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morpheus.js
Commit 37187ac9 authored by jgould's avatar jgould
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tcga cluster ids

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js/morpheus-latest.min.js
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src/io/tcga_util.js
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morpheus.TcgaUtil = function() { morpheus.TcgaUtil = function () {
}; };
morpheus.TcgaUtil.DISEASE_STUDIES = { morpheus.TcgaUtil.DISEASE_STUDIES = {
'LAML' : 'Acute Myeloid Leukemia', 'LAML': 'Acute Myeloid Leukemia',
'ACC' : 'Adrenocortical carcinoma', 'ACC': 'Adrenocortical carcinoma',
'BLCA' : 'Bladder Urothelial Carcinoma', 'BLCA': 'Bladder Urothelial Carcinoma',
'LGG' : 'Brain Lower Grade Glioma', 'LGG': 'Brain Lower Grade Glioma',
'BRCA' : 'Breast invasive carcinoma', 'BRCA': 'Breast invasive carcinoma',
'CESC' : 'Cervical squamous cell carcinoma and endocervical adenocarcinoma', 'CESC': 'Cervical squamous cell carcinoma and endocervical adenocarcinoma',
'CHOL' : 'Cholangiocarcinoma', 'CHOL': 'Cholangiocarcinoma',
'LCML' : 'Chronic Myelogenous Leukemia', 'LCML': 'Chronic Myelogenous Leukemia',
'COAD' : 'Colon adenocarcinoma', 'COAD': 'Colon adenocarcinoma',
'CNTL' : 'Controls', 'CNTL': 'Controls',
'ESCA' : 'Esophageal carcinoma ', 'ESCA': 'Esophageal carcinoma ',
'FPPP' : 'FFPE Pilot Phase II', 'FPPP': 'FFPE Pilot Phase II',
'GBM' : 'Glioblastoma multiforme', 'GBM': 'Glioblastoma multiforme',
'HNSC' : 'Head and Neck squamous cell carcinoma', 'HNSC': 'Head and Neck squamous cell carcinoma',
'KICH' : 'Kidney Chromophobe', 'KICH': 'Kidney Chromophobe',
'KIRC' : 'Kidney renal clear cell carcinoma', 'KIRC': 'Kidney renal clear cell carcinoma',
'KIRP' : 'Kidney renal papillary cell carcinoma', 'KIRP': 'Kidney renal papillary cell carcinoma',
'LIHC' : 'Liver hepatocellular carcinoma', 'LIHC': 'Liver hepatocellular carcinoma',
'LUAD' : 'Lung adenocarcinoma', 'LUAD': 'Lung adenocarcinoma',
'LUSC' : 'Lung squamous cell carcinoma', 'LUSC': 'Lung squamous cell carcinoma',
'DLBC' : 'Lymphoid Neoplasm Diffuse Large B-cell Lymphoma', 'DLBC': 'Lymphoid Neoplasm Diffuse Large B-cell Lymphoma',
'MESO' : 'Mesothelioma', 'MESO': 'Mesothelioma',
'MISC' : 'Miscellaneous', 'MISC': 'Miscellaneous',
'OV' : 'Ovarian serous cystadenocarcinoma', 'OV': 'Ovarian serous cystadenocarcinoma',
'PAAD' : 'Pancreatic adenocarcinoma', 'PAAD': 'Pancreatic adenocarcinoma',
'PCPG' : 'Pheochromocytoma and Paraganglioma', 'PCPG': 'Pheochromocytoma and Paraganglioma',
'PRAD' : 'Prostate adenocarcinoma', 'PRAD': 'Prostate adenocarcinoma',
'READ' : 'Rectum adenocarcinoma', 'READ': 'Rectum adenocarcinoma',
'SARC' : 'Sarcoma', 'SARC': 'Sarcoma',
'SKCM' : 'Skin Cutaneous Melanoma', 'SKCM': 'Skin Cutaneous Melanoma',
'STAD' : 'Stomach adenocarcinoma', 'STAD': 'Stomach adenocarcinoma',
'TGCT' : 'Testicular Germ Cell Tumors', 'TGCT': 'Testicular Germ Cell Tumors',
'THYM' : 'Thymoma', 'THYM': 'Thymoma',
'THCA' : 'Thyroid carcinoma', 'THCA': 'Thyroid carcinoma',
'UCS' : 'Uterine Carcinosarcoma', 'UCS': 'Uterine Carcinosarcoma',
'UCEC' : 'Uterine Corpus Endometrial Carcinoma', 'UCEC': 'Uterine Corpus Endometrial Carcinoma',
'UVM' : 'Uveal Melanoma', 'UVM': 'Uveal Melanoma',
'KIPAN' : 'Pan-Kidney Cohort', 'KIPAN': 'Pan-Kidney Cohort',
'COADREAD' : 'Colonrectal adenocarcinoma', 'COADREAD': 'Colonrectal adenocarcinoma',
'GBMLGG' : 'Glioma', 'GBMLGG': 'Glioma',
'STES' : 'Stomach and Esophageal Carcinoma' 'STES': 'Stomach and Esophageal Carcinoma'
}; };
morpheus.TcgaUtil.SAMPLE_TYPES = { morpheus.TcgaUtil.SAMPLE_TYPES = {
'01' : 'Primary solid Tumor', '01': 'Primary solid Tumor',
'02' : 'Recurrent Solid Tumor', '02': 'Recurrent Solid Tumor',
'03' : 'Primary Blood Derived Cancer - Peripheral Blood', '03': 'Primary Blood Derived Cancer - Peripheral Blood',
'04' : 'Recurrent Blood Derived Cancer - Bone Marrow', '04': 'Recurrent Blood Derived Cancer - Bone Marrow',
'05' : 'Additional - New Primary', '05': 'Additional - New Primary',
'06' : 'Metastatic', '06': 'Metastatic',
'07' : 'Additional Metastatic', '07': 'Additional Metastatic',
'08' : 'Human Tumor Original Cells', '08': 'Human Tumor Original Cells',
'09' : 'Primary Blood Derived Cancer - Bone Marrow', '09': 'Primary Blood Derived Cancer - Bone Marrow',
'10' : 'Blood Derived Normal', '10': 'Blood Derived Normal',
'11' : 'Solid Tissue Normal', '11': 'Solid Tissue Normal',
'12' : 'Buccal Cell Normal', '12': 'Buccal Cell Normal',
'13' : 'EBV Immortalized Normal', '13': 'EBV Immortalized Normal',
'14' : 'Bone Marrow Normal', '14': 'Bone Marrow Normal',
'20' : 'Control Analyte', '20': 'Control Analyte',
'40' : 'Recurrent Blood Derived Cancer - Peripheral Blood', '40': 'Recurrent Blood Derived Cancer - Peripheral Blood',
'50' : 'Cell Lines', '50': 'Cell Lines',
'60' : 'Primary Xenograft Tissue', '60': 'Primary Xenograft Tissue',
'61' : 'Cell Line Derived Xenograft Tissue' '61': 'Cell Line Derived Xenograft Tissue'
}; };
morpheus.TcgaUtil.barcode = function(s) { morpheus.TcgaUtil.barcode = function (s) {
var tokens = s.split('-'); var tokens = s.split('-');
var id = tokens[2]; var id = tokens[2];
var sampleType; var sampleType;
// e.g. TCGA-AC-A23H-01A-11D-A159-09
if (tokens.length > 3) { if (tokens.length > 3) {
sampleType = tokens[3]; sampleType = tokens[3];
if (sampleType.length > 2) { if (sampleType.length > 2) {
sampleType = sampleType.substring(0, 2); sampleType = sampleType.substring(0, 2);
} }
sampleType = morpheus.TcgaUtil.SAMPLE_TYPES[sampleType]; sampleType = morpheus.TcgaUtil.SAMPLE_TYPES[sampleType];
} else { } else {
sampleType = morpheus.TcgaUtil.SAMPLE_TYPES['01']; sampleType = morpheus.TcgaUtil.SAMPLE_TYPES['01'];
} }
return { return {
id : id.toLowerCase(), id: id.toLowerCase(),
sampleType : sampleType sampleType: sampleType
}; };
}; };
morpheus.TcgaUtil.getDataset = function(options) { morpheus.TcgaUtil.setIdAndSampleType = function (dataset) {
var idVector = dataset.getColumnMetadata().get(0);
var participantId = dataset.getColumnMetadata().add('participant_id');
var sampleType = dataset.getColumnMetadata().add('sample_type');
for (var i = 0, size = idVector.size(); i < size; i++) {
var barcode = morpheus.TcgaUtil.barcode(idVector.getValue(i));
idVector.setValue(i, barcode.id + '-' + barcode.sampleType);
sampleType.setValue(i, barcode.sampleType);
participantId.setValue(i, barcode.id);
}
};
morpheus.TcgaUtil.getDataset = function (options) {
var promises = []; var promises = [];
var datasets = []; var datasets = [];
var returnDeferred = $.Deferred(); var returnDeferred = $.Deferred();
function splitId(dataset) {
var idVector = dataset.getRowMetadata().get(0);
for (var i = 0, size = idVector.size(); i < size; i++) {
var id = idVector.getValue(i);
var index = id.indexOf('|');
idVector.setValue(i, id.substring(0, index));
}
}
function setIdAndSampleType(dataset) {
var idVector = dataset.getColumnMetadata().get(0);
var participantId = dataset.getColumnMetadata().add('participant_id');
var sampleType = dataset.getColumnMetadata().add('sample_type');
for (var i = 0, size = idVector.size(); i < size; i++) {
var barcode = morpheus.TcgaUtil.barcode(idVector.getValue(i));
if (barcode.sampleType !== undefined) {
idVector.setValue(i, barcode.id + '-' + barcode.sampleType);
sampleType.setValue(i, barcode.sampleType);
} else {
idVector.setValue(i, barcode.id);
}
participantId.setValue(i, barcode.id);
}
}
if (options.mrna) { if (options.mrna) {
// id + type // id + type
var mrna = $.Deferred(); var mrna = $.Deferred();
promises.push(mrna); promises.push(mrna);
new morpheus.TxtReader().read(options.mrna, function(err, dataset) { new morpheus.TxtReader().read(options.mrna, function (err, dataset) {
if (err) { if (err) {
console.log('Error reading file:' + err); console.log('Error reading file:' + err);
} else { } else {
datasets.push(dataset); datasets.push(dataset);
// splitId(dataset); morpheus.TcgaUtil.setIdAndSampleType(dataset);
setIdAndSampleType(dataset);
} }
mrna.resolve(); mrna.resolve();
}); });
...@@ -134,18 +122,18 @@ morpheus.TcgaUtil.getDataset = function(options) { ...@@ -134,18 +122,18 @@ morpheus.TcgaUtil.getDataset = function(options) {
if (options.mutation) { if (options.mutation) {
var mutation = $.Deferred(); var mutation = $.Deferred();
promises.push(mutation); promises.push(mutation);
new morpheus.MafFileReader().read(options.mutation, function(err, new morpheus.MafFileReader().read(options.mutation, function (err,
dataset) { dataset) {
if (err) { if (err) {
console.log('Error reading file:' + err); console.log('Error reading file:' + err);
} else { } else {
datasets.push(dataset); datasets.push(dataset);
setIdAndSampleType(dataset); morpheus.TcgaUtil.setIdAndSampleType(dataset);
} }
mutation.resolve(); mutation.resolve();
}); });
var sigGenesAnnotation = morpheus.Util.readLines(options.sigGenes); var sigGenesAnnotation = morpheus.Util.readLines(options.sigGenes);
sigGenesAnnotation.done(function(lines) { sigGenesAnnotation.done(function (lines) {
sigGenesLines = lines; sigGenesLines = lines;
}); });
promises.push(sigGenesAnnotation); promises.push(sigGenesAnnotation);
...@@ -154,15 +142,15 @@ morpheus.TcgaUtil.getDataset = function(options) { ...@@ -154,15 +142,15 @@ morpheus.TcgaUtil.getDataset = function(options) {
var gistic = $.Deferred(); var gistic = $.Deferred();
promises.push(gistic); promises.push(gistic);
new morpheus.GisticReader().read(options.gistic, new morpheus.GisticReader().read(options.gistic,
function(err, dataset) { function (err, dataset) {
if (err) { if (err) {
console.log('Error reading file:' + err); console.log('Error reading file:' + err);
} else { } else {
datasets.push(dataset); datasets.push(dataset);
setIdAndSampleType(dataset); morpheus.TcgaUtil.setIdAndSampleType(dataset);
} }
gistic.resolve(); gistic.resolve();
}); });
} }
if (options.gisticGene) { if (options.gisticGene) {
...@@ -170,14 +158,14 @@ morpheus.TcgaUtil.getDataset = function(options) { ...@@ -170,14 +158,14 @@ morpheus.TcgaUtil.getDataset = function(options) {
promises.push(gisticGene); promises.push(gisticGene);
new morpheus.TxtReader({ new morpheus.TxtReader({
dataColumnStart : 3 dataColumnStart: 3
}).read(options.gisticGene, function(err, dataset) { }).read(options.gisticGene, function (err, dataset) {
if (err) { if (err) {
console.log('Error reading file:' + err); console.log('Error reading file:' + err);
} else { } else {
datasets.push(dataset); datasets.push(dataset);
setIdAndSampleType(dataset); morpheus.TcgaUtil.setIdAndSampleType(dataset);
} }
gisticGene.resolve(); gisticGene.resolve();
}); });
...@@ -186,12 +174,12 @@ morpheus.TcgaUtil.getDataset = function(options) { ...@@ -186,12 +174,12 @@ morpheus.TcgaUtil.getDataset = function(options) {
if (options.seg) { if (options.seg) {
var seg = $.Deferred(); var seg = $.Deferred();
promises.push(seg); promises.push(seg);
new morpheus.SegTabReader().read(options.seg, function(err, dataset) { new morpheus.SegTabReader().read(options.seg, function (err, dataset) {
if (err) { if (err) {
console.log('Error reading file:' + err); console.log('Error reading file:' + err);
} else { } else {
datasets.push(dataset); datasets.push(dataset);
setIdAndSampleType(dataset); morpheus.TcgaUtil.setIdAndSampleType(dataset);
} }
seg.resolve(); seg.resolve();
}); });
...@@ -201,14 +189,13 @@ morpheus.TcgaUtil.getDataset = function(options) { ...@@ -201,14 +189,13 @@ morpheus.TcgaUtil.getDataset = function(options) {
var rppa = $.Deferred(); var rppa = $.Deferred();
promises.push(rppa); promises.push(rppa);
new morpheus.TxtReader().read(options.rppa, function(err, dataset) { new morpheus.TxtReader().read(options.rppa, function (err, dataset) {
if (err) { if (err) {
console.log('Error reading file:' + err); console.log('Error reading file:' + err);
} else { } else {
datasets.push(dataset); datasets.push(dataset);
setIdAndSampleType(dataset); morpheus.TcgaUtil.setIdAndSampleType(dataset);
} }
// splitId(dataset);
rppa.resolve(); rppa.resolve();
}); });
...@@ -218,13 +205,13 @@ morpheus.TcgaUtil.getDataset = function(options) { ...@@ -218,13 +205,13 @@ morpheus.TcgaUtil.getDataset = function(options) {
// id + type // id + type
var methylation = $.Deferred(); var methylation = $.Deferred();
promises.push(methylation); promises.push(methylation);
new morpheus.TxtReader({}).read(options.methylation, function(err, new morpheus.TxtReader({}).read(options.methylation, function (err,
dataset) { dataset) {
if (err) { if (err) {
console.log('Error reading file:' + err); console.log('Error reading file:' + err);
} else { } else {
datasets.push(dataset); datasets.push(dataset);
setIdAndSampleType(dataset); morpheus.TcgaUtil.setIdAndSampleType(dataset);
} }
methylation.resolve(); methylation.resolve();
}); });
...@@ -233,7 +220,7 @@ morpheus.TcgaUtil.getDataset = function(options) { ...@@ -233,7 +220,7 @@ morpheus.TcgaUtil.getDataset = function(options) {
var mrnaClustPromise = morpheus.Util.readLines(options.mrnaClust); var mrnaClustPromise = morpheus.Util.readLines(options.mrnaClust);
promises.push(mrnaClustPromise); promises.push(mrnaClustPromise);
var sampleIdToClusterId; var sampleIdToClusterId;
mrnaClustPromise.done(function(lines) { mrnaClustPromise.done(function (lines) {
// SampleName cluster silhouetteValue // SampleName cluster silhouetteValue
// SampleName cluster silhouetteValue // SampleName cluster silhouetteValue
// TCGA-OR-A5J1-01 1 0.00648776228925048 // TCGA-OR-A5J1-01 1 0.00648776228925048
...@@ -246,107 +233,107 @@ morpheus.TcgaUtil.getDataset = function(options) { ...@@ -246,107 +233,107 @@ morpheus.TcgaUtil.getDataset = function(options) {
for (; lineNumber < lines.length; lineNumber++) { for (; lineNumber < lines.length; lineNumber++) {
var tokens = lines[lineNumber].split(tab); var tokens = lines[lineNumber].split(tab);
var barcode = morpheus.TcgaUtil.barcode(tokens[0]); var barcode = morpheus.TcgaUtil.barcode(tokens[0]);
sampleIdToClusterId.set(barcode.id, tokens[1]); sampleIdToClusterId.set(barcode.id + '-' + barcode.sampleType, tokens[1]);
} }
}); });
var annotationCallbacks = []; var annotationCallbacks = [];
var annotationDef = null; var annotationDef = null;
if (options.columnAnnotations) { if (options.columnAnnotations) {
annotationDef = morpheus.DatasetUtil.annotate({ annotationDef = morpheus.DatasetUtil.annotate({
annotations : options.columnAnnotations, annotations: options.columnAnnotations,
isColumns : true isColumns: true
}); });
promises.push(annotationDef); promises.push(annotationDef);
annotationDef.done(function(array) { annotationDef.done(function (array) {
annotationCallbacks = array; annotationCallbacks = array;
}); });
} }
$.when.apply($, promises).then( $.when.apply($, promises).then(
function() { function () {
var datasetToReturn = null; var datasetToReturn = null;
if (datasets.length === 1) { if (datasets.length === 1) {
var sourceName = datasets[0].getName(); var sourceName = datasets[0].getName();
var sourceVector = datasets[0].getRowMetadata().add( var sourceVector = datasets[0].getRowMetadata().add(
'Source'); 'Source');
for (var i = 0; i < sourceVector.size(); i++) { for (var i = 0; i < sourceVector.size(); i++) {
sourceVector.setValue(i, sourceName); sourceVector.setValue(i, sourceName);
} }
datasetToReturn = datasets[0]; datasetToReturn = datasets[0];
} else { } else {
var maxIndex = 0; var maxIndex = 0;
var maxColumns = datasets[0].getColumnCount(); var maxColumns = datasets[0].getColumnCount();
// use dataset with most columns as the reference or // use dataset with most columns as the reference or
// mutation data // mutation data
for (var i = 1; i < datasets.length; i++) { for (var i = 1; i < datasets.length; i++) {
if (datasets[i].getColumnCount() > maxColumns) { if (datasets[i].getColumnCount() > maxColumns) {
maxColumns = datasets[i].getColumnCount(); maxColumns = datasets[i].getColumnCount();
maxIndex = i; maxIndex = i;
}
if (datasets[i].getName() === 'mutations_merged.maf') {
maxColumns = Number.MAX_VALUE;
maxIndex = i;
}
} }
var datasetIndices = []; if (datasets[i].getName() === 'mutations_merged.maf') {
datasetIndices.push(maxIndex); maxColumns = Number.MAX_VALUE;
for (var i = 0; i < datasets.length; i++) { maxIndex = i;
if (i !== maxIndex) {
datasetIndices.push(i);
}
} }
}
var joined = new morpheus.JoinedDataset( var datasetIndices = [];
datasets[datasetIndices[0]], datasetIndices.push(maxIndex);
datasets[datasetIndices[1]], 'id', 'id'); for (var i = 0; i < datasets.length; i++) {
for (var i = 2; i < datasetIndices.length; i++) { if (i !== maxIndex) {
joined = new morpheus.JoinedDataset(joined, datasetIndices.push(i);
datasets[datasetIndices[i]], 'id', 'id');
} }
datasetToReturn = joined;
} }
var clusterIdVector = datasetToReturn.getColumnMetadata().add( var joined = new morpheus.JoinedDataset(
'mRNAseq_cluster'); datasets[datasetIndices[0]],
var idVector = datasetToReturn.getColumnMetadata().getByName( datasets[datasetIndices[1]], 'id', 'id');
'participant_id'); for (var i = 2; i < datasetIndices.length; i++) {
for (var j = 0, size = idVector.size(); j < size; j++) { joined = new morpheus.JoinedDataset(joined,
clusterIdVector.setValue(j, sampleIdToClusterId datasets[datasetIndices[i]], 'id', 'id');
.get(idVector.getValue(j)));
} }
// view in space of mutation sample ids only datasetToReturn = joined;
if (options.mutation) { }
var sourceToIndices = morpheus.VectorUtil
.createValueToIndicesMap(datasetToReturn
.getRowMetadata().getByName('Source'));
var mutationDataset = new morpheus.SlicedDatasetView(
datasetToReturn, sourceToIndices
.get('mutations_merged.maf'));
new morpheus.OpenFileTool()
.annotate(sigGenesLines, mutationDataset, false,
null, 'id', 'gene', [ 'q' ]);
var qVector = mutationDataset.getRowMetadata().getByName(
'q');
var qValueVector = mutationDataset.getRowMetadata()
.getByName('q_value');
if (qValueVector == null) {
qValueVector = mutationDataset.getRowMetadata().add(
'q_value');
}
for (var i = 0, size = qValueVector.size(); i < size; i++) {
qValueVector.setValue(i, qVector.getValue(i));
}
mutationDataset.getRowMetadata().remove( var clusterIdVector = datasetToReturn.getColumnMetadata().add(
morpheus.MetadataUtil.indexOf(mutationDataset 'mRNAseq_cluster');
.getRowMetadata(), 'q')); var idVector = datasetToReturn.getColumnMetadata().getByName(
'id');
for (var j = 0, size = idVector.size(); j < size; j++) {
clusterIdVector.setValue(j, sampleIdToClusterId
.get(idVector.getValue(j)));
}
// view in space of mutation sample ids only
if (options.mutation) {
var sourceToIndices = morpheus.VectorUtil
.createValueToIndicesMap(datasetToReturn
.getRowMetadata().getByName('Source'));
var mutationDataset = new morpheus.SlicedDatasetView(
datasetToReturn, sourceToIndices
.get('mutations_merged.maf'));
new morpheus.OpenFileTool()
.annotate(sigGenesLines, mutationDataset, false,
null, 'id', 'gene', ['q']);
var qVector = mutationDataset.getRowMetadata().getByName(
'q');
var qValueVector = mutationDataset.getRowMetadata()
.getByName('q_value');
if (qValueVector == null) {
qValueVector = mutationDataset.getRowMetadata().add(
'q_value');
} }
if (annotationDef) { for (var i = 0, size = qValueVector.size(); i < size; i++) {
annotationCallbacks.forEach(function(f) { qValueVector.setValue(i, qVector.getValue(i));
f(datasetToReturn);
});
} }
returnDeferred.resolve(datasetToReturn);
}); mutationDataset.getRowMetadata().remove(
morpheus.MetadataUtil.indexOf(mutationDataset
.getRowMetadata(), 'q'));
}
if (annotationDef) {
annotationCallbacks.forEach(function (f) {
f(datasetToReturn);
});
}
returnDeferred.resolve(datasetToReturn);
});
return returnDeferred; return returnDeferred;
}; };
\ No newline at end of file
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