Author: scooter
Date: 2011-02-25 18:20:31 -0800 (Fri, 25 Feb 2011)
New Revision: 24242
Added:
csplugins/trunk/ucsf/scooter/nodeCharts/examples/heatstrip.com
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/HeatStrip.java
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/LinearGradientPaintFactory.java
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/examples/bar2.com
csplugins/trunk/ucsf/scooter/nodeCharts/pom.xml
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/NodeChartCommandHandler.java
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/ValueUtils.java
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/resources/nodeCharts/plugin.props
Log:
Added HeatStrips
Modified: csplugins/trunk/ucsf/scooter/nodeCharts/examples/bar2.com
===================================================================
--- csplugins/trunk/ucsf/scooter/nodeCharts/examples/bar2.com 2011-02-26
00:28:15 UTC (rev 24241)
+++ csplugins/trunk/ucsf/scooter/nodeCharts/examples/bar2.com 2011-02-26
02:20:31 UTC (rev 24242)
@@ -1,3 +1,2 @@
-nodecharts bar nodelist="all" attributelist="gal1RGexp,gal4RGexp,gal80Rexp"
colorlist="up:cyan,down:yellow"
-
+nodecharts bar nodelist="all" attributelist="gal1RGexp,gal4RGexp,gal80Rexp"
colorlist="up:red,down:green" showlabels="false"
network view update
Added: csplugins/trunk/ucsf/scooter/nodeCharts/examples/heatstrip.com
===================================================================
--- csplugins/trunk/ucsf/scooter/nodeCharts/examples/heatstrip.com
(rev 0)
+++ csplugins/trunk/ucsf/scooter/nodeCharts/examples/heatstrip.com
2011-02-26 02:20:31 UTC (rev 24242)
@@ -0,0 +1,3 @@
+nodecharts heatstrip nodelist="all"
attributelist="gal1RGexp,gal4RGexp,gal80Rexp" colorlist="redgreen"
normalize="true" showlabels="false"
+
+network view update
Modified: csplugins/trunk/ucsf/scooter/nodeCharts/pom.xml
===================================================================
--- csplugins/trunk/ucsf/scooter/nodeCharts/pom.xml 2011-02-26 00:28:15 UTC
(rev 24241)
+++ csplugins/trunk/ucsf/scooter/nodeCharts/pom.xml 2011-02-26 02:20:31 UTC
(rev 24242)
@@ -14,7 +14,7 @@
<groupId>cytoscape.csplugins</groupId>
<artifactId>nodeCharts</artifactId>
<packaging>jar</packaging>
- <version>0.93</version>
+ <version>0.94</version>
<name>Node Charts Plugin</name>
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/NodeChartCommandHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/NodeChartCommandHandler.java
2011-02-26 00:28:15 UTC (rev 24241)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/NodeChartCommandHandler.java
2011-02-26 02:20:31 UTC (rev 24242)
@@ -58,6 +58,7 @@
// nodeChart imports
import nodeCharts.view.NodeChartViewer;
import nodeCharts.view.BarChart;
+import nodeCharts.view.HeatStrip;
import nodeCharts.view.LineChart;
import nodeCharts.view.PieChart;
import nodeCharts.view.StripeChart;
@@ -80,9 +81,11 @@
public static final String NETWORK = "network";
public static final String NODE = "node";
public static final String NODELIST = "nodelist";
+ public static final String NORMALIZE = "normalize";
public static final String POSITION = "position";
public static final String SCALE = "scale";
public static final String SELECTED = "selected";
+ public static final String SHOWLABELS = "showlabels";
public static final String VALUES = "valuelist";
public NodeChartCommandHandler(String namespace, CyLogger logger) {
@@ -93,6 +96,7 @@
// Register each command
register(new BarChart());
+ register(new HeatStrip());
register(new LineChart());
register(new PieChart());
register(new StripeChart());
@@ -185,6 +189,23 @@
labels = ValueUtils.getStringList(args.get(LABELS));
}
+ boolean showLabels = true;
+ if (args.containsKey(SHOWLABELS)) {
+ showLabels =
ValueUtils.getBooleanValue(args.get(SHOWLABELS));
+ }
+
+ boolean normalize = false;
+ List<Double>maxValues = null;
+ if (args.containsKey(NORMALIZE)) {
+ normalize =
ValueUtils.getBooleanValue(args.get(NORMALIZE));
+ if (normalize && args.containsKey(ATTRIBUTELIST)) {
+ for (CyNode node: nodeList) {
+ values =
ValueUtils.getDataFromAttributes (node, args.get(ATTRIBUTELIST), labels);
+ maxValues =
ValueUtils.arrayMax(maxValues, values);
+ }
+ }
+ }
+
double scale = 0.90;
if (args.containsKey(SCALE)) {
try {
@@ -203,12 +224,18 @@
throw new CyCommandException("unknown position
keyword or illegal position expression: "+position);
}
+ if (!showLabels)
+ labels = null;
+
// OK, do it!
for (CyNode node: nodeList) {
// If we've got an attributelist, we need to get our
values now since they will change based on
// the node
- if (args.containsKey(ATTRIBUTELIST))
+ if (args.containsKey(ATTRIBUTELIST)) {
values = ValueUtils.getDataFromAttributes
(node, args.get(ATTRIBUTELIST), labels);
+ if (normalize)
+ ValueUtils.normalize(values, maxValues);
+ }
List<CustomGraphic> cgList =
viewer.getCustomGraphics(args, values, labels, node, view, pos, scale);
ViewUtils.addCustomGraphics(cgList, node, view);
@@ -228,9 +255,11 @@
addArgument(viewer.getName(), NETWORK, CURRENT);
addArgument(viewer.getName(), NODE);
addArgument(viewer.getName(), NODELIST);
+ addArgument(viewer.getName(), NORMALIZE, "false");
addArgument(viewer.getName(), POSITION);
addArgument(viewer.getName(), VALUES);
addArgument(viewer.getName(), SCALE, "0.90");
+ addArgument(viewer.getName(), SHOWLABELS, "true");
// Get the specific commands handled by the viewer
Map<String,String> args = viewer.getOptions();
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/ValueUtils.java
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/ValueUtils.java
2011-02-26 00:28:15 UTC (rev 24241)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/ValueUtils.java
2011-02-26 02:20:31 UTC (rev 24242)
@@ -100,7 +100,7 @@
}
if (attributeArray.length == 1) {
// Handle the case where we were given a single, list
attribute
- if (labels.size() == 0) {
+ if (labels == null || labels.size() == 0) {
throw new CyCommandException("Labels must be
specified if attribute is a list");
}
String attr = attributeArray[0].trim();
@@ -140,7 +140,7 @@
}
}
}
- if (labels.size() == 0)
+ if (labels != null && labels.size() == 0)
labels.addAll(Arrays.asList(attributeArray));
return result;
}
@@ -190,6 +190,25 @@
return new ArrayList<String>();
}
+ /**
+ * Return the boolean equivalent of the input
+ *
+ * @param input an input value that is supposed to be Boolean
+ * @return the boolean value it represents
+ */
+ public static boolean getBooleanValue(Object input) {
+ if (input instanceof Boolean)
+ return ((Boolean)input).booleanValue();
+ return Boolean.parseBoolean(input.toString());
+ }
+
+ /**
+ * Return the double equivalent of the input
+ *
+ * @param input an input value that is supposed to be a double
+ * @return the a double value it represents
+ * @throws NumberFormatException is the value is illegal
+ */
public static double getDoubleValue(Object input) throws
NumberFormatException {
if (input instanceof Double)
return ((Double)input).doubleValue();
@@ -200,6 +219,28 @@
throw new NumberFormatException("input can not be converted to
double");
}
+ public static List<Double> arrayMax(List<Double> maxValues,
List<Double> values) {
+ // Initialize, if necessary
+ if (maxValues == null) {
+ maxValues = new ArrayList<Double>(values.size());
+ for (Double d: values)
+ maxValues.add(Math.abs(d));
+ return maxValues;
+ }
+
+ // OK, now we need to actually do the work...
+ for (int index = 0; index < values.size(); index++) {
+ maxValues.set(index, Math.max(maxValues.get(index),
Math.abs(values.get(index))));
+ }
+ return maxValues;
+ }
+
+ public static void normalize(List<Double> values, List<Double>
maxValues) {
+ for (int index = 0; index < values.size(); index++) {
+ values.set(index,
values.get(index)/maxValues.get(index));
+ }
+ }
+
/**
* Takes a map of objects indexed by a string keyword and returns
* a map of strings indexed by that keyword. This involves figuring
@@ -240,6 +281,8 @@
private static final String RAINBOW = "rainbow";
private static final String RANDOM = "random";
private static final String UP = "up:";
+ private static final String ZERO = "zero:";
+ private static final double EPSILON = 1E-8f;
public static List<Color> convertInputToColor(Object input,
List<Double>values) throws CyCommandException {
int nColors = values.size();
@@ -263,9 +306,13 @@
// Look for up/down special case
if (colorArray.length == 2 &&
(colorArray[0].toLowerCase().startsWith(UP) ||
- colorArray[1].toLowerCase().startsWith(DOWN))) {
+ colorArray[0].toLowerCase().startsWith(DOWN))) {
return parseUpDownColor(colorArray, values);
-
+ } else if (colorArray.length == 3 &&
+ (colorArray[0].toLowerCase().startsWith(UP) ||
+ colorArray[0].toLowerCase().startsWith(DOWN) ||
+ colorArray[0].toLowerCase().startsWith(ZERO))) {
+ return parseUpDownColor(colorArray, values);
} else if (colorArray.length > 1)
return parseColorList(colorArray);
else
@@ -274,24 +321,38 @@
throw new CyCommandException("unknown type for color
list");
}
+ public static List<Color> parseUpDownColor(String[] colorArray) throws
CyCommandException {
+ if (colorArray.length < 2)
+ throw new CyCommandException("Up/Down color spec must
have at least 2 colors");
+
+ String [] colors = new String[3];
+ colors[2] = "black";
+ for (int index = 0; index < colorArray.length; index++) {
+ if (colorArray[index].toLowerCase().startsWith(UP)) {
+ colors[0] =
colorArray[index].substring(UP.length());
+ } else if
(colorArray[index].toLowerCase().startsWith(DOWN)) {
+ colors[1] =
colorArray[index].substring(DOWN.length());
+ } else if
(colorArray[index].toLowerCase().startsWith(ZERO)) {
+ colors[2] =
colorArray[index].substring(ZERO.length());
+ }
+ }
+ return parseColorList(colors);
+ }
+
private static List<Color> parseUpDownColor(String[] colorArray,
List<Double>values) throws CyCommandException {
- String [] colors = new String[2];
- if (colorArray[0].toLowerCase().startsWith(UP)) {
- colors[0] = colorArray[0].substring(UP.length());
- colors[1] = colorArray[1].substring(DOWN.length());
- } else {
- colors[1] = colorArray[0].substring(DOWN.length());
- colors[0] = colorArray[1].substring(UP.length());
- }
- List<Color> upDownColors = parseColorList(colors);
+ List<Color> upDownColors = parseUpDownColor(colorArray);
Color up = upDownColors.get(0);
Color down = upDownColors.get(1);
+ Color zero = upDownColors.get(2);
+
List<Color> results = new ArrayList<Color>(values.size());
for (Double v: values) {
- if (v < 0.0)
+ if (v < EPSILON)
results.add(down);
+ else if (v > EPSILON)
+ results.add(up);
else
- results.add(up);
+ results.add(zero);
}
return results;
}
Added:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/HeatStrip.java
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/HeatStrip.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/HeatStrip.java
2011-02-26 02:20:31 UTC (rev 24242)
@@ -0,0 +1,183 @@
+package nodeCharts.view;
+
+import giny.view.Position;
+
+import java.awt.Color;
+import java.awt.Shape;
+import java.awt.geom.Area;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import nodeCharts.command.NodeChartCommandHandler;
+import nodeCharts.command.ValueUtils;
+import nodeCharts.view.ViewUtils.TextAlignment;
+import cytoscape.CyNode;
+import cytoscape.command.CyCommandException;
+import cytoscape.render.stateful.CustomGraphic;
+import cytoscape.render.stateful.PaintFactory;
+import cytoscape.view.CyNetworkView;
+
+/**
+ * creates a list of custom graphics where each custom graphic represents a
+ * bar of a heat strip. The data for this is of the format: value1:value2:....
+ * The colors are specified as a colorlist triple: up:zero:down, or a quad
+ * up:zero:down:missing, or a keyword: redgreen, yellowcyan. If nothing
+ * is specified, yellowcyan is assumed
+ *
+ * Bar starts at centerline of node and goes upwards (for positive value) or
+ * downwards (for negative values)
+ *
+ */
+public class HeatStrip implements NodeChartViewer {
+ private static final String COLORS = "colorlist";
+ private static final String SEPARATION = "separation";
+ private static final String REDGREEN = "redgreen";
+ private static final String YELLOWCYAN = "yellowcyan";
+
+ float[] dist = {0.0f, 0.5f, 1.0f};
+ Color[] redGreen = {Color.GREEN, Color.BLACK, Color.RED};
+ Color[] yellowCyan = {Color.CYAN, Color.BLACK, Color.YELLOW};
+
+
+ public String getName() {
+ return "heatstrip";
+ }
+
+ public String getDescription() {
+ return "Display the values passed as arguments as a heat strip
on the node";
+ }
+
+ public Map<String, String> getOptions() {
+ Map<String, String> options = new HashMap<String, String>();
+ options.put(COLORS, "yellowcyan");
+ options.put(SEPARATION, "");
+ return options;
+ }
+
+ public List<CustomGraphic> getCustomGraphics(Map<String, Object> args,
+ List<Double> values, List<String> labels, CyNode node,
+ CyNetworkView view, Object position, double scale)
throws CyCommandException {
+
+ Color[] colorScale = null;
+
+ // Get our colors
+ String colorSpec = args.get(COLORS).toString();
+ if (colorSpec.equalsIgnoreCase(YELLOWCYAN)) {
+ colorScale = yellowCyan;
+ } else if (colorSpec.equalsIgnoreCase(REDGREEN)) {
+ colorScale = redGreen;
+ } else {
+ colorScale = new Color[3];
+ String [] colorArray = colorSpec.split(",");
+ List<Color> colors =
ValueUtils.parseUpDownColor(colorArray);
+ colorScale[0] = colors.get(0);
+ colorScale[2] = colors.get(1);
+ colorScale[1] = colors.get(2);
+ }
+ int separation = 0;
+ Object separationObj = args.get(SEPARATION);
+ if (separationObj instanceof String)
+ {
+ if (! separationObj.equals(""))
+ {
+ separation =
Integer.parseInt(separationObj.toString());
+ }
+ }
+
+ int nbrSlices = values.size();
+ List<CustomGraphic> cgList = new ArrayList<CustomGraphic>();
+
+ // We need to get our bounding box in order to scale our graphic
+ // properly
+ Rectangle2D bbox = ViewUtils.getNodeBoundingBox(node, view,
position, scale);
+ double height = bbox.getHeight();
+ double width = bbox.getWidth();
+
+ double x = bbox.getX();
+ double y = bbox.getY();
+
+ double yMid = y + (0.5 * height);
+
+ // System.out.println("Node bounding box = " + bbox);
+ // divide width into equal size segments
+ double slice = (width / values.size()) - (values.size() *
separation) + separation; // only have n-1 separators
+// System.out.println("slice = " + slice);
+
+
+ double min = 0.000001; // endure no division by zero
+ double max = -0.000001;
+ for (double i : values) {
+ min = Math.min(min, i);
+ max = Math.max(max, i);
+ }
+
+ // make the graph symmetrical around max and min, set to the
larger (maybe will be too influenced by outliers?)
+ if (Math.abs(max) > Math.abs(min))
+ {
+ min = -1.0 * max;
+ }
+ else
+ {
+ max = -1.0 * min;
+ }
+
+ Rectangle2D [] barArray = new Rectangle2D[values.size()];
+ double maxY = 0.0;
+ PaintFactory pf = new LinearGradientPaintFactory(x, y+height,
x, y, colorScale, dist);
+
+ for (int i = 0; i < values.size(); i++) {
+ double px1 = x + (i * slice);
+ double w = slice;
+ double val = values.get(i);
+ double py1 = y + (0.5 * height);
+ if (val > 0.0) // positive, work down to midpoint
+ {
+ py1 = py1 - ((0.5 * height) * (val / max));
+ }
+ else // negative, work down from midpoint
+ {
+ val = -val;
+ }
+
+ double h = (0.5 * height) * (val / max);
+
+ barArray[i] = new Rectangle2D.Double(px1, py1, w, h);
+ // System.out.println ("Got rectangle from: " + px1 +
"," + py1 + " of width " + w + " and height " + h);
+ maxY = Math.max(maxY, barArray[i].getMaxY());
+
+ CustomGraphic c = new CustomGraphic(barArray[i], pf);
+// System.out.println("added custome graphic for line from
" + drect.getP1() + " to " + .getP2());
+ cgList.add(c);
+ }
+
+ if (labels != null && labels.size() > 0) {
+ // Now, create the labels. We want to do this here so
we can adjust the label for the slice
+ for (int i = 0; i < values.size(); i++) {
+
+ // add labels
+ TextAlignment tAlign = TextAlignment.ALIGN_LEFT;
+
+ // Now, create the label. Put the label on the
outer edge of the circle.
+ Point2D labelPosition = new
Point2D.Double(barArray[i].getCenterX(), maxY);
+ // vals[1] =
ViewUtils.getLabelCustomGraphic(label, null, 0, 0, labelPosition, tAlign, view);
+ Shape textShape =
ViewUtils.getLabelShape(labels.get(i), null, 0, 0, view);
+
+ double maxHeight = barArray[i].getWidth();
+ textShape = ViewUtils.positionLabel(textShape,
labelPosition, tAlign, maxHeight, 0.0, 70.0);
+ if (textShape == null) continue;
+
+ // vals[1] = new CustomGraphic(textArea, new
DefaultPaintFactory(Color.BLACK));
+ CustomGraphic c1 = new
CustomGraphic(textShape, new DefaultPaintFactory(Color.BLACK));
+ cgList.add(c1);
+ }
+ }
+ return cgList;
+ }
+
+
+}
Added:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/LinearGradientPaintFactory.java
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/LinearGradientPaintFactory.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/LinearGradientPaintFactory.java
2011-02-26 02:20:31 UTC (rev 24242)
@@ -0,0 +1,55 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2010 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package nodeCharts.view;
+
+import java.awt.Color;
+import java.awt.Paint;
+import java.awt.LinearGradientPaint;
+import java.awt.geom.Rectangle2D;
+
+import cytoscape.render.stateful.PaintFactory;
+
+class LinearGradientPaintFactory implements PaintFactory {
+ private final LinearGradientPaint paint;
+
+ public LinearGradientPaintFactory(double startx, double starty, double
endx, double endy,
+ final Color[] colorArray, final float[]
stopArray) {
+ paint = new LinearGradientPaint((float)startx, (float)starty,
(float)endx, (float)endy,
+ stopArray, colorArray);
+ }
+
+ public Paint getPaint(final Rectangle2D bound) {
+ // System.out.println("MyPaintFactory returning: "+color);
+ return paint;
+ }
+}
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/resources/nodeCharts/plugin.props
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/resources/nodeCharts/plugin.props
2011-02-26 00:28:15 UTC (rev 24241)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/resources/nodeCharts/plugin.props
2011-02-26 02:20:31 UTC (rev 24242)
@@ -11,7 +11,7 @@
pluginDescription=Paint a chart on a node
# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
-pluginVersion=0.93
+pluginVersion=0.94
# Compatible Cytoscape version
cytoscapeVersion=2.8
@@ -29,6 +29,6 @@
projectURL=http://www.rbvi.ucsf.edu/Research/cytoscape/
# Date this plugin/plugin version was released
-releaseDate=December 21, 2010
+releaseDate=February 25, 2011
# -- The following properties should be set ONLY BY CORE PLUGINS -- #
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
