net.maizegenetics.analysis.chart.TableReportManhattanDataset Maven / Gradle / Ivy
/*
* TableReportManhattanDataset
*/
package net.maizegenetics.analysis.chart;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import net.maizegenetics.analysis.association.AssociationConstants;
import net.maizegenetics.util.TableReport;
import org.jfree.data.Range;
import org.jfree.data.xy.DefaultTableXYDataset;
/**
*
* @author yz79
* @author Terry Casstevens
*/
public class TableReportManhattanDataset extends DefaultTableXYDataset {
private String[] seriesNames;
private int[] seriesOffsets;
private String myTrait;
private int numberYAxes;
private String[] myChromNames;
private Object[] myColumnNames;
private double[] myPValues;
private double[] myLogPValues;
private double myMaxLogValue;
private long[] myPositions;
private String[] myMarkers;
private HashMap myLookupTable;
private int myPValueColumnIndex = -1;
private int myChromColumnIndex = -1;
private int myPositionColumnIndex = -1;
private int myMarkerColumnIndex = -1;
private int myTraitColumnIndex = -1;
private final int myNumRows;
private final int myStartIndex;
private final int myEndIndex;
private final List myActualPositions = new ArrayList<>();
public TableReportManhattanDataset(TableReport theTable, int start, int end) {
numberYAxes = 0;
myStartIndex = start;
myEndIndex = end;
myNumRows = myEndIndex - start;
setTableReport(theTable);
}
@Override
public Range getDomainBounds(boolean includeInterval) {
return new Range(getDomainLowerBound(includeInterval), getDomainUpperBound(includeInterval));
}
@Override
public double getDomainUpperBound(boolean includeInterval) {
return myPositions[myNumRows - 1];
}
@Override
public double getDomainLowerBound(boolean includeInterval) {
return myPositions[0];
}
public Range getRangeBounds() {
return new Range(0.0, myMaxLogValue);
}
@Override
public int getItemCount(int parm1) {
return seriesOffsets[parm1 + 1] - seriesOffsets[parm1];
}
@Override
public Number getX(int series, int item) {
return myPositions[seriesOffsets[series] + item];
}
@Override
public int getSeriesCount() {
return numberYAxes;
}
@Override
public Number getY(int series, int item) {
return myLogPValues[seriesOffsets[series] + item];
}
public String getSeriesName(int series) {
return seriesNames[series];
}
@Override
public String getSeriesKey(int series) {
return seriesNames[series];
}
public String getXName() {
return "Position";
}
public List getActualPostions() {
return myActualPositions;
}
private void setTraitColumnIndex() {
for (int i = 0; i < myColumnNames.length; i++) {
if (myColumnNames[i].equals(AssociationConstants.STATS_HEADER_TRAIT)) {
myTraitColumnIndex = i;
return;
}
}
}
private void setPValueColumnIndex() {
for (int i = 0; i < myColumnNames.length; i++) {
if (myColumnNames[i].equals(AssociationConstants.STATS_HEADER_P_VALUE)) {
myPValueColumnIndex = i;
return;
}
}
throw new IllegalArgumentException("No P-values in selected data");
}
private void setChromColumnIndex() {
for (int i = 0; i < myColumnNames.length; i++) {
if (myColumnNames[i].equals(AssociationConstants.STATS_HEADER_CHR)) {
myChromColumnIndex = i;
return;
}
}
throw new IllegalArgumentException("No Chromosome names in selected data");
}
private void setMarkerColumnIndex() {
for (int i = 0; i < myColumnNames.length; i++) {
if (myColumnNames[i].equals(AssociationConstants.STATS_HEADER_MARKER)) {
myMarkerColumnIndex = i;
return;
}
}
}
private void setPositionColumnIndex() {
for (int i = 0; i < myColumnNames.length; i++) {
if (myColumnNames[i].equals(AssociationConstants.STATS_HEADER_POSITION)) {
myPositionColumnIndex = i;
return;
}
}
throw new IllegalArgumentException("No positions in selected data");
}
private void setMarkers(TableReport myTableReport) {
for (int i = 0; i < myMarkers.length; i++) {
myMarkers[i] = ((String) myTableReport.getValueAt(myStartIndex + i, myMarkerColumnIndex));
}
}
private void setPValues(TableReport myTableReport) {
Object temp = myTableReport.getValueAt(myStartIndex, myPValueColumnIndex);
if (temp instanceof Double) {
for (int i = 0; i < myPValues.length; i++) {
myPValues[i] = ((Double) myTableReport.getValueAt(myStartIndex + i, myPValueColumnIndex));
if (myPValues[i] == 0) {
myPValues[i] = Double.MIN_VALUE;
}
myLookupTable.put(myPValues[i], i);
}
} else if (temp instanceof String) {
for (int i = 0; i < myPValues.length; i++) {
myPValues[i] = Double.parseDouble((String) myTableReport.getValueAt(myStartIndex + i, myPValueColumnIndex));
if (myPValues[i] == 0) {
myPValues[i] = Double.MIN_VALUE;
}
myLookupTable.put(myPValues[i], i);
}
} else {
throw new IllegalStateException("TableReportManhattanDataset: setPValues: Unknown data type of P values: " + temp.getClass().getName());
}
}
private void setPositions(TableReport myTableReport) {
long offset = 0;
int currentPosition = 0;
int previousPosition = 0;
String currentChrom = "";
List offsets = new ArrayList<>();
// GLM positions formatted as int
boolean isNewChromosome = true;
List chromosomeNames = new ArrayList<>();
for (int i = 0; i < myNumRows; i++) {
currentPosition = Integer.valueOf((myTableReport.getValueAt(myStartIndex + i, myPositionColumnIndex)).toString());
myChromNames[i] = myTableReport.getValueAt(myStartIndex + i, myChromColumnIndex).toString();
if (!currentChrom.equals(myChromNames[i])) {
numberYAxes++;
currentChrom = myChromNames[i];
chromosomeNames.add(currentChrom);
previousPosition = 0;
offsets.add(i);
isNewChromosome = true;
}
myPositions[i] = currentPosition - previousPosition + offset;
if (isNewChromosome) {
myActualPositions.add(myPositions[i] - currentPosition);
isNewChromosome = false;
}
previousPosition = currentPosition;
offset = myPositions[i];
}
offsets.add(myNumRows);
seriesOffsets = new int[numberYAxes + 1];
for (int i = 0; i < numberYAxes + 1; i++) {
seriesOffsets[i] = offsets.get(i);
}
seriesNames = new String[numberYAxes];
chromosomeNames.toArray(seriesNames);
}
private void setTrait(TableReport table) {
myTrait = (String) table.getValueAt(myStartIndex, myTraitColumnIndex);
}
public String getMarker(int series, int item) {
return myMarkers[seriesOffsets[series] + item];
}
public String[] getChroms() {
return myChromNames;
}
public String getTrait() {
return myTrait;
}
private void setLogPValues() {
for (int i = 0; i < myLogPValues.length; i++) {
myLogPValues[i] = -Math.log10(myPValues[i]);
if (myLogPValues[i] > myMaxLogValue) {
myMaxLogValue = myLogPValues[i];
}
}
}
public void setTableReport(TableReport theTable) {
myColumnNames = theTable.getTableColumnNames();
setPValueColumnIndex();
setChromColumnIndex();
setPositionColumnIndex();
setMarkerColumnIndex();
setTraitColumnIndex();
myPValues = new double[myNumRows];
myLogPValues = new double[myNumRows];
myChromNames = new String[myNumRows];
myPositions = new long[myNumRows];
myMarkers = new String[myNumRows];
myLookupTable = new HashMap<>(myNumRows);
setPValues(theTable);
setLogPValues();
setPositions(theTable);
setMarkers(theTable);
setTrait(theTable);
}
}