private void saveCluster(File file, Experiment experiment, IData data, int[] rows)
throws Exception {
PrintWriter out = new PrintWriter(new FileOutputStream(file));
String[] fieldNames = data.getFieldNames();
out.print("Original row");
out.print("\t");
for (int i = 0; i < fieldNames.length; i++) {
out.print(fieldNames[i]);
// if (i < fieldNames.length - 1) {
out.print("\t");
// }
}
for (int i = 0; i < geneGroupMeans[0].length; i++) {
out.print("Group" + (i + 1) + " mean\t");
out.print("Group" + (i + 1) + " std.dev.\t");
}
// out.print("\t");
out.print("F ratio");
out.print("\t");
out.print("SS(Groups)\t");
out.print("SS(Error)\t");
out.print("df (Groups)\t");
out.print("df (Error)\t");
out.print("raw p value\t");
out.print("adj p value");
// out.print("UniqueID\tName");
for (int i = 0; i < experiment.getNumberOfSamples(); i++) {
out.print("\t");
out.print(data.getFullSampleName(experiment.getSampleIndex(i)));
}
out.print("\n");
for (int i = 0; i < rows.length; i++) {
out.print(Integer.toString(experiment.getGeneIndexMappedToData(rows[i]) + 1));
// out.print(data.getUniqueId(rows[i]));
out.print("\t");
// out.print(data.getGeneName(rows[i]));
for (int k = 0; k < fieldNames.length; k++) {
out.print(data.getElementAttribute(experiment.getGeneIndexMappedToData(rows[i]), k));
// if (k < fieldNames.length - 1) {
out.print("\t");
// }
}
for (int j = 0; j < geneGroupMeans[rows[i]].length; j++) {
out.print(geneGroupMeans[rows[i]][j] + "\t");
out.print(geneGroupSDs[rows[i]][j] + "\t");
}
// out.print("\t");
out.print("" + ((Float) fValues.get(rows[i])).floatValue());
out.print("\t");
out.print("" + ((Float) ssGroups.get(rows[i])).floatValue());
out.print("\t");
out.print("" + ((Float) ssError.get(rows[i])).floatValue());
out.print("\t");
out.print("" + ((Float) dfNumValues.get(rows[i])).floatValue());
out.print("\t");
out.print("" + ((Float) dfDenomValues.get(rows[i])).floatValue());
out.print("\t");
out.print("" + ((Float) rawPValues.get(rows[i])).floatValue());
out.print("\t");
out.print("" + ((Float) adjPValues.get(rows[i])).floatValue());
for (int j = 0; j < experiment.getNumberOfSamples(); j++) {
out.print("\t");
out.print(Float.toString(experiment.get(rows[i], j)));
}
out.print("\n");
}
out.flush();
out.close();
}
/**
* Gathers data for a set of genes
*
* @param geneIndices
*/
private void getChartData(int[] geneIndices, int multigeneIndex) {
try {
lowerOutliers[multigeneIndex] = new float[clusterCount][];
upperOutliers[multigeneIndex] = new float[clusterCount][];
expressionSDs[multigeneIndex] = new float[clusterCount];
expressionAverages[multigeneIndex] = new float[clusterCount];
expressionMedian[multigeneIndex] = new float[clusterCount];
expressionQ1[multigeneIndex] = new float[clusterCount];
expressionQ3[multigeneIndex] = new float[clusterCount];
expressionIQR[multigeneIndex] = new float[clusterCount];
expressionLowerWhisker[multigeneIndex] = new float[clusterCount];
expressionUpperWhisker[multigeneIndex] = new float[clusterCount];
for (int i = 0; i < clusterCount; i++) {
float average = 0;
float sum = 0;
int membership = 0;
for (int j = 0; j < clusters[i].length; j++) {
for (int k = 0; k < geneIndices.length; k++) {
average = average + experiment.get(geneIndices[k], clusters[i][j]);
membership++;
}
}
average = average / (float) membership;
expressionAverages[multigeneIndex][i] = average;
for (int j = 0; j < clusters[i].length; j++) {
for (int k = 0; k < geneIndices.length; k++) {
sum =
sum + (float) Math.pow(experiment.get(geneIndices[k], clusters[i][j]) - average, 2);
}
}
sum = sum / (float) membership;
expressionSDs[multigeneIndex][i] = (float) Math.sqrt(sum);
// get box plot stuff
float[] expression = new float[clusters[i].length * geneIndices.length];
int expindex = 0;
for (int j = 0; j < clusters[i].length; j++) {
for (int k = 0; k < geneIndices.length; k++) {
expression[expindex++] = (experiment.get(geneIndices[k], clusters[i][j]));
}
}
Arrays.sort(expression);
expressionMedian[multigeneIndex][i] = getMedian(expression);
float[] lower = new float[expression.length / 2];
float[] upper = new float[expression.length / 2];
for (int j = 0; j < lower.length; j++) {
lower[j] = expression[j];
upper[upper.length - 1 - j] = expression[expression.length - 1 - j];
}
expressionQ1[multigeneIndex][i] = getMedian(lower);
expressionQ3[multigeneIndex][i] = getMedian(upper);
expressionIQR[multigeneIndex][i] =
expressionQ3[multigeneIndex][i] - expressionQ1[multigeneIndex][i];
expressionLowerWhisker[multigeneIndex][i] =
expressionQ1[multigeneIndex][i] - 1.5f * expressionIQR[multigeneIndex][i];
expressionUpperWhisker[multigeneIndex][i] =
expressionQ3[multigeneIndex][i] + 1.5f * expressionIQR[multigeneIndex][i];
int upperCount = 0;
int lowerCount = 0;
for (int index = 0; index < expression.length; index++) {
if (expression[index] < expressionLowerWhisker[multigeneIndex][i]) lowerCount++;
if (expression[index] > expressionUpperWhisker[multigeneIndex][i]) upperCount++;
}
lowerOutliers[multigeneIndex][i] = new float[lowerCount];
upperOutliers[multigeneIndex][i] = new float[upperCount];
for (int j = 0; j < lowerOutliers[multigeneIndex][i].length; j++) {
lowerOutliers[multigeneIndex][i][j] = expression[j];
}
for (int j = 0; j < upperOutliers[multigeneIndex][i].length; j++) {
upperOutliers[multigeneIndex][i][j] = expression[expression.length - 1 - j];
}
}
} catch (Exception e) {
System.out.println("data problem");
e.printStackTrace();
for (int i = 0; i < clusterCount; i++) {
expressionAverages[multigeneIndex][i] = (float) Math.random();
expressionSDs[multigeneIndex][i] = (float) Math.random() / 10f;
}
}
}