/dataset_util.js
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morpheus.DatasetUtil = function() { morpheus.DatasetUtil = function () {
}; };
morpheus.DatasetUtil.min = function(dataset, seriesIndex) { morpheus.DatasetUtil.min = function (dataset, seriesIndex) {
seriesIndex = seriesIndex || 0; seriesIndex = seriesIndex || 0;
var min = Number.MAX_VALUE; var min = Number.MAX_VALUE;
for (var i = 0, rows = dataset.getRowCount(); i < rows; i++) { for (var i = 0, rows = dataset.getRowCount(); i < rows; i++) {
...@@ -14,14 +14,14 @@ morpheus.DatasetUtil.min = function(dataset, seriesIndex) { ...@@ -14,14 +14,14 @@ morpheus.DatasetUtil.min = function(dataset, seriesIndex) {
} }
return min; return min;
}; };
morpheus.DatasetUtil.slicedView = function(dataset, rows, columns) { morpheus.DatasetUtil.slicedView = function (dataset, rows, columns) {
return new morpheus.SlicedDatasetView(dataset, rows, columns); return new morpheus.SlicedDatasetView(dataset, rows, columns);
}; };
morpheus.DatasetUtil.transposedView = function(dataset) { morpheus.DatasetUtil.transposedView = function (dataset) {
return dataset instanceof morpheus.TransposedDatasetView ? dataset return dataset instanceof morpheus.TransposedDatasetView ? dataset
.getDataset() : new morpheus.TransposedDatasetView(dataset); .getDataset() : new morpheus.TransposedDatasetView(dataset);
}; };
morpheus.DatasetUtil.max = function(dataset, seriesIndex) { morpheus.DatasetUtil.max = function (dataset, seriesIndex) {
seriesIndex = seriesIndex || 0; seriesIndex = seriesIndex || 0;
var max = -Number.MAX_VALUE; var max = -Number.MAX_VALUE;
for (var i = 0, rows = dataset.getRowCount(); i < rows; i++) { for (var i = 0, rows = dataset.getRowCount(); i < rows; i++) {
...@@ -36,7 +36,7 @@ morpheus.DatasetUtil.max = function(dataset, seriesIndex) { ...@@ -36,7 +36,7 @@ morpheus.DatasetUtil.max = function(dataset, seriesIndex) {
return max; return max;
}; };
morpheus.DatasetUtil.getDatasetReader = function(ext, options) { morpheus.DatasetUtil.getDatasetReader = function (ext, options) {
var datasetReader; var datasetReader;
if (ext === 'maf') { if (ext === 'maf') {
datasetReader = new morpheus.MafFileReader(); datasetReader = new morpheus.MafFileReader();
...@@ -63,23 +63,23 @@ morpheus.DatasetUtil.getDatasetReader = function(ext, options) { ...@@ -63,23 +63,23 @@ morpheus.DatasetUtil.getDatasetReader = function(ext, options) {
return datasetReader; return datasetReader;
}; };
morpheus.DatasetUtil.readDatasetArray = function(options) { morpheus.DatasetUtil.readDatasetArray = function (options) {
var retDef = $.Deferred(); var retDef = $.Deferred();
var loadedDatasets = []; var loadedDatasets = [];
var promises = []; var promises = [];
_.each(options.dataset, function(option, i) { _.each(options.dataset, function (option, i) {
var p = option.dataset.file ? morpheus.DatasetUtil.read( var p = option.dataset.file ? morpheus.DatasetUtil.read(
option.dataset.file, option.dataset.options) option.dataset.file, option.dataset.options)
: morpheus.DatasetUtil.read(option.dataset); : morpheus.DatasetUtil.read(option.dataset);
p.index = i; p.index = i;
p.done(function(dataset) { p.done(function (dataset) {
loadedDatasets[this.index] = dataset; loadedDatasets[this.index] = dataset;
}); });
p.fail(function(err) { p.fail(function (err) {
var message = [ 'Error opening ' var message = ['Error opening '
+ (option.dataset.file ? morpheus.Util + (option.dataset.file ? morpheus.Util
.getFileName(option.dataset.file) : morpheus.Util .getFileName(option.dataset.file) : morpheus.Util
.getFileName(option.dataset)) + '.' ]; .getFileName(option.dataset)) + '.'];
if (err.message) { if (err.message) {
message.push('<br />Cause: '); message.push('<br />Cause: ');
message.push(err.message); message.push(err.message);
...@@ -94,35 +94,35 @@ morpheus.DatasetUtil.readDatasetArray = function(options) { ...@@ -94,35 +94,35 @@ morpheus.DatasetUtil.readDatasetArray = function(options) {
} }
$.when $.when
.apply($, promises) .apply($, promises)
.then( .then(
function() { function () {
var joined; var joined;
if (loadedDatasets.length > 1) { if (loadedDatasets.length > 1) {
joined = new morpheus.JoinedDataset( joined = new morpheus.JoinedDataset(
loadedDatasets[0], loadedDatasets[1], 'id', loadedDatasets[0], loadedDatasets[1], 'id',
'id'); 'id');
for (var i = 2; i < loadedDatasets.length; i++) { for (var i = 2; i < loadedDatasets.length; i++) {
joined = new morpheus.JoinedDataset(joined, joined = new morpheus.JoinedDataset(joined,
loadedDatasets[i], 'id', 'id'); loadedDatasets[i], 'id', 'id');
} }
} else { } else {
// add Source // add Source
joined = loadedDatasets[0]; joined = loadedDatasets[0];
var sourceVector = joined.getRowMetadata().add( var sourceVector = joined.getRowMetadata().add(
'Source'); 'Source');
var name = joined.getName(); var name = joined.getName();
for (var i = 0, nrows = sourceVector.size(); i < nrows; i++) { for (var i = 0, nrows = sourceVector.size(); i < nrows; i++) {
sourceVector.setValue(i, name); sourceVector.setValue(i, name);
} }
} }
retDef.resolve(joined); retDef.resolve(joined);
}); });
return retDef; return retDef;
}; };
/** /**
* Annotate a dataset from external file or text. * Annotate a dataset from external file or text.
* *
* @param options.annotations - * @param options.annotations -
* Array of file, datasetField, and fileField. * Array of file, datasetField, and fileField.
* @param options.isColumns - * @param options.isColumns -
...@@ -130,53 +130,53 @@ morpheus.DatasetUtil.readDatasetArray = function(options) { ...@@ -130,53 +130,53 @@ morpheus.DatasetUtil.readDatasetArray = function(options) {
* @return A jQuery Deferred object that resolves to an array of functions to * @return A jQuery Deferred object that resolves to an array of functions to
* execute with a dataset parameter. * execute with a dataset parameter.
*/ */
morpheus.DatasetUtil.annotate = function(options) { morpheus.DatasetUtil.annotate = function (options) {
var retDef = $.Deferred(); var retDef = $.Deferred();
var promises = []; var promises = [];
var functions = []; var functions = [];
var isColumns = options.isColumns; var isColumns = options.isColumns;
_.each(options.annotations, function(ann) { _.each(options.annotations, function (ann) {
if (morpheus.Util.isArray(ann.file)) { // already parsed text if (morpheus.Util.isArray(ann.file)) { // already parsed text
functions.push(function(dataset) { functions.push(function (dataset) {
new morpheus.OpenFileTool().annotate(ann.file, dataset, new morpheus.OpenFileTool().annotate(ann.file, dataset,
isColumns, null, ann.datasetField, ann.fileField, isColumns, null, ann.datasetField, ann.fileField,
ann.include); ann.include);
}); });
} else { } else {
var result = morpheus.Util.readLines(ann.file); var result = morpheus.Util.readLines(ann.file);
var fileName = morpheus.Util.getFileName(ann.file); var fileName = morpheus.Util.getFileName(ann.file);
var deferred = $.Deferred(); var deferred = $.Deferred();
promises.push(deferred); promises.push(deferred);
result.fail(function(message) { result.fail(function (message) {
deferred.reject(message); deferred.reject(message);
}); });
result.done(function(lines) { result.done(function (lines) {
if (morpheus.Util.endsWith(fileName, '.gmt')) { if (morpheus.Util.endsWith(fileName, '.gmt')) {
var sets = new morpheus.GmtReader().parseLines(lines); var sets = new morpheus.GmtReader().parseLines(lines);
functions.push(function(dataset) { functions.push(function (dataset) {
new morpheus.OpenFileTool().annotate(null, dataset, new morpheus.OpenFileTool().annotate(null, dataset,
isColumns, sets, ann.datasetField, isColumns, sets, ann.datasetField,
ann.fileField); ann.fileField);
}); });
deferred.resolve(); deferred.resolve();
} else if (morpheus.Util.endsWith(fileName, '.cls')) { } else if (morpheus.Util.endsWith(fileName, '.cls')) {
functions.push(function(dataset) { functions.push(function (dataset) {
new morpheus.OpenFileTool().annotateCls(null, dataset, new morpheus.OpenFileTool().annotateCls(null, dataset,
fileName, isColumns, lines); fileName, isColumns, lines);
}); });
deferred.resolve(); deferred.resolve();
} else { } else {
functions.push(function(dataset) { functions.push(function (dataset) {
new morpheus.OpenFileTool().annotate(lines, dataset, new morpheus.OpenFileTool().annotate(lines, dataset,
isColumns, null, ann.datasetField, isColumns, null, ann.datasetField,
ann.fileField, ann.include); ann.fileField, ann.include);
}); });
deferred.resolve(); deferred.resolve();
} }
}); });
} }
}); });
$.when.apply($, promises).then(function() { $.when.apply($, promises).then(function () {
retDef.resolve(functions); retDef.resolve(functions);
}); });
return retDef; return retDef;
...@@ -186,10 +186,10 @@ morpheus.DatasetUtil.annotate = function(options) { ...@@ -186,10 +186,10 @@ morpheus.DatasetUtil.annotate = function(options) {
* a File or url * a File or url
* @return A promise that resolves to Dataset * @return A promise that resolves to Dataset
*/ */
morpheus.DatasetUtil.read = function(fileOrUrl, options) { morpheus.DatasetUtil.read = function (fileOrUrl, options) {
var isFile = fileOrUrl instanceof File; var isFile = fileOrUrl instanceof File;
var isString = _.isString(fileOrUrl); var isString = _.isString(fileOrUrl);
var ext = morpheus.Util.getExtension(morpheus.Util.getFileName(fileOrUrl)); var ext = options && options.extension ? options.extension : morpheus.Util.getExtension(morpheus.Util.getFileName(fileOrUrl));
var datasetReader = morpheus.DatasetUtil.getDatasetReader(ext, options); var datasetReader = morpheus.DatasetUtil.getDatasetReader(ext, options);
if (isString || isFile) { // URL or file if (isString || isFile) { // URL or file
...@@ -198,32 +198,32 @@ morpheus.DatasetUtil.read = function(fileOrUrl, options) { ...@@ -198,32 +198,32 @@ morpheus.DatasetUtil.read = function(fileOrUrl, options) {
if (options && options.background) { if (options && options.background) {
var path = morpheus.Util.getScriptPath(); var path = morpheus.Util.getScriptPath();
var blob = new Blob( var blob = new Blob(
[ 'self.onmessage = function(e) {' ['self.onmessage = function(e) {'
+ 'importScripts(e.data.path);' + 'importScripts(e.data.path);'
+ 'var ext = morpheus.Util.getExtension(morpheus.Util' + 'var ext = morpheus.Util.getExtension(morpheus.Util'
+ '.getFileName(e.data.fileOrUrl));' + '.getFileName(e.data.fileOrUrl));'
+ 'var datasetReader = morpheus.DatasetUtil.getDatasetReader(ext,' + 'var datasetReader = morpheus.DatasetUtil.getDatasetReader(ext,'
+ ' e.data.options);' + ' e.data.options);'
+ 'datasetReader.read(e.data.fileOrUrl, function(err,dataset) {' + 'datasetReader.read(e.data.fileOrUrl, function(err,dataset) {'
+ ' self.postMessage(dataset);' + ' });' + '}' ]); + ' self.postMessage(dataset);' + ' });' + '}']);
// Obtain a blob URL reference to our worker 'file'. // Obtain a blob URL reference to our worker 'file'.
var blobURL = window.URL.createObjectURL(blob); var blobURL = window.URL.createObjectURL(blob);
var worker = new Worker(blobURL); // blobURL); var worker = new Worker(blobURL); // blobURL);
worker.addEventListener('message', function(e) { worker.addEventListener('message', function (e) {
// wrap in dataset object // wrap in dataset object
deferred.resolve(morpheus.Dataset.fromJson(e.data)); deferred.resolve(morpheus.Dataset.fromJson(e.data));
window.URL.revokeObjectURL(blobURL); window.URL.revokeObjectURL(blobURL);
}, false); }, false);
// start the worker // start the worker
worker.postMessage({ worker.postMessage({
path : path, path: path,
fileOrUrl : fileOrUrl, fileOrUrl: fileOrUrl,
options : options options: options
}); });
} else { } else {
datasetReader.read(fileOrUrl, function(err, dataset) { datasetReader.read(fileOrUrl, function (err, dataset) {
if (err) { if (err) {
deferred.reject(err); deferred.reject(err);
} else { } else {
...@@ -234,7 +234,7 @@ morpheus.DatasetUtil.read = function(fileOrUrl, options) { ...@@ -234,7 +234,7 @@ morpheus.DatasetUtil.read = function(fileOrUrl, options) {
} }
var pr = deferred.promise(); var pr = deferred.promise();
pr.toString = function() { pr.toString = function () {
return '' + fileOrUrl; return '' + fileOrUrl;
}; };
return pr; return pr;
...@@ -259,11 +259,11 @@ morpheus.DatasetUtil.read = function(fileOrUrl, options) { ...@@ -259,11 +259,11 @@ morpheus.DatasetUtil.read = function(fileOrUrl, options) {
* correspond to the column indices in the dataset * correspond to the column indices in the dataset
* @param options.metadataFields * @param options.metadataFields
* An array of row metadata fields to include from the dataset * An array of row metadata fields to include from the dataset
* *
*/ */
morpheus.DatasetUtil.toObjectArray = function(dataset, options) { morpheus.DatasetUtil.toObjectArray = function (dataset, options) {
var columns = options.columns || [ 0 ]; var columns = options.columns || [0];
var columnFields = options.columnFields || [ 'value' ]; var columnFields = options.columnFields || ['value'];
if (columnFields.length !== columns.length) { if (columnFields.length !== columns.length) {
throw 'columns.length !== columnFields.length'; throw 'columns.length !== columnFields.length';
} }
...@@ -293,19 +293,19 @@ morpheus.DatasetUtil.toObjectArray = function(dataset, options) { ...@@ -293,19 +293,19 @@ morpheus.DatasetUtil.toObjectArray = function(dataset, options) {
} }
return array; return array;
}; };
morpheus.DatasetUtil.fixL1K = function(dataset) { morpheus.DatasetUtil.fixL1K = function (dataset) {
var names = { var names = {
'cell_id' : 'Cell Line', 'cell_id': 'Cell Line',
'pert_idose' : 'Dose (\u00B5M)', 'pert_idose': 'Dose (\u00B5M)',
'pert_iname' : 'Name', 'pert_iname': 'Name',
'pert_itime' : 'Time (hr)', 'pert_itime': 'Time (hr)',
'distil_ss' : 'Signature Strength', 'distil_ss': 'Signature Strength',
'pert_type' : 'Type', 'pert_type': 'Type',
'cell_lineage' : 'Lineage', 'cell_lineage': 'Lineage',
'cell_histology' : 'Histology', 'cell_histology': 'Histology',
'cell_type' : 'Cell Type' 'cell_type': 'Cell Type'
}; };
var fixNames = function(metadata) { var fixNames = function (metadata) {
for (var i = 0, count = metadata.getMetadataCount(); i < count; i++) { for (var i = 0, count = metadata.getMetadataCount(); i < count; i++) {
var v = metadata.get(i); var v = metadata.get(i);
var name = v.getName(); var name = v.getName();
...@@ -317,7 +317,7 @@ morpheus.DatasetUtil.fixL1K = function(dataset) { ...@@ -317,7 +317,7 @@ morpheus.DatasetUtil.fixL1K = function(dataset) {
}; };
fixNames(dataset.getRowMetadata()); fixNames(dataset.getRowMetadata());
fixNames(dataset.getColumnMetadata()); fixNames(dataset.getColumnMetadata());
var fix666 = function(metadata) { var fix666 = function (metadata) {
for (var i = 0, count = metadata.getMetadataCount(); i < count; i++) { for (var i = 0, count = metadata.getMetadataCount(); i < count; i++) {
var v = metadata.get(i); var v = metadata.get(i);
if (v.getName() == 'Dose (\u00B5M)') { // convert to number if (v.getName() == 'Dose (\u00B5M)') { // convert to number
...@@ -347,9 +347,9 @@ morpheus.DatasetUtil.fixL1K = function(dataset) { ...@@ -347,9 +347,9 @@ morpheus.DatasetUtil.fixL1K = function(dataset) {
}; };
fix666(dataset.getRowMetadata()); fix666(dataset.getRowMetadata());
fix666(dataset.getColumnMetadata()); fix666(dataset.getColumnMetadata());
var fixCommas = function(metadata) { var fixCommas = function (metadata) {
var regex = /(,)([^ ])/g; var regex = /(,)([^ ])/g;
_.each([ 'Lineage', 'Histology' ], function(name) { _.each(['Lineage', 'Histology'], function (name) {
var v = metadata.getByName(name); var v = metadata.getByName(name);
if (v != null) { if (v != null) {
for (var i = 0, size = v.size(); i < size; i++) { for (var i = 0, size = v.size(); i < size; i++) {
...@@ -364,7 +364,7 @@ morpheus.DatasetUtil.fixL1K = function(dataset) { ...@@ -364,7 +364,7 @@ morpheus.DatasetUtil.fixL1K = function(dataset) {
fixCommas(dataset.getRowMetadata()); fixCommas(dataset.getRowMetadata());
fixCommas(dataset.getColumnMetadata()); fixCommas(dataset.getColumnMetadata());
}; };
morpheus.DatasetUtil.geneSetsToDataset = function(name, sets) { morpheus.DatasetUtil.geneSetsToDataset = function (name, sets) {
var uniqueIds = new morpheus.Map(); var uniqueIds = new morpheus.Map();
for (var i = 0, length = sets.length; i < length; i++) { for (var i = 0, length = sets.length; i < length; i++) {
var ids = sets[i].ids; var ids = sets[i].ids;
...@@ -374,9 +374,9 @@ morpheus.DatasetUtil.geneSetsToDataset = function(name, sets) { ...@@ -374,9 +374,9 @@ morpheus.DatasetUtil.geneSetsToDataset = function(name, sets) {
} }
var uniqueIdsArray = uniqueIds.keys(); var uniqueIdsArray = uniqueIds.keys();
var dataset = new morpheus.Dataset({ var dataset = new morpheus.Dataset({
name : name, name: name,
rows : uniqueIdsArray.length, rows: uniqueIdsArray.length,
columns : sets.length columns: sets.length
}); });
var columnIds = dataset.getColumnMetadata().add('id'); var columnIds = dataset.getColumnMetadata().add('id');
for (var i = 0, length = sets.length; i < length; i++) { for (var i = 0, length = sets.length; i < length; i++) {
...@@ -396,29 +396,29 @@ morpheus.DatasetUtil.geneSetsToDataset = function(name, sets) { ...@@ -396,29 +396,29 @@ morpheus.DatasetUtil.geneSetsToDataset = function(name, sets) {
return dataset; return dataset;
}; };
morpheus.DatasetUtil.DATASET_FILE_FORMATS = '<a target="_blank" href="http://support.lincscloud.org/hc/en-us/articles/202105453-GCT-Gene-Cluster-Text-Format-">GCT 1.3</a>, ' morpheus.DatasetUtil.DATASET_FILE_FORMATS = '<a target="_blank" href="http://support.lincscloud.org/hc/en-us/articles/202105453-GCT-Gene-Cluster-Text-Format-">GCT 1.3</a>, '
+ '<a target="_blank" href="http://www.broadinstitute.org/cancer/software/genepattern/gp_guides/file-formats/sections/gct">GCT 1.2</a>, ' + '<a target="_blank" href="http://www.broadinstitute.org/cancer/software/genepattern/gp_guides/file-formats/sections/gct">GCT 1.2</a>, '
+ '<a target="_blank" href="https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification">MAF</a>, ' + '<a target="_blank" href="https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification">MAF</a>, '
+ '<a target="_blank", href="http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29">GMT</a>, ' + '<a target="_blank", href="http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29">GMT</a>, '
+ ' or a tab-delimited text file'; + ' or a tab-delimited text file';
morpheus.DatasetUtil.BASIC_DATASET_FILE_FORMATS = '<a target="_blank" href="http://support.lincscloud.org/hc/en-us/articles/202105453-GCT-Gene-Cluster-Text-Format-">GCT 1.3</a>, ' morpheus.DatasetUtil.BASIC_DATASET_FILE_FORMATS = '<a target="_blank" href="http://support.lincscloud.org/hc/en-us/articles/202105453-GCT-Gene-Cluster-Text-Format-">GCT 1.3</a>, '
+ '<a target="_blank" href="http://www.broadinstitute.org/cancer/software/genepattern/gp_guides/file-formats/sections/gct">GCT 1.2</a>, ' + '<a target="_blank" href="http://www.broadinstitute.org/cancer/software/genepattern/gp_guides/file-formats/sections/gct">GCT 1.2</a>, '
+ ' or a tab-delimited text file'; + ' or a tab-delimited text file';
morpheus.DatasetUtil.GCT_FILE_FORMAT = '<a target="_blank" href="http://support.lincscloud.org/hc/en-us/articles/202105453-GCT-Gene-Cluster-Text-Format-">GCT 1.3</a>'; morpheus.DatasetUtil.GCT_FILE_FORMAT = '<a target="_blank" href="http://support.lincscloud.org/hc/en-us/articles/202105453-GCT-Gene-Cluster-Text-Format-">GCT 1.3</a>';
morpheus.DatasetUtil.ANNOTATION_FILE_FORMATS = 'an xlsx file, tab-delimited text file, or a <a target="_blank" href="http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29">GMT file</a>'; morpheus.DatasetUtil.ANNOTATION_FILE_FORMATS = 'an xlsx file, tab-delimited text file, or a <a target="_blank" href="http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29">GMT file</a>';
morpheus.DatasetUtil.DENDROGRAM_FILE_FORMATS = 'a <a href="http://en.wikipedia.org/wiki/Newick_format" target="_blank">Newick</a> file'; morpheus.DatasetUtil.DENDROGRAM_FILE_FORMATS = 'a <a href="http://en.wikipedia.org/wiki/Newick_format" target="_blank">Newick</a> file';
morpheus.DatasetUtil.OPEN_FILE_FORMATS = '<a target="_blank" href="http://support.lincscloud.org/hc/en-us/articles/202105453-GCT-Gene-Cluster-Text-Format-">GCT 1.3</a>, ' morpheus.DatasetUtil.OPEN_FILE_FORMATS = '<a target="_blank" href="http://support.lincscloud.org/hc/en-us/articles/202105453-GCT-Gene-Cluster-Text-Format-">GCT 1.3</a>, '
+ '<a target="_blank" href="http://www.broadinstitute.org/cancer/software/genepattern/gp_guides/file-formats/sections/gct">GCT 1.2</a>, ' + '<a target="_blank" href="http://www.broadinstitute.org/cancer/software/genepattern/gp_guides/file-formats/sections/gct">GCT 1.2</a>, '
+ '<a target="_blank" href="https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification">MAF</a>, ' + '<a target="_blank" href="https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification">MAF</a>, '
+ '<a target="_blank", href="http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29">GMT</a>, ' + '<a target="_blank", href="http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29">GMT</a>, '
+ ' a tab-delimited text file, or a <a href="http://en.wikipedia.org/wiki/Newick_format" target="_blank">Newick</a> file'; + ' a tab-delimited text file, or a <a href="http://en.wikipedia.org/wiki/Newick_format" target="_blank">Newick</a> file';
morpheus.DatasetUtil.getRootDataset = function(dataset) { morpheus.DatasetUtil.getRootDataset = function (dataset) {
while (dataset.getDataset) { while (dataset.getDataset) {
dataset = dataset.getDataset(); dataset = dataset.getDataset();
} }
return dataset; return dataset;
}; };
morpheus.DatasetUtil.getSeriesIndex = function(dataset, name) { morpheus.DatasetUtil.getSeriesIndex = function (dataset, name) {
for (var i = 0, nseries = dataset.getSeriesCount(); i < nseries; i++) { for (var i = 0, nseries = dataset.getSeriesCount(); i < nseries; i++) {
if (name === dataset.getName(i)) { if (name === dataset.getName(i)) {
return i; return i;
...@@ -426,12 +426,12 @@ morpheus.DatasetUtil.getSeriesIndex = function(dataset, name) { ...@@ -426,12 +426,12 @@ morpheus.DatasetUtil.getSeriesIndex = function(dataset, name) {
} }
return -1; return -1;
}; };
morpheus.DatasetUtil.getSeriesNames = function(dataset) { morpheus.DatasetUtil.getSeriesNames = function (dataset) {
var names = []; var names = [];
for (var i = 0, nseries = dataset.getSeriesCount(); i < nseries; i++) { for (var i = 0, nseries = dataset.getSeriesCount(); i < nseries; i++) {
names.push(dataset.getName(i)); names.push(dataset.getName(i));
} }
names.sort(function(a, b) { names.sort(function (a, b) {
a = a.toLowerCase(); a = a.toLowerCase();
b = b.toLowerCase(); b = b.toLowerCase();
return (a < b ? -1 : (a === b ? 0 : 1)); return (a < b ? -1 : (a === b ? 0 : 1));
...@@ -442,7 +442,7 @@ morpheus.DatasetUtil.getSeriesNames = function(dataset) { ...@@ -442,7 +442,7 @@ morpheus.DatasetUtil.getSeriesNames = function(dataset) {
/** /**
* Search dataset values. * Search dataset values.
*/ */
morpheus.DatasetUtil.searchValues = function(dataset, text, cb) { morpheus.DatasetUtil.searchValues = function (dataset, text, cb) {
if (text === '') { if (text === '') {
return; return;
} }
...@@ -454,7 +454,7 @@ morpheus.DatasetUtil.searchValues = function(dataset, text, cb) { ...@@ -454,7 +454,7 @@ morpheus.DatasetUtil.searchValues = function(dataset, text, cb) {
for (var i = 0, nrows = dataset.getRowCount(); i < nrows; i++) { for (var i = 0, nrows = dataset.getRowCount(); i < nrows; i++) {
for (var k = 0, nseries = dataset.getSeriesCount(); k < nseries; k++) { for (var k = 0, nseries = dataset.getSeriesCount(); k < nseries; k++) {
if (dataset.getDataType(i, k) === 'object') { if (dataset.getDataType(i, k) === 'object') {
seriesIndices.push([ i, k ]); seriesIndices.push([i, k]);
} }
} }
} }
...@@ -474,8 +474,8 @@ morpheus.DatasetUtil.searchValues = function(dataset, text, cb) { ...@@ -474,8 +474,8 @@ morpheus.DatasetUtil.searchValues = function(dataset, text, cb) {
} }
var fields = _val == null ? [] : _.keys(_val); var fields = _val == null ? [] : _.keys(_val);
var predicates = morpheus.Util.createSearchPredicates({ var predicates = morpheus.Util.createSearchPredicates({
tokens : tokens, tokens: tokens,
fields : fields fields: fields
}); });
var npredicates = predicates.length; var npredicates = predicates.length;
...@@ -500,7 +500,7 @@ morpheus.DatasetUtil.searchValues = function(dataset, text, cb) { ...@@ -500,7 +500,7 @@ morpheus.DatasetUtil.searchValues = function(dataset, text, cb) {
break; break;
} }
} else { // try all fields } else { // try all fields
for ( var name in object) { for (var name in object) {
var value = object[name]; var value = object[name];
if (value != null && predicate.accept(value)) { if (value != null && predicate.accept(value)) {
if (cb(value, pair[0], j) === false) { if (cb(value, pair[0], j) === false) {
...@@ -522,17 +522,17 @@ morpheus.DatasetUtil.searchValues = function(dataset, text, cb) { ...@@ -522,17 +522,17 @@ morpheus.DatasetUtil.searchValues = function(dataset, text, cb) {
/** /**
* Search dataset values. * Search dataset values.
*/ */
morpheus.DatasetUtil.autocompleteValues = function(dataset) { morpheus.DatasetUtil.autocompleteValues = function (dataset) {
return function(tokens, cb) { return function (tokens, cb) {
var token = tokens != null && tokens.length > 0 ? tokens[tokens.selectionStartIndex] var token = tokens != null && tokens.length > 0 ? tokens[tokens.selectionStartIndex]
: ''; : '';
token = $.trim(token); token = $.trim(token);
var seriesIndices = []; var seriesIndices = [];
for (var i = 0, nrows = dataset.getRowCount(); i < nrows; i++) { for (var i = 0, nrows = dataset.getRowCount(); i < nrows; i++) {
for (var k = 0, nseries = dataset.getSeriesCount(); k < nseries; k++) { for (var k = 0, nseries = dataset.getSeriesCount(); k < nseries; k++) {
if (dataset.getDataType(i, k) === 'object') { if (dataset.getDataType(i, k) === 'object') {
seriesIndices.push([ i, k ]); seriesIndices.push([i, k]);
} }
} }
} }
...@@ -553,15 +553,15 @@ morpheus.DatasetUtil.autocompleteValues = function(dataset) { ...@@ -553,15 +553,15 @@ morpheus.DatasetUtil.autocompleteValues = function(dataset) {
var matches = []; var matches = [];
var fields = _val == null ? [] : _.keys(_val); var fields = _val == null ? [] : _.keys(_val);
if (token === '') { if (token === '') {
fields.sort(function(a, b) { fields.sort(function (a, b) {
return (a === b ? 0 : (a < b ? -1 : 1)); return (a === b ? 0 : (a < b ? -1 : 1));
}); });
fields.forEach(function(field) { fields.forEach(function (field) {
matches.push({ matches.push({
value : field + ':', value: field + ':',
label : '<span style="font-weight:300;">' + field label: '<span style="font-weight:300;">' + field
+ ':</span>', + ':</span>',
show : true show: true
}); });
}); });
return cb(matches); return cb(matches);
...@@ -573,9 +573,9 @@ morpheus.DatasetUtil.autocompleteValues = function(dataset) { ...@@ -573,9 +573,9 @@ morpheus.DatasetUtil.autocompleteValues = function(dataset) {
if (token.charCodeAt(semi - 1) !== 92) { // \: if (token.charCodeAt(semi - 1) !== 92) { // \:
var possibleField = $.trim(token.substring(0, semi)); var possibleField = $.trim(token.substring(0, semi));
if (possibleField.length > 0 && possibleField[0] === '"' if (possibleField.length > 0 && possibleField[0] === '"'
&& possibleField[token.length - 1] === '"') { && possibleField[token.length - 1] === '"') {
possibleField = possibleField.substring(1, possibleField = possibleField.substring(1,
possibleField.length - 1); possibleField.length - 1);
} }
var index = fields.indexOf(possibleField); var index = fields.indexOf(possibleField);
if (index !== -1) { if (index !== -1) {
...@@ -602,7 +602,7 @@ morpheus.DatasetUtil.autocompleteValues = function(dataset) { ...@@ -602,7 +602,7 @@ morpheus.DatasetUtil.autocompleteValues = function(dataset) {
if (field !== null) { if (field !== null) {
var val = object[field]; var val = object[field];
if (val != null) { if (val != null) {
var id = new morpheus.Identifier([ val, field ]); var id = new morpheus.Identifier([val, field]);
if (!set.has(id) && regex.test(val)) { if (!set.has(id) && regex.test(val)) {
set.add(id); set.add(id);
if (set.size() === max) { if (set.size() === max) {
...@@ -611,9 +611,9 @@ morpheus.DatasetUtil.autocompleteValues = function(dataset) { ...@@ -611,9 +611,9 @@ morpheus.DatasetUtil.autocompleteValues = function(dataset) {
} }
} }
} else { // search all fields } else { // search all fields
for ( var name in object) { for (var name in object) {
var val = object[name]; var val = object[name];
var id = new morpheus.Identifier([ val, name ]); var id = new morpheus.Identifier([val, name]);
if (!set.has(id) && regex.test(val)) { if (!set.has(id) && regex.test(val)) {
set.add(id); set.add(id);
if (set.size() === max) { if (set.size() === max) {
...@@ -626,25 +626,25 @@ morpheus.DatasetUtil.autocompleteValues = function(dataset) { ...@@ -626,25 +626,25 @@ morpheus.DatasetUtil.autocompleteValues = function(dataset) {
} }
} }
} }
set.forEach(function(id) { set.forEach(function (id) {
var array = id.getArray(); var array = id.getArray();
var field = array[1]; var field = array[1];
var val = array[0]; var val = array[0];
matches.push({ matches.push({
value : field + ':' + val, value: field + ':' + val,
label : '<span style="font-weight:300;">' + field + ':</span>' label: '<span style="font-weight:300;">' + field + ':</span>'
+ '<span style="font-weight:900;">' + val + '</span>' + '<span style="font-weight:900;">' + val + '</span>'
}); });
}); });
if (field == null) { if (field == null) {
fields.forEach(function(field) { fields.forEach(function (field) {
if (regex.test(field)) { if (regex.test(field)) {
matches.push({ matches.push({
value : field + ':', value: field + ':',
label : '<span style="font-weight:300;">' + field label: '<span style="font-weight:300;">' + field
+ ':</span>', + ':</span>',
show : true show: true
}); });
} }
}); });
...@@ -700,72 +700,72 @@ morpheus.DatasetUtil.autocompleteValues = function(dataset) { ...@@ -700,72 +700,72 @@ morpheus.DatasetUtil.autocompleteValues = function(dataset) {
// json.push('}'); // end json object // json.push('}'); // end json object
// return json.join(''); // return json.join('');
// }; // };
morpheus.DatasetUtil.fill = function(dataset, value, seriesIndex) { morpheus.DatasetUtil.fill = function (dataset, value, seriesIndex) {
seriesIndex = seriesIndex || 0; seriesIndex = seriesIndex || 0;
for (var i = 0, nrows = dataset.getRowCount(), ncols = dataset for (var i = 0, nrows = dataset.getRowCount(), ncols = dataset
.getColumnCount(); i < nrows; i++) { .getColumnCount(); i < nrows; i++) {
for (var j = 0; j < ncols; j++) { for (var j = 0; j < ncols; j++) {
dataset.setValue(i, j, value, seriesIndex); dataset.setValue(i, j, value, seriesIndex);
} }
} }
}; };
morpheus.DatasetUtil.shallowCopy = function(dataset) { morpheus.DatasetUtil.shallowCopy = function (dataset) {
// make a shallow copy of the dataset, metadata is immutable via the UI // make a shallow copy of the dataset, metadata is immutable via the UI
var rowMetadataModel = morpheus.MetadataUtil.shallowCopy(dataset var rowMetadataModel = morpheus.MetadataUtil.shallowCopy(dataset
.getRowMetadata()); .getRowMetadata());
var columnMetadataModel = morpheus.MetadataUtil.shallowCopy(dataset var columnMetadataModel = morpheus.MetadataUtil.shallowCopy(dataset
.getColumnMetadata()); .getColumnMetadata());
dataset.getRowMetadata = function() { dataset.getRowMetadata = function () {
return rowMetadataModel; return rowMetadataModel;
}; };
dataset.getColumnMetadata = function() { dataset.getColumnMetadata = function () {
return columnMetadataModel; return columnMetadataModel;
}; };
return dataset; return dataset;
}; };
morpheus.DatasetUtil.copy = function(dataset) { morpheus.DatasetUtil.copy = function (dataset) {
var newDataset = new morpheus.Dataset({ var newDataset = new morpheus.Dataset({
name : dataset.getName(), name: dataset.getName(),
rows : dataset.getRowCount(), rows: dataset.getRowCount(),
columns : dataset.getColumnCount(), columns: dataset.getColumnCount(),
dataType : 'object' dataType: 'object'
}); });
for (var seriesIndex = 0, nseries = dataset.getSeriesCount(); seriesIndex < nseries; seriesIndex++) { for (var seriesIndex = 0, nseries = dataset.getSeriesCount(); seriesIndex < nseries; seriesIndex++) {
if (seriesIndex > 0) { if (seriesIndex > 0) {
newDataset.addSeries({ newDataset.addSeries({
name : dataset.getName(seriesIndex), name: dataset.getName(seriesIndex),
rows : dataset.getRowCount(), rows: dataset.getRowCount(),
columns : dataset.getColumnCount(), columns: dataset.getColumnCount(),
dataType : 'object' dataType: 'object'
}); });
} }
for (var i = 0, nrows = dataset.getRowCount(), ncols = dataset for (var i = 0, nrows = dataset.getRowCount(), ncols = dataset
.getColumnCount(); i < nrows; i++) { .getColumnCount(); i < nrows; i++) {
for (var j = 0; j < ncols; j++) { for (var j = 0; j < ncols; j++) {
newDataset.setValue(i, j, dataset.getValue(i, j, seriesIndex), newDataset.setValue(i, j, dataset.getValue(i, j, seriesIndex),
seriesIndex); seriesIndex);
} }
} }
} }
var rowMetadataModel = morpheus.MetadataUtil.shallowCopy(dataset var rowMetadataModel = morpheus.MetadataUtil.shallowCopy(dataset
.getRowMetadata()); .getRowMetadata());
var columnMetadataModel = morpheus.MetadataUtil.shallowCopy(dataset var columnMetadataModel = morpheus.MetadataUtil.shallowCopy(dataset
.getColumnMetadata()); .getColumnMetadata());
newDataset.getRowMetadata = function() { newDataset.getRowMetadata = function () {
return rowMetadataModel; return rowMetadataModel;
}; };
newDataset.getColumnMetadata = function() { newDataset.getColumnMetadata = function () {
return columnMetadataModel; return columnMetadataModel;
}; };
return newDataset; return newDataset;
}; };
morpheus.DatasetUtil.toString = function(dataset, value, seriesIndex) { morpheus.DatasetUtil.toString = function (dataset, value, seriesIndex) {
seriesIndex = seriesIndex || 0; seriesIndex = seriesIndex || 0;
var s = []; var s = [];
for (var i = 0, nrows = dataset.getRowCount(), ncols = dataset for (var i = 0, nrows = dataset.getRowCount(), ncols = dataset
.getColumnCount(); i < nrows; i++) { .getColumnCount(); i < nrows; i++) {
for (var j = 0; j < ncols; j++) { for (var j = 0; j < ncols; j++) {
if (j > 0) { if (j > 0) {
s.push(', '); s.push(', ');
...@@ -776,7 +776,7 @@ morpheus.DatasetUtil.toString = function(dataset, value, seriesIndex) { ...@@ -776,7 +776,7 @@ morpheus.DatasetUtil.toString = function(dataset, value, seriesIndex) {
} }
return s.join(''); return s.join('');
}; };
morpheus.DatasetUtil.getNonEmptyRows = function(dataset) { morpheus.DatasetUtil.getNonEmptyRows = function (dataset) {
var rowsToKeep = []; var rowsToKeep = [];
for (var i = 0, nrows = dataset.getRowCount(); i < nrows; i++) { for (var i = 0, nrows = dataset.getRowCount(); i < nrows; i++) {
var keep = false; var keep = false;
......
src/tools/chart_tool2.js
View file @ bc8c2428
...@@ -228,6 +228,7 @@ morpheus.ChartTool2 = function (chartOptions) { ...@@ -228,6 +228,7 @@ morpheus.ChartTool2 = function (chartOptions) {
morpheus.ChartTool2.getPlotlyDefaults = function () { morpheus.ChartTool2.getPlotlyDefaults = function () {
var layout = { var layout = {
hovermode: 'closest',
autosize: false, autosize: false,
paper_bgcolor: 'rgb(255,255,255)', paper_bgcolor: 'rgb(255,255,255)',
plot_bgcolor: 'rgb(229,229,229)', plot_bgcolor: 'rgb(229,229,229)',
......
src/ui/heat_map.js
View file @ bc8c2428
...@@ -621,9 +621,14 @@ morpheus.HeatMap.showTool = function (tool, controller, callback) { ...@@ -621,9 +621,14 @@ morpheus.HeatMap.showTool = function (tool, controller, callback) {
} }
} }
} }
var toolName = tool.toString();
var parenIndex = toolName.indexOf('(');
if (parenIndex !== -1) {
toolName = toolName.substring(0, parenIndex).trim();
}
morpheus.Util.trackEvent({ morpheus.Util.trackEvent({
eventCategory: 'Tool', eventCategory: 'Tool',
eventAction: tool.toString() eventAction: toolName
}); });
}; };
morpheus.HeatMap.getSpaces = function (groupByKeys, length, gapSize) { morpheus.HeatMap.getSpaces = function (groupByKeys, length, gapSize) {
...@@ -863,6 +868,10 @@ morpheus.HeatMap.prototype = { ...@@ -863,6 +868,10 @@ morpheus.HeatMap.prototype = {
project.setRowSortKeys(sortKeys, true); project.setRowSortKeys(sortKeys, true);
this.scrollTop(0); this.scrollTop(0);
} }
morpheus.Util.trackEvent({
eventCategory: 'Tool',
eventAction: isColumns ? 'sortRowsBasedOnSelection' : 'sortColumnsBasedOnSelection'
});
}, },
getToolbarElement: function () { getToolbarElement: function () {
......
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