public static void saveAsCGHInput(Dataset dataset, String outFileName)
throws IOException, InvalidIndexException {
dataset.load();
List<String> sampleNames = dataset.getSampleNames();
String header = "#ID\tChr\tStart\tEnd\t" + ListUtils.toString(sampleNames, "\t") + "\n";
StringBuilder line = new StringBuilder();
;
List<String> lines = new ArrayList<String>();
DataFrame featureDataFrame = dataset.getFeatureData().getDataFrame();
DataFrame dataFrame = new DataFrame();
dataFrame.setRowNames(featureDataFrame.getColumn("ProbeName"));
dataFrame.addColumn(featureDataFrame.getColumn("loc.chromosome"));
dataFrame.addColumn(featureDataFrame.getColumn("loc.start"));
dataFrame.addColumn(featureDataFrame.getColumn("loc.end"));
for (int i = 0; i < sampleNames.size(); i++) {
dataFrame.addColumn(ArrayUtils.toStringList(dataset.getDoubleMatrix().getColumn(i)));
}
System.out.println("---> writting " + outFileName);
IOUtils.write(new File(outFileName), header + dataFrame.toString(true, false));
// System.out.println("feature column names = " +
// ListUtils.toString(dataset.getFeatureData().getDataFrame().getColumn("ProbeUID")));
// line.append("#ID\tChr\tStart\tEnd\t").append(ListUtils.toString(dataset.getSampleNames(),
// "\t"));
// lines.add(line.toString());
//
// for(int i=0 ; i<dataset.getRowDimension() ; i++) {
//
// }
//
//
// IOUtils.write(new File(outFileName), lines);
}
@Override
protected void execute() {
try {
// update status
jobStatus.addStatusMessage("10", "Preparing data");
// infrared connector
// DBConnector dbConnector = new DBConnector(species, new File(babelomicsHomePath +
// "/conf/infrared.properties"));
// prepare params
prepare();
// run fatigo's
if (filterList.size() == 0 && !isYourAnnotations) {
throw new ParseException("No biological database selected (eg. --go-bp)");
} else {
// save id lists
IOUtils.write(outdir + "/ranked_list.txt", rankedList.toString());
result.addOutputItem(
new Item(
"ranked_list",
"ranked_list.txt",
"Ranked list",
Item.TYPE.FILE,
Arrays.asList("RANKED_LIST", "CLEAN"),
new HashMap<String, String>(),
"Input data"));
// order ranked list and save genes and rank separately
// FatiScan fatiscan = new
// FatiScan(rankedList,null,dbConnector,FatiScan.DEFAULT_NUMBER_OF_PARTITIONS,testMode,outputFormat,order,duplicatesMode);
FatiScan fatiscan =
new FatiScan(
rankedList,
null,
null,
FatiScan.DEFAULT_NUMBER_OF_PARTITIONS,
testMode,
outputFormat,
order,
duplicatesMode);
fatiscan.prepareLists();
IOUtils.write(outdir + "/id_list.txt", fatiscan.getIdList());
result.addOutputItem(
new Item(
"id_list",
"id_list.txt",
"Id list (sorted)",
Item.TYPE.FILE,
Arrays.asList("IDLIST", "SORTED"),
new HashMap<String, String>(),
"Input data"));
IOUtils.write(outdir + "/statistic.txt", ListUtils.toStringArray(fatiscan.getStatistic()));
result.addOutputItem(
new Item(
"statistic",
"statistic.txt",
"Statistic (sorted)",
Item.TYPE.FILE,
Arrays.asList("STATISTIC", "SORTED"),
new HashMap<String, String>(),
"Input data"));
// significant count
significantCount = new ArrayList<StringBuilder>();
for (int i = 0; i < DEFAULT_PVALUES.length; i++) {
significantCount.add(new StringBuilder("#DB\tNº of significant terms\n"));
}
// annotation report
annotationReport = new StringBuilder();
annotationReport.append("#DB").append("\t").append("Number of annotations").append("\n");
// do fatiscans
double progress = 20;
double inc = 60.0 / filterList.size();
for (FunctionalFilter filter : filterList) {
doTest(rankedList, filter, method);
jobStatus.addStatusMessage("" + progress, "Executing test");
progress += inc;
}
// update status
jobStatus.addStatusMessage("90", "Executing test");
if (isYourAnnotations) {
doYourAnnotationsTest(rankedList, yourAnnotations, method);
}
// update status
jobStatus.addStatusMessage("95", "Saving results");
saveAnnotationsReport();
// save significant count table
for (int i = 0; i < DEFAULT_PVALUES.length; i++) {
IOUtils.write(
outdir + "/significant_count_" + pvalueFormatter.format(DEFAULT_PVALUES[i]) + ".txt",
significantCount.get(i).toString());
}
result
.getOutputItems()
.add(
3,
new Item(
"significant",
"significant_count_${pvalue}.txt",
"Number of significant terms per DB",
Item.TYPE.FILE,
Arrays.asList("TABLE,SUMMARY_TABLE,SIGNIFICANT_COUNT_TABLE"),
new HashMap<String, String>(),
"Significant Results"));
result.addMetaItem(new Item("flags", "SHOW_PVALUES", "", TYPE.MESSAGE));
}
} catch (Exception e) {
e.printStackTrace();
}
}
private void saveGeneSetAnalysisResults(GeneSetAnalysis gsea, FunctionalDbDescriptor filterInfo)
throws IOException {
String fileName = filterInfo.getName() + ".txt";
String annotFileName = filterInfo.getName() + ".annot";
// save statistic results
IOUtils.write(outdir + "/" + fileName, ListUtils.toString(gsea.resultsToStringList(), "\n"));
result.addOutputItem(
new Item(
filterInfo.getName(),
fileName,
filterInfo.getTitle(),
Item.TYPE.FILE,
Arrays.asList(filterInfo.getPrefix().toUpperCase() + "_TERM"),
new HashMap<String, String>(),
"All results"));
// save significant results
int numberOfSignificantTerms;
List<GeneSetAnalysisTestResult> significant;
String formattedPValue;
for (int i = 0; i < DEFAULT_PVALUES.length; i++) {
formattedPValue = pvalueFormatter.format(DEFAULT_PVALUES[i]);
significant = gsea.getSignificant(DEFAULT_PVALUES[i]);
if (significant != null && significant.size() > 0) {
IOUtils.write(
outdir + "/significant_" + filterInfo.getName() + "_" + formattedPValue + ".txt",
gsea.significantResultsToStringList(significant, DEFAULT_PVALUES[i]));
numberOfSignificantTerms = significant.size();
} else {
numberOfSignificantTerms = 0;
}
significantCount
.get(i)
.append(filterInfo.getTitle())
.append("\t")
.append(numberOfSignificantTerms)
.append("\n");
if (numberOfSignificantTerms > 0) {
// go graph
if (filterInfo.getPrefix().equalsIgnoreCase("go")) {
try {
String limitMessage = "";
boolean outOfbounds = createGseaGoGraph(significant, DEFAULT_PVALUES[i], filterInfo);
if (outOfbounds) limitMessage = " just most 100 significant terms";
Item item =
new Item(
"go_graph_significant_" + filterInfo.getName() + "_" + formattedPValue,
"go_graph_" + filterInfo.getName() + "_" + formattedPValue + "_graphimage.png",
filterInfo.getTitle()
+ " DAG (significant terms, pvalue<"
+ formattedPValue
+ ") "
+ limitMessage,
Item.TYPE.IMAGE,
Arrays.asList("SIGNIFICANT,THUMBNAIL,GO_GRAPH_VIZ_JNLP"),
new HashMap<String, String>(),
"Significant Results." + filterInfo.getTitle());
item.setContext("pvalue==" + formattedPValue);
result.getOutputItems().add(4, item);
} catch (GoGraphException gge) {
Item item =
new Item(
"go_graph_significant_" + filterInfo.getName() + "_" + formattedPValue,
"Graph not found",
filterInfo.getTitle()
+ " DAG (significant terms, pvalue<"
+ formattedPValue
+ ")",
Item.TYPE.MESSAGE,
Arrays.asList("ERROR"),
new HashMap<String, String>(),
"Significant Results." + filterInfo.getTitle());
item.setContext("pvalue==" + formattedPValue);
result.getOutputItems().add(4, item);
}
}
// table
Item item =
new Item(
"significant_" + filterInfo.getName(),
"significant_" + filterInfo.getName() + "_" + formattedPValue + ".txt",
filterInfo.getTitle() + " significant terms (pvalue<" + formattedPValue + ")",
Item.TYPE.FILE,
Arrays.asList(
"SIGNIFICANT",
"TABLE",
gsea.getMethod().toUpperCase() + "_TABLE",
filterInfo.getPrefix().toUpperCase() + "_TERM"),
new HashMap<String, String>(),
"Significant Results." + filterInfo.getTitle());
item.setContext("pvalue==" + formattedPValue);
result.getOutputItems().add(4, item);
} else {
Item item =
new Item(
"significant_" + filterInfo.getName(),
"No significant terms for current pvalue " + formattedPValue,
filterInfo.getTitle() + " significant terms (pvalue<" + formattedPValue + ")",
Item.TYPE.MESSAGE,
Arrays.asList("WARNING"),
new HashMap<String, String>(),
"Significant Results." + filterInfo.getTitle());
item.setContext("pvalue==" + formattedPValue);
result.getOutputItems().add(4, item);
}
}
// annotations report
addAnnotationReport(gsea, filterInfo.getTitle());
// save annotations
if (gsea.getAnnotations() != null && gsea.getAnnotations().size() > 0) {
IOUtils.write(outdir + "/" + annotFileName, gsea.getAnnotations().toString());
result.addOutputItem(
new Item(
"annot_" + filterInfo.getName(),
annotFileName,
"Annotations for " + filterInfo.getTitle(),
Item.TYPE.FILE,
Arrays.asList("ANNOTATION"),
new HashMap<String, String>(),
"Annotation files"));
} else {
result.addOutputItem(
new Item(
"annot_" + filterInfo.getName(),
"no annotations found for input ids",
"Annotations for " + filterInfo.getTitle(),
Item.TYPE.MESSAGE,
Arrays.asList("WARNING"),
new HashMap<String, String>(),
"Annotation files"));
}
}
/**
* @throws InvalidColumnIndexException
* @throws IOException
*/
public void executeLimma() {
Limma limma = null;
if (classValues.size() > 2) {
limma = new Limma(babelomicsHomePath + "/bin/diffexp/limma_multiclasses.r");
} else if (classValues.size() == 2) {
limma = new Limma(babelomicsHomePath + "/bin/diffexp/limma_twoclasses.r");
} else if (classValues.size() == 1) {
limma = new Limma(babelomicsHomePath + "/bin/diffexp/limma_oneclass.r");
} else {
abort(
"testmismatched_executelimma_classcomparison",
"test " + test + " not supported for " + classValues.size() + "-class test",
"test " + test + " not supported for " + classValues.size() + "-class test",
"test " + test + " not supported for " + classValues.size() + "-class test");
}
// System.out.println("dataset = " + dataset.toString());
System.out.println("class name = " + className);
limma.setInputFilename(dataset.getDatasetFile().getAbsolutePath());
limma.setClasses(dataset.getVariables().getByName(className).getValues());
limma.setContrast(classValues);
try {
Dataset subDataset = dataset.getSubDataset(className, classValues);
// apply test and multiple test correction according
//
TestResultList<LimmaTestResult> res = limma.compute();
DiffExpressionUtils.multipleTestCorrection(res, correction);
// create output file
//
int[] columnOrder =
ListUtils.order(subDataset.getVariables().getByName(className).getValues());
int[] rowOrder = ListUtils.order(ArrayUtils.toList(res.getStatistics()), true);
DataFrame dataFrame = new DataFrame(subDataset.getFeatureNames().size(), 0);
dataFrame.addColumn(
"statistic",
ListUtils.toStringList(
ListUtils.ordered(ArrayUtils.toList(res.getStatistics()), rowOrder)));
dataFrame.addColumn(
"p-value",
ListUtils.toStringList(ListUtils.ordered(ArrayUtils.toList(res.getPValues()), rowOrder)));
dataFrame.addColumn(
"adj. p-value",
ListUtils.toStringList(
ListUtils.ordered(ArrayUtils.toList(res.getAdjPValues()), rowOrder)));
dataFrame.setRowNames(ListUtils.ordered(subDataset.getFeatureNames(), rowOrder));
FeatureData featureData = new FeatureData(dataFrame);
File file = new File(outdir + "/" + test + ".txt");
featureData.save(file);
if (file.exists()) {
result.addOutputItem(
new Item(
test + "file",
file.getName(),
"Limma output file",
TYPE.FILE,
new ArrayList<String>(2),
new HashMap<String, String>(2),
"Limma output files"));
}
// getting significative genes
//
DiffExpressionUtils.addSignificativeResults(
subDataset,
test,
"statistic",
res.getStatistics(),
"adj. p-value",
res.getAdjPValues(),
"p-value",
res.getPValues(),
null,
null,
null,
null,
className,
columnOrder,
pValue,
maxDisplay,
this);
DiffExpressionUtils.createFatiScanRedirection(dataFrame, test, "statistic", result, outdir);
} catch (Exception e) {
e.printStackTrace();
abort(
"exception_executelimma_classcomparison",
"error running limma",
"error running limma: " + e.toString(),
"error running limma: " + e.toString());
}
}
public void executeAnova() {
DoubleMatrix matrix = null;
List<String> vars = new ArrayList<String>();
List<Integer> indices = new ArrayList<Integer>();
List<String> values = dataset.getVariables().getByName(className).getValues();
if (values.size() == classValues.size()) {
matrix = dataset.getDoubleMatrix();
vars = values;
} else {
for (int i = 0; i < values.size(); i++) {
if (classValues.contains(values.get(i))) {
indices.add(i);
vars.add(values.get(i));
}
}
matrix = dataset.getSubMatrixByColumns(ListUtils.toIntArray(indices));
}
try {
Dataset subDataset = dataset.getSubDataset(className, classValues);
// apply test and multiple test correction according
//
AnovaTest anova = new AnovaTest(matrix, vars);
TestResultList<AnovaTestResult> res = anova.compute();
DiffExpressionUtils.multipleTestCorrection(res, correction);
// create output file
//
int[] columnOrder =
ListUtils.order(subDataset.getVariables().getByName(className).getValues());
int[] rowOrder = ListUtils.order(ArrayUtils.toList(res.getStatistics()), true);
DataFrame dataFrame = new DataFrame(subDataset.getFeatureNames().size(), 0);
dataFrame.addColumn(
"statistic",
ListUtils.toStringList(
ListUtils.ordered(ArrayUtils.toList(res.getStatistics()), rowOrder)));
dataFrame.addColumn(
"p-value",
ListUtils.toStringList(ListUtils.ordered(ArrayUtils.toList(res.getPValues()), rowOrder)));
dataFrame.addColumn(
"adj. p-value",
ListUtils.toStringList(
ListUtils.ordered(ArrayUtils.toList(res.getAdjPValues()), rowOrder)));
dataFrame.setRowNames(ListUtils.ordered(subDataset.getFeatureNames(), rowOrder));
FeatureData featureData = new FeatureData(dataFrame);
File file = new File(outdir + "/" + test + ".txt");
featureData.save(file);
if (file.exists()) {
result.addOutputItem(
new Item(
test + "file",
file.getName(),
"Anova output file",
TYPE.FILE,
new ArrayList<String>(2),
new HashMap<String, String>(2),
"Anova output files"));
}
// getting significative genes
//
DiffExpressionUtils.addSignificativeResults(
subDataset,
test,
"statistic",
res.getStatistics(),
"adj. p-value",
res.getAdjPValues(),
"p-value",
res.getPValues(),
null,
null,
null,
null,
className,
columnOrder,
pValue,
maxDisplay,
this);
DiffExpressionUtils.createFatiScanRedirection(dataFrame, test, "statistic", result, outdir);
} catch (Exception e) {
e.printStackTrace();
abort(
"exception_executeanova_classcomparison",
"error running anova",
"error running anova: " + e.getMessage(),
"error running anova: " + e.getMessage());
}
}
@Override
public void execute() {
List<String> values = null;
// init
//
test = commandLine.getOptionValue("test", null);
className = commandLine.getOptionValue("class-name", null);
values =
(commandLine.hasOption("class-values")
? StringUtils.toList(commandLine.getOptionValue("class-values", null), ",")
: null);
correction = commandLine.getOptionValue("correction", "fdr");
String pValueParam = commandLine.getOptionValue("p-value", "0.05");
String foldChangeValueParam = commandLine.getOptionValue("fold-change-value", "2");
String datasetParam = commandLine.getOptionValue("dataset");
if (className != null) {
if (values == null) {
values = ListUtils.unique(dataset.getVariables().getByName(className).getValues());
} else {
values = ListUtils.unique(values);
}
classValues = new ArrayList<String>();
for (String val : values) {
if (val != null && val.trim().length() > 0) {
classValues.add(val.trim());
}
}
}
if ("fold-change".equalsIgnoreCase(test) || "fold_change".equalsIgnoreCase(test)) {
try {
foldChangeValue = Double.parseDouble(foldChangeValueParam);
} catch (NumberFormatException e) {
foldChangeValue = 0.05;
}
} else {
try {
pValue = Double.parseDouble(pValueParam);
if (pValue > 1 || pValue < 0) {
pValue = 0.05;
}
} catch (NumberFormatException e) {
pValue = 0.05;
}
}
// input parameters
//
result.addOutputItem(
new Item(
"dataset_input_param",
(datasetParam == null ? "" : new File(datasetParam).getName()),
"Dataset file name",
Item.TYPE.MESSAGE,
Arrays.asList("INPUT_PARAM"),
new HashMap<String, String>(),
"Input parameters"));
result.addOutputItem(
new Item(
"test_input_param",
test,
"Test",
Item.TYPE.MESSAGE,
Arrays.asList("INPUT_PARAM"),
new HashMap<String, String>(),
"Input parameters"));
result.addOutputItem(
new Item(
"class_input_param",
(className == null ? "" : className)
+ " ["
+ ListUtils.toString(classValues, ", ")
+ "]",
"Class",
Item.TYPE.MESSAGE,
Arrays.asList("INPUT_PARAM"),
new HashMap<String, String>(),
"Input parameters"));
if ("fold_change".equalsIgnoreCase(test) || "fold-change".equalsIgnoreCase(test)) {
result.addOutputItem(
new Item(
"fold_change_value_input_param",
foldChangeValueParam,
"Fold-change value",
Item.TYPE.MESSAGE,
Arrays.asList("INPUT_PARAM"),
new HashMap<String, String>(),
"Input parameters"));
} else {
result.addOutputItem(
new Item(
"correction_input_param",
correction,
"Multiple-test correction",
Item.TYPE.MESSAGE,
Arrays.asList("INPUT_PARAM"),
new HashMap<String, String>(),
"Input parameters"));
result.addOutputItem(
new Item(
"pvalue_input_param",
pValueParam,
"Adjusted p-value",
Item.TYPE.MESSAGE,
Arrays.asList("INPUT_PARAM"),
new HashMap<String, String>(),
"Input parameters"));
}
// check input parameters
//
if (datasetParam == null) {
abort(
"missingdataset_execute_classcomparison",
"Missing dataset",
"Missing dataset",
"Missing dataset");
}
if (className == null) {
abort(
"classnamemissing_execute_classcomparison",
"class name missing",
"class name missing",
"class name missing");
}
if (classValues == null) {
abort(
"classvaluesmissing_execute_classcomparison",
"class values missing",
"class values missing",
"class values missing");
}
if (test == null) {
abort(
"testmissing_execute_classcomparison",
"class comparison test missing",
"class comparison test missing",
"class comparison test missing");
}
// reading dataset
//
File datasetFile = new File(datasetParam);
try {
dataset = new Dataset(datasetFile);
if (!dataset.load() && !dataset.validate()) {
abort(
"exception_execute_classcomparison",
"Error",
"Error loading dataset "
+ datasetFile.getName()
+ ": "
+ dataset.getMessages().getErrorString(""),
"");
}
} catch (Exception e) {
abort(
"exception_execute_clustering",
"Error",
"Error reading dataset " + datasetFile.getName(),
"");
}
// executing test
//
updateJobStatus("40", "computing " + test);
if ("limma".equalsIgnoreCase(test)) {
executeLimma();
} else if ("t".equalsIgnoreCase(test)) {
if (classValues.size() == 2) {
executeT();
} else {
abort(
"testmismatched_execute_classcomparison",
"test " + test + " not supported for " + classValues.size() + "-class test",
"test " + test + " not supported for " + classValues.size() + "-class test",
"test " + test + " not supported for " + classValues.size() + "-class test");
}
} else if ("fold_change".equalsIgnoreCase(test) || "fold-change".equalsIgnoreCase(test)) {
if (classValues.size() == 2) {
executeFoldChange();
} else {
abort(
"testmismatched_execute_classcomparison",
"test " + test + " not supported for " + classValues.size() + "-class test",
"test " + test + " not supported for " + classValues.size() + "-class test",
"test " + test + " not supported for " + classValues.size() + "-class test");
}
} else if ("anova".equalsIgnoreCase(test)) {
if (classValues.size() > 2) {
executeAnova();
} else {
abort(
"testmismatched_execute_classcomparison",
"test " + test + " not supported for " + classValues.size() + "-class test",
"test " + test + " not supported for " + classValues.size() + "-class test",
"test " + test + " not supported for " + classValues.size() + "-class test");
}
} else {
abort(
"testunknown_execute_classcomparison",
"unknown test " + test,
"unknown test " + test,
"unknown test " + test);
}
}
private void setFoldChangeResults(
Dataset subDataset, String test, String testLabel, double[] res, String className)
throws InvalidIndexException, IOException {
// int[] columnOrder =
// ListUtils.order(subDataset.getVariables().getByName(className).getValues());
int[] rowOrder = ListUtils.order(ArrayUtils.toList(res), true);
DataFrame dataFrame = new DataFrame(subDataset.getFeatureNames().size(), 0);
dataFrame.addColumn(test, ListUtils.ordered(ArrayUtils.toStringList(res), rowOrder));
dataFrame.setRowNames(ListUtils.ordered(subDataset.getFeatureNames(), rowOrder));
FeatureData featureData = new FeatureData(dataFrame);
File file = new File(outdir + "/" + test + "_foldchange.txt");
IOUtils.write(file, dataFrame.toString(true, true));
/** Get significative terms, babelomics 5 * */
List<String> featureNames = new ArrayList<String>();
List<String> featureValues = new ArrayList<String>();
List<String> featureNamesUp = new ArrayList<String>();
List<String> featureNamesDown = new ArrayList<String>();
for (String rowName : dataFrame.getRowNames()) {
List<String> row = dataFrame.getRow(rowName);
double stats = Double.parseDouble(row.get(0));
if (Math.abs(stats) >= foldChangeValue) {
featureNames.add(rowName);
featureValues.add(row.get(0));
if (stats >= 0) featureNamesUp.add(rowName);
else featureNamesDown.add(rowName);
}
}
dataFrame = new DataFrame(featureNames.size(), 0);
dataFrame.addColumn(test, featureValues);
dataFrame.setRowNames(featureNames);
List<Integer> sigRowIndexes = new ArrayList<Integer>();
for (String feat : featureNames) {
int idx = 0;
for (String featSub : subDataset.getFeatureNames()) {
if (feat.equalsIgnoreCase(featSub)) sigRowIndexes.add(idx);
idx++;
}
}
DoubleMatrix doubleMatrix =
new DoubleMatrix(dataFrame.getRowDimension(), subDataset.getColumnDimension());
for (int i = 0; i < sigRowIndexes.size(); i++) {
doubleMatrix.setRow(i, subDataset.getDoubleMatrix().getRow(sigRowIndexes.get(i)));
}
File fileXX = new File(outdir + "/" + test + "_foldchange_significative_dataset.txt");
Dataset sigDataset = new Dataset(subDataset.getSampleNames(), featureNames, doubleMatrix);
sigDataset.save(fileXX);
File fileAux = new File(outdir + "/" + test + "_foldchange_significative_table.txt");
IOUtils.write(fileAux, dataFrame.toString(true, true));
fileAux = new File(outdir + "/" + test + "_foldchange_significative_table_up.txt");
IOUtils.write(fileAux, featureNamesUp);
fileAux = new File(outdir + "/" + test + "_foldchange_significative_table_down.txt");
IOUtils.write(fileAux, featureNamesDown);
// fileAux = new File(outdir + "/" + test + "_foldchange_significative_dataset.txt");
// IOUtils.write(fileAux, featureNamesDown);
//
// List<String> featuresUp = new ArrayList<String>();
// List<String> featuresDown = new ArrayList<String>();
// for (String rowName : dataFrame.getRowNames()) {
// List<String> row = dataFrame.getRow(rowName);
// double stats = Double.parseDouble(row.get(0));
// if(stats>=foldChangeValue){
//
//
//// featuresUp.add(rowName);
//// else
//// featuresDown.add(rowName);
// }
// }
// file = new File(tool.getOutdir() + "/" + test + "_significative_table_up.txt");
// IOUtils.write(file, featuresUp);
// file = new File(tool.getOutdir() + "/" + test + "_significative_table_down.txt");
// IOUtils.write(file, featuresDown);
// featureData.save(file);
if (file.exists()) {
result.addOutputItem(
new Item(
test + "_foldchange",
file.getName(),
testLabel + " fold-change output file",
TYPE.FILE,
new ArrayList<String>(),
new HashMap<String, String>(),
testLabel + " fold-change.Output files"));
String json =
"{\\\"paramfilename\\\": \\\"input_params.txt\\\", \\\"testfilename\\\": \\\""
+ file.getName()
+ "\\\"}";
result.addOutputItem(
new Item(
"diff_expr_" + StringUtils.randomString(8),
json,
"Significative results",
TYPE.FILE,
StringUtils.toList("DIFF_EXPRESSION_VIEWER"),
new HashMap<String, String>(),
testLabel + " fold-change. Significative results"));
DiffExpressionUtils.createFatiScanRedirection(
dataFrame, test, test, result, outdir, testLabel + " fold-change.");
}
/*
List<Double> orderedRes = ListUtils.ordered(ArrayUtils.toList(res), rowOrder);
int posValues = 0;
int negValues = 0;
for(int i=0 ; i<orderedRes.size() ; i++) {
if (Math.abs(orderedRes.get(i))>foldChangeValue) {
if (orderedRes.get(i)>0) {
posValues++;
} else {
negValues++;
}
}
}
if (posValues + negValues == 0) {
result.addOutputItem(new Item("no_sig_results", "No significative results (fold-change value = " + foldChangeValue + ")", "Significative results", TYPE.MESSAGE, new ArrayList<String>(), new HashMap<String, String>(2), testLabel + " fold-change.Significative results"));
return;
}
int halfDisplay = maxDisplay/2;
int posValuesToDisplay = posValues;
int negValuesToDisplay = negValues;
if (posValues + negValues > maxDisplay) {
if (Math.min(posValues, negValues)>halfDisplay) {
posValuesToDisplay = halfDisplay;
negValuesToDisplay = halfDisplay;
} else {
posValuesToDisplay = posValues>negValues ? (maxDisplay-negValues) : posValues;
negValuesToDisplay = negValues>posValues ? (maxDisplay-posValues) : negValues;
}
}
int nbToDisplay = posValuesToDisplay + negValuesToDisplay;
DoubleMatrix doubleMatrix = new DoubleMatrix(nbToDisplay, subDataset.getColumnDimension());
int rowIndex = 0;
int negLimit = rowOrder.length-negValuesToDisplay;
List<Integer> sigRowIndexes = new ArrayList<Integer>();
for(int i=0 ; i<rowOrder.length ; i++) {
if (i<posValuesToDisplay || i>=negLimit) {
doubleMatrix.setRow(rowIndex++, subDataset.getDoubleMatrix().getRow(rowOrder[i]));
//System.out.println(subDataset.getFeatureNames().get(sigOrder[i]));
sigRowIndexes.add(rowOrder[i]);
}
}
file = new File(outdir + "/" + test +"_fold_change_significative_dataset.txt");
Dataset sigDataset = new Dataset(subDataset.getSampleNames(), ListUtils.subList(subDataset.getFeatureNames(), ListUtils.toIntArray(sigRowIndexes)), doubleMatrix);
sigDataset.setVariables(subDataset.getVariables());
sigDataset.validate();
sigDataset.save(file);
if (file.exists()) {
String tags = "datamatrix,expression";
result.addOutputItem(new Item(test + "_sig_dataset", file.getName(), "Significative values dataset (fold-change value = " + foldChangeValue + ")", TYPE.DATA, StringUtils.toList(tags, ","), new HashMap<String, String>(2), testLabel + " fold-change.Significative results"));
File redirectionFile = new File(outdir + "/clustering.redirection");
DiffExpressionUtils.createClusteringRedirectionFile(redirectionFile, file);
if ( redirectionFile.exists() ) {
tags = "REDIRECTION(" + redirectionFile.getName() + ":Send to Clustering tool...)";
result.addOutputItem(new Item(test + "_sig_dataset", file.getName(), "Significative values dataset (fold-change value = " + foldChangeValue + ")", TYPE.FILE, StringUtils.toList(tags, ","), new HashMap<String, String>(2), testLabel + " fold-change.Significative results"));
}
}
rowOrder = ListUtils.order(ListUtils.subList(ArrayUtils.toList(res), ListUtils.toIntArray(sigRowIndexes)), true);
DataFrame sigDataFrame = new DataFrame(sigDataset.getFeatureNames().size(), 0);
sigDataFrame.addColumn(test, ListUtils.toStringList(ListUtils.ordered(ListUtils.subList(ArrayUtils.toList(res), ListUtils.toIntArray(sigRowIndexes)), rowOrder)));
sigDataFrame.setRowNames(ListUtils.ordered(ListUtils.subList(subDataset.getFeatureNames(), ListUtils.toIntArray(sigRowIndexes)), rowOrder));
// adding table to results
//
file = new File(outdir + "/" + test + "fold_change_significative_table.txt");
IOUtils.write(file, sigDataFrame.toString(true, true));
if ( file.exists() ) {
result.addOutputItem(new Item(test + "fold_change_table", file.getName(), "Significative values table (fold-change value = " + foldChangeValue + ")", TYPE.FILE, StringUtils.toList("TABLE," + test.toUpperCase() + "_FOLD_CHANGE_TABLE", ","), new HashMap<String, String>(2), testLabel + " fold-change.Significative results"));
}
// adding heatmap to results
//
Canvas sigHeatmap = DiffExpressionUtils.generateHeatmap(sigDataset, className, columnOrder, rowOrder, testLabel, ListUtils.toDoubleArray(ListUtils.subList(ArrayUtils.toList(res), ListUtils.toIntArray(sigRowIndexes))), null, null);
if (sigHeatmap == null) {
printError("ioexception_execute_fold_change_classcomparison", "ERROR", "Error generating " + test + " fold-change heatmap image");
} else {
try {
File sigHeatmapFile = new File(outdir + "/" + test + "fold_change_heatmap_significative.png");
sigHeatmap.save(sigHeatmapFile.getAbsolutePath());
if (sigHeatmapFile.exists()) {
result.addOutputItem(new Item(test + "_fold_change_heatmap_significative", sigHeatmapFile.getName(), testLabel + " fold-change heatmap with significative values (fold-change value = " + foldChangeValue + ")", TYPE.IMAGE, new ArrayList<String>(2), new HashMap<String, String>(2), testLabel + " fold-change.Significative results"));
}
} catch (IOException e) {
printError("ioexception_execute_fold_change_classcomparison", "ERROR", "Error saving " + test + " fold-change heatmap image");
}
}
DiffExpressionUtils.createFatiGoRedirection(dataFrame.getRowNames(), dataFrame.getColumnAsDoubleArray(test), test, result, outdir, testLabel + " fold-change.");
DiffExpressionUtils.createFatiScanRedirection(sigDataFrame, test, test, result, outdir, testLabel + " fold-change.");
*/
}
public void executeT() {
int[] cols = dataset.getColumnIndexesByVariableValue(className, classValues.get(0));
DoubleMatrix sample1 = dataset.getSubMatrixByColumns(cols);
cols = dataset.getColumnIndexesByVariableValue(className, classValues.get(1));
DoubleMatrix sample2 = dataset.getSubMatrixByColumns(cols);
try {
Dataset subDataset = dataset.getSubDataset(className, classValues);
// apply test and multiple test correction according
//
TTest tTest = new TTest();
TestResultList<TTestResult> res = tTest.tTest(sample1, sample2);
DiffExpressionUtils.multipleTestCorrection(res, correction);
// create output file
//
int[] columnOrder =
ListUtils.order(subDataset.getVariables().getByName(className).getValues());
int[] rowOrder = ListUtils.order(ArrayUtils.toList(res.getStatistics()), true);
DataFrame dataFrame = new DataFrame(subDataset.getFeatureNames().size(), 0);
dataFrame.addColumn(
"statistic",
ListUtils.toStringList(
ListUtils.ordered(ArrayUtils.toList(res.getStatistics()), rowOrder)));
dataFrame.addColumn(
"p-value",
ListUtils.toStringList(ListUtils.ordered(ArrayUtils.toList(res.getPValues()), rowOrder)));
dataFrame.addColumn(
"adj. p-value",
ListUtils.toStringList(
ListUtils.ordered(ArrayUtils.toList(res.getAdjPValues()), rowOrder)));
dataFrame.setRowNames(ListUtils.ordered(subDataset.getFeatureNames(), rowOrder));
FeatureData featureData = new FeatureData(dataFrame);
File file = new File(outdir + "/t.txt");
featureData.save(file);
if (file.exists()) {
result.addOutputItem(
new Item(
"tfile",
file.getName(),
"T-test output file",
TYPE.FILE,
new ArrayList<String>(),
new HashMap<String, String>(),
"T-test output files"));
}
// getting significative genes
//
DiffExpressionUtils.addSignificativeResults(
subDataset,
test,
"statistic",
res.getStatistics(),
"adj. p-value",
res.getAdjPValues(),
"p-value",
res.getPValues(),
null,
null,
null,
null,
className,
columnOrder,
pValue,
maxDisplay,
this);
DiffExpressionUtils.createFatiScanRedirection(dataFrame, test, "statistic", result, outdir);
} catch (Exception e) {
e.printStackTrace();
abort("exception_executet_classcomparison", "ERROR", "Error running t-test", "");
}
}
