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