/** Invoked by the framework when this viewer is selected. */
public void onSelected(IFramework framework) {
geneClusterCB.removeAllItems();
for (int i = 0; i < framework.getClusterRepository(0).size(); i++) {
if (framework.getClusterRepository(0).getCluster(i + 1) == null) break;
Cluster cluster = framework.getClusterRepository(0).getCluster(i + 1);
geneClusterCB.addItem(
"Cluster #: " + cluster.getSerialNumber() + ", " + cluster.getClusterLabel());
}
}
private void populateGeneListComboBoxes() {
geneClusterCB = new JComboBox();
geneClusterCB.removeAllItems();
for (int i = 0; i < framework.getClusterRepository(0).size(); i++) {
if (framework.getClusterRepository(0).getCluster(i + 1) == null) break;
Cluster cluster = framework.getClusterRepository(0).getCluster(i + 1);
geneClusterCB.addItem(
"Cluster #: " + cluster.getSerialNumber() + ", " + cluster.getClusterLabel());
}
geneClusterCB.setVisible(false);
geneClusterCB.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
repaint();
}
});
geneAnnotationCB = new JComboBox(framework.getData().getAllFilledAnnotationFields());
geneAnnotationCB.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
if (chartTypeCB.getSelectedIndex() > 1) // this method only applies for single gene
return;
geneCB.removeAllItems();
int selected = Math.max(geneAnnotationCB.getSelectedIndex(), 0);
int numGenes =
framework
.getData()
.getAnnotationList(framework.getData().getAllFilledAnnotationFields()[selected])
.length;
StringExt[] stringext = new StringExt[numGenes];
String[] geneNames =
framework
.getData()
.getAnnotationList(
framework.getData().getAllFilledAnnotationFields()[selected]);
for (int i = 0; i < numGenes; i++) stringext[i] = new StringExt(geneNames[i]);
DefaultComboBoxModel cbm = new DefaultComboBoxModel(stringext);
geneCB.setModel(cbm);
}
});
geneCB =
new JComboBox(
framework
.getData()
.getAnnotationList(framework.getData().getAllFilledAnnotationFields()[0]));
geneCB.setMaximumSize(new Dimension(150, geneCB.getHeight()));
geneCB.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
repaint();
}
});
}
public void paint(Graphics g) {
super.paint(g);
if (clusterCount == 0) return;
boolean ismultigene = !isSingleGene;
Graphics2D g2 = (Graphics2D) g;
multigeneCount = 1;
Cluster cluster = null;
if (ismultigene) {
try {
if (!inAnalysis) {
int begin = geneClusterCB.getSelectedItem().toString().indexOf(":");
int end = geneClusterCB.getSelectedItem().toString().indexOf(",");
sn = geneClusterCB.getSelectedItem().toString().substring(begin + 2, end);
cluster = framework.getClusterRepository(0).getCluster(Integer.parseInt(sn));
geneIndices = cluster.getIndices();
}
} catch (Exception e) {
e.printStackTrace();
System.out.println("Gene Cluster Problem");
return;
}
if (geneIndices == null || geneIndices.length < 1) return;
if (aggregateGeneCluster) multigeneCount = 1;
else multigeneCount = geneIndices.length;
}
int chartTop = chartTopHeight;
lowerOutliers = new float[multigeneCount][][];
upperOutliers = new float[multigeneCount][][];
expressionSDs = new float[multigeneCount][];
expressionAverages = new float[multigeneCount][];
expressionMedian = new float[multigeneCount][];
expressionQ1 = new float[multigeneCount][];
expressionQ3 = new float[multigeneCount][];
expressionIQR = new float[multigeneCount][];
expressionLowerWhisker = new float[multigeneCount][];
expressionUpperWhisker = new float[multigeneCount][];
chartTitles = new String[multigeneCount];
int maxString = 0;
for (int i = 0; i < clusterNames.length; i++) {
maxString = Math.max(maxString, g.getFontMetrics().stringWidth(clusterNames[i]));
}
chartGap = maxString + 50;
// for only drawing the visible area- dramatic speed improvements
Rectangle bounds = g.getClipBounds();
int indexBegin = (int) Math.max(-3 + bounds.y / (chartHeight + chartGap), 0f);
int indexEnd =
(int) Math.min(multigeneCount, 3 + (bounds.y + bounds.height) / (chartHeight + chartGap));
for (int multigeneIndex = indexBegin; multigeneIndex < indexEnd; multigeneIndex++) {
if (ismultigene) {
if (aggregateGeneCluster) {
getChartData(geneIndices, multigeneIndex);
if (inAnalysis) chartTitles[multigeneIndex] = geneClusterLabel;
else chartTitles[multigeneIndex] = cluster.getClusterLabel();
} else {
getChartData(geneIndices[multigeneIndex], multigeneIndex);
chartTitles[multigeneIndex] =
framework.getData()
.getElementAnnotation(
geneIndices[multigeneIndex], framework.getData().getFieldNames()[0])[0];
}
} else {
getChartData(geneCB.getSelectedIndex(), multigeneIndex);
chartTitles[multigeneIndex] = geneCB.getSelectedItem().toString();
}
float maxHeight = 0;
float minHeight = Float.POSITIVE_INFINITY;
for (int i = 0; i < clusterCount; i++) {
if (this.isBoxPlot) {
for (int j = 0; j < this.upperOutliers[multigeneIndex][i].length; j++) {
maxHeight = Math.max(upperOutliers[multigeneIndex][i][j], maxHeight);
}
maxHeight = Math.max(expressionUpperWhisker[multigeneIndex][i], maxHeight);
} else {
maxHeight =
Math.max(
expressionAverages[multigeneIndex][i] + this.expressionSDs[multigeneIndex][i],
maxHeight);
}
}
for (int i = 0; i < clusterCount; i++) {
if (this.isBoxPlot) {
for (int j = 0; j < this.lowerOutliers[multigeneIndex][i].length; j++) {
minHeight = Math.min(lowerOutliers[multigeneIndex][i][j], minHeight);
}
minHeight = Math.min(expressionLowerWhisker[multigeneIndex][i], minHeight);
} else minHeight = 0f; // Math.min(expressionAverages[i], minHeight);
}
maxHeight++;
float topgridline;
float bottomgridline;
if (this.autoScale) {
topgridline = (int) maxHeight + (int) maxHeight % 2;
bottomgridline = (int) minHeight - (int) minHeight % 2 - 2;
if (!isBoxPlot) bottomgridline = 0f;
fixedTop = topgridline;
fixedBottom = bottomgridline;
} else {
topgridline = fixedTop;
bottomgridline = fixedBottom;
if (!isBoxPlot) bottomgridline = 0f;
}
float gridrange = topgridline - bottomgridline;
// draw everything
// grid
g2.setColor(Color.black);
g2.drawLine(
chartleft - 5,
chartHeight + chartTop,
chartleft + clusterCount * chartIncrement,
chartHeight + chartTop); // horizontal line bottom
g2.drawLine(chartleft, chartTop, chartleft, chartHeight + chartTop + 5); // vertical line left
g2.setColor(Color.gray);
g2.drawLine(chartleft - 7, chartTop, chartleft, chartTop); // horizontal line ticktop
g2.drawLine(
chartleft - 5,
chartTop + chartHeight / 4,
chartleft,
chartTop + chartHeight / 4); // horizontal line tick75%
g2.drawLine(
chartleft - 7,
chartTop + chartHeight / 2,
chartleft,
chartTop + chartHeight / 2); // horizontal line tickMid
g2.drawLine(
chartleft - 5,
chartTop + 3 * chartHeight / 4,
chartleft,
chartTop + 3 * chartHeight / 4); // horizontal line tick25%
if (showGridlines) {
g2.setColor(Color.gray);
g2.drawLine(
chartleft,
chartTop,
chartleft + chartIncrement * clusterCount,
chartTop); // horizontal line grid
g2.drawLine(
chartleft,
chartTop + chartHeight / 4,
chartleft + chartIncrement * clusterCount,
chartTop + chartHeight / 4); // horizontal line grid
g2.drawLine(
chartleft,
chartTop + chartHeight / 2,
chartleft + chartIncrement * clusterCount,
chartTop + chartHeight / 2); // horizontal line grid
g2.drawLine(
chartleft,
chartTop + 3 * chartHeight / 4,
chartleft + chartIncrement * clusterCount,
chartTop + 3 * chartHeight / 4); // horizontal line grid
}
g2.setColor(Color.black);
g2.drawString(
Float.toString(bottomgridline + gridrange),
chartleft - 40,
chartTop + 3); // vertical axis label
g2.drawString(
Float.toString(bottomgridline + gridrange * 3f / 4f),
chartleft - 40,
(chartTop + 3) + chartHeight / 4); // vertical axis label
g2.drawString(
Float.toString(bottomgridline + gridrange / 2f),
chartleft - 40,
(chartTop + 3) + chartHeight / 2); // vertical axis label
g2.drawString(
Float.toString(bottomgridline + gridrange / 4f),
chartleft - 40,
(chartTop + 3) + (3 * chartHeight / 4)); // vertical axis label
g2.drawString(
Float.toString(bottomgridline),
chartleft - 40,
(chartTop + 3) + (chartHeight)); // vertical axis label
Font font = g2.getFont();
g2.setFont(new Font("Helvetica", Font.BOLD, 16));
g2.drawString(
chartTitles[multigeneIndex],
chartleft + chartIncrement / 2,
chartTop - 15); // Gene/group Name label
g2.setFont(font);
g2.rotate(-Math.PI / 2);
g2.drawString(
"Expression", -((chartTop + 3) + 2 * chartHeight / 3), (chartleft - 60)); // y-axis Label
g2.rotate(Math.PI / 2);
for (int i = 0; i < this.clusterCount; i++) {
int xorigin = (int) ((.25f + (float) i) * chartIncrement) + chartleft;
int yorigin = chartHeight + chartTop;
int barWidth = chartIncrement / 2;
int barHeight =
(int) ((expressionAverages[multigeneIndex][i]) * ((float) chartHeight) / gridrange);
int errorBarHeight =
(int) (expressionSDs[multigeneIndex][i] * ((float) chartHeight) / gridrange);
int boxBottom =
(int)
((-bottomgridline + expressionQ1[multigeneIndex][i])
* ((float) chartHeight)
/ gridrange);
int boxTop =
(int)
((-bottomgridline + expressionQ3[multigeneIndex][i])
* ((float) chartHeight)
/ gridrange);
int boxMedian =
(int)
((-bottomgridline + expressionMedian[multigeneIndex][i])
* ((float) chartHeight)
/ gridrange);
int boxLowerWhisker =
(int)
((-bottomgridline + expressionLowerWhisker[multigeneIndex][i])
* ((float) chartHeight)
/ gridrange);
int boxUpperWhisker =
(int)
((-bottomgridline + expressionUpperWhisker[multigeneIndex][i])
* ((float) chartHeight)
/ gridrange);
g2.setColor(Color.gray);
g2.drawLine(
xorigin + 3 * barWidth / 2,
yorigin,
xorigin + 3 * barWidth / 2,
yorigin + 5); // vertical tickmark
g2.setColor(Color.black);
g2.rotate(-Math.PI / 2);
g2.drawString(
clusterNames[i],
-(yorigin + 5) - g.getFontMetrics().stringWidth(clusterNames[i]),
(xorigin + barWidth / 2)); // cluster names
g2.rotate(Math.PI / 2);
if (!isBoxPlot) { // bar graph
g2.setColor(clusterColors[i]);
g2.fillRect(xorigin, yorigin - barHeight, barWidth, barHeight); // box
g2.setColor(Color.black);
g2.drawRect(xorigin, yorigin - barHeight, barWidth, barHeight); // box outline
g2.drawLine(
xorigin + barWidth / 2,
yorigin - barHeight - errorBarHeight,
xorigin + barWidth / 2,
yorigin - barHeight); // vertical errorbar
g2.drawLine(
xorigin + barWidth / 4,
yorigin - barHeight - errorBarHeight,
xorigin + 3 * barWidth / 4,
yorigin - barHeight - errorBarHeight); // horizontal error bar
} else if (isBoxPlot) { // box plot
g2.setColor(clusterColors[i]);
g2.fillRect(xorigin, yorigin - boxTop, barWidth, boxTop - boxBottom); // box
g2.setColor(Color.black);
g2.drawRect(xorigin, yorigin - boxTop, barWidth, boxTop - boxBottom); // box outline
g2.drawLine(
xorigin, yorigin - boxMedian, xorigin + barWidth, yorigin - boxMedian); // median line
g2.drawLine(
xorigin + barWidth / 2,
yorigin - boxTop,
xorigin + barWidth / 2,
yorigin - boxUpperWhisker); // vertical whisker upper
g2.drawLine(
xorigin + barWidth / 2,
yorigin - boxBottom,
xorigin + barWidth / 2,
yorigin - boxLowerWhisker); // vertical whisker lower
g2.drawLine(
xorigin + barWidth / 4,
yorigin - boxUpperWhisker,
xorigin + 3 * barWidth / 4,
yorigin - boxUpperWhisker); // horizontal whisker upper
g2.drawLine(
xorigin + barWidth / 4,
yorigin - boxLowerWhisker,
xorigin + 3 * barWidth / 4,
yorigin - boxLowerWhisker); // horizontal whisker lower
// draw outliers
int circleWidth = 6;
for (int j = 0; j < upperOutliers[multigeneIndex][i].length; j++) {
g2.drawOval(
xorigin + barWidth / 2 - circleWidth / 2,
yorigin
- (int)
((float) ((-bottomgridline + upperOutliers[multigeneIndex][i][j]))
* ((float) chartHeight)
/ gridrange)
- circleWidth / 2,
circleWidth,
circleWidth);
}
for (int j = 0; j < lowerOutliers[multigeneIndex][i].length; j++) {
g2.drawOval(
xorigin + barWidth / 2 - circleWidth / 2,
yorigin
- (int)
((float) ((-bottomgridline + lowerOutliers[multigeneIndex][i][j]))
* ((float) chartHeight)
/ gridrange)
- circleWidth / 2,
circleWidth,
circleWidth);
}
} else {
System.out.println("unknown chart type");
}
}
chartTop =
chartTopHeight
+ (multigeneIndex + 1) * (chartHeight + chartGap); // moves top down for next graph
}
jScrollBar.setUnitIncrement(chartHeight + chartGap);
int viewerHeight = chartTopHeight + (multigeneCount) * (chartHeight + chartGap);
this.setSize(new Dimension(this.getWidth(), viewerHeight));
this.setPreferredSize(new Dimension(this.getWidth(), viewerHeight));
}