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"));
}
}
