package gem;
import gem.parser.TabDelimitedFileParser;
import gem.util.Binomial;
import gem.util.Kronometre;
import org.apache.batik.dom.GenericDOMImplementation;
import org.apache.batik.svggen.SVGGraphics2D;
import org.w3c.dom.DOMImplementation;
import org.w3c.dom.Document;
import javax.imageio.ImageIO;
import java.awt.*;
import java.awt.image.BufferedImage;
import java.io.*;
import java.util.*;
import java.util.List;
/**
* This class draws a plot of results, focusing a specific tissue in expO dataset, color-coding
* genes with their relative expression in that tissue.
*
* @author Ozgun Babur
*/
public class PlotForTissue2 implements Constants
{
public static final AlphaComposite text =
AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 1f);
public static final AlphaComposite box =
AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.5f);
public static final Font modfont = new Font("Verdana", Font.PLAIN, 24);
public static final Font labelfont = new Font("Verdana", Font.PLAIN, 12);
public static final Font idfont = new Font("Verdana", Font.PLAIN, 10);
static String factorName;
static boolean[] posCancer;
static boolean[] posNormal;
static Map<Gene, Double> gene2change = new HashMap<Gene, Double>();
static Map<Gene, Double> gene2rankCh = new HashMap<Gene, Double>();
static Map<String, Integer> tar2modNum = new HashMap<String, Integer>();
static Map<Gene, Integer> normalMap = new HashMap<Gene, Integer>();
static List<String> expnames;
static String comtype;
static int rowStart = 60;
static final double FOLLOW_PVAL_THR = 0.1;
//public static Font upFont;
//public static Font downFont;
public static void main(String[] args) throws Throwable
{
Kronometre kron = new Kronometre();
String file = "result/Result_fdr0.05_var1.0_AR_expo_prostate";
comtype = "33";
String plat = "GPL8300";
List<Triplet> trips = Triplet.readTripsAndAssociate(file + ".xls",
"resource/expop/expop_1.txt", "resource/expop/expop_2.txt", "resource/expop/expop_3.txt");
// List<Triplet> trips = Triplet.readTrips(file + ".xls");
Iterator<Triplet> iter = trips.iterator();
while (iter.hasNext())
{
Triplet t = iter.next();
if (t.fac_id.startsWith("M")) iter.remove();
}
System.out.println("trips.size() = " + trips.size());
// CrossPlatformMapper.associateAndClean(trips, "resource/expop/nikidata.txt");
// CrossPlatformMapper.associateWithGSE6919(trips, plat);
// trips = Triplet.selectModulator(trips, "SPDEF");
posCancer = CellTypeMatcher.getCancerProstateInExpop(comtype);
// posNormal = CellTypeMatcher.getCancerProstateInExpop(comtype + "_primary");
posNormal = CellTypeMatcher.getBenignProstateInExpop(comtype);
// posCancer = CrossPlatformMapper.getPosInGSE6919(plat, false);
// posNormal = CrossPlatformMapper.getPosInGSE6919(plat, true);
// CellTypeMatcher.randomizeInside(posCancer, posNormal);
boolean[] pos = CellTypeMatcher.takeOR(posNormal, posCancer);
CellTypeMatcher.replaceValsToRanks(trips, pos);
fillChangeMaps(trips);
keepMostChangedTargetIsoforms(trips);
fillMappingsAfter(trips);
generateSVG(trips, file + "_in" + comtype);
// generatePNG(trips, file);
// printScores(trips);
kron.stop();
kron.print();
}
private static void fillMappingsAfter(Collection<Triplet> trips)
{
for (Triplet t : trips)
{
double gamma = Difference.calcGamma(t);
String tarNm = t.getTSym() + (gamma > 0 ? "+" : "-");
if (!tar2modNum.containsKey(tarNm)) tar2modNum.put(tarNm, 0);
tar2modNum.put(tarNm, tar2modNum.get(tarNm) + 1);
}
}
private static void fillChangeMaps(Collection<Triplet> trips)
{
TabDelimitedFileParser parser =
new TabDelimitedFileParser("resource/expop/deviated-in-cancer-AR.txt");
Map<String, String> deviationMap = parser.getOneToOneMap("ID", "PresenceInNormal");
for (Triplet t : trips)
{
if (!gene2change.containsKey(t.M)) putToChangeMap(t.M);
if (!gene2change.containsKey(t.F)) putToChangeMap(t.F);
if (!gene2change.containsKey(t.T)) putToChangeMap(t.T);
if (!normalMap.containsKey(t.T))
{
double pres = .5;
if (deviationMap.containsKey(t.T.id))
{
pres = Double.parseDouble(deviationMap.get(t.T.id));
}
normalMap.put(t.T, pres > .8 ? 1 : pres < .2 ? -1 : 0);
}
}
expnames = CellTypeMatcher.readSampleNames("resource/expop/expop_expnames.txt");
}
// static Map<String, Double> remmap = new HashMap<String, Double>();
private static void putToChangeMap(Gene gene)
{
gene2change.put(gene, CellTypeMatcher.getChangeBetweenTissues(gene, posNormal, posCancer));
gene2rankCh.put(gene, CellTypeMatcher.getMeanChange(gene, posNormal, posCancer));
// double ch;
// if (remmap.containsKey(gene.geneid)) ch = remmap.get(gene.geneid);
// else
// {
// ch = Math.random() < .5 ? 0.2 : 0.8;
// remmap.put(gene.geneid, ch);
// }
// gene2change.put(gene, ch);
}
private static void keepMostChangedTargetIsoforms(List<Triplet> trips)
{
System.out.println("trips.size() = " + trips.size());
Map<String, Triplet> select = new HashMap<String, Triplet>();
Map<String, Double> max = new HashMap<String, Double>();
for (Triplet t : trips)
{
if (noChange(t.T)) continue;
// double ch = Math.abs(gene2change.get(t.T) - 0.5);
double ch = Math.abs(gene2rankCh.get(t.T));
String key = t.M.geneid + "-" + t.F.id + "-" + t.T.geneid + (ch>0?"+":"-");
if (!select.containsKey(key) || max.get(key) < ch)
{
select.put(key, t);
max.put(key, ch);
}
}
for (String key : new HashSet<String>(select.keySet()))
{
key = key.substring(0, key.length()-1);
if (select.containsKey(key + "+") && select.containsKey(key + "-"))
{
select.remove(key + "+");
select.remove(key + "-");
}
}
trips.clear();
trips.addAll(select.values());
System.out.println("trips.size() = " + trips.size());
}
public static String getExpLabel(int index)
{
String s = posNormal[index] ? "N" : posCancer[index] ? "C" : "?";
String name = expnames.get(index);
s += "-" + CellTypeMatcher.getExpClass(name) + "-" + name;
return s;
}
private static void saveGroupValues(Group group)
{
List<Gene> genes = new ArrayList<Gene>(group.getSize() + 1);
genes.add(group.getFirstMod());
for (List<Triplet> trips : group.cats.values())
{
for (Triplet t : trips)
{
genes.add(t.T);
}
}
try
{
String file = "result/group_vals/" + group.getName().replace("|", "-");
BufferedWriter writer = new BufferedWriter(new FileWriter(file + ".txt"));
writer.write("Genes/Exps");
for (int i = 0; i < posNormal.length; i++)
{
if (posNormal[i] || posCancer[i]) writer.write("\t" + getExpLabel(i));
}
for (Gene gene : genes)
{
if (!noChange(gene)) writeGeneValues(writer, gene);
}
writer.close();
// List<Integer> indexes = Hierarchical.getCancerSubtype(genes, posNormal, posCancer);
// writer = new BufferedWriter(new FileWriter(file + " - subtype.txt"));
//
// for (Integer index : indexes)
// {
// writer.write(index + "\n");
// }
//
// writer.close();
}
catch (IOException e)
{
e.printStackTrace();
}
}
private static void writeGeneValues(BufferedWriter writer, Gene gene)
throws IOException
{
writer.write("\n" + gene.getPrintable());
for (int i = 0; i < posNormal.length; i++)
{
if (posNormal[i] || posCancer[i]) writer.write("\t" + gene.value[i]);
}
}
public void paint(Graphics2D g2d, List<Group> modlist, Gene factor)
{
// printSignatureCommons(modlist);
Collections.sort(modlist);
int i = 0;
Group[][] page = new Group[(modlist.size()/5)+ (modlist.size()%5==0 ? 0 : 1)][5];
for (Group mod : modlist)
{
page[i/5][i%5]=mod;
i++;
}
for (int rowi = 0; rowi < page.length; rowi++)
{
Group[] row = page[rowi];
int top = 0;
int bottom = 0;
for (Group mod : row)
{
if (mod!=null)
{
top = Math.max(top, mod.getTop());
bottom = Math.max(bottom, mod.getBottom());
}
}
int rowCenter = rowStart + 20 * top + 12;
int rowbottom = rowCenter + 20 * bottom + 84;
setText(g2d);
g2d.setFont(modfont);
String facName = factor.getSymbol();
FontMetrics fm = g2d.getFontMetrics();
int width = fm.stringWidth(facName);
g2d.setPaint(getColor(
// factor.calcPresenceOnTissue(posCancer),
gene2change.get(factor),
UP_COLOR, DOWN_COLOR, NOTR_COLOR));
g2d.fillRect(18, rowCenter - 12, width+4, 24);
setText(g2d);
g2d.drawString(facName, 20, rowCenter + 10);
g2d.setFont(idfont);
String[] id = factor.id.split("\\|");
g2d.drawString (id[0], 20 + width + 6, rowCenter - 2);
g2d.drawString (id[1], 20 + width + 6, rowCenter + 12);
g2d.drawString("activates",60,rowCenter-20);
g2d.drawString("inhibits",60,rowCenter+30);
for (int col = 0; col < row.length; col++)
{
Group group = row[col];
if (group!=null)
{
drawGroup(g2d, group, 60 + 240 * col, rowStart, rowCenter, rowbottom);
System.out.println(group);
}
}
rowStart = rowbottom;
}
}
private void drawGroup(Graphics2D g2d, Group mod, int x,
int rowstart, int rowCenter, int rowbottom)
{
// if (mod.getFirstFac().id.startsWith("A"))
// saveGroupValues(mod);
mod.sortMembers();
boolean showIsoforms = mod.getName().contains("|");
g2d.setColor(Color.LIGHT_GRAY);
g2d.drawRect(x+54,rowstart-50,220,rowbottom-rowstart-20);
g2d.setFont(modfont);
String name = mod.getName();
if (showIsoforms) name = name.substring(0, name.indexOf("|"));
FontMetrics fm = g2d.getFontMetrics();
int width = fm.stringWidth(name);
int margin= ((240 - width) / 2) + (showIsoforms ? 14 : 54);
g2d.setComposite(text);
paintPresenceBox(g2d, mod.getChangeListOfMod(), x+margin, rowstart - 44, width, 30);
setText(g2d);
if (showIsoforms)
{
String[] nm = mod.getName().split("\\|");
assert nm.length == 3 : "name = " + mod.getName();
g2d.drawString (nm[0], x+margin, rowstart-20);
g2d.setFont(idfont);
g2d.drawString (nm[1], x+margin+width+6, rowstart-32);
g2d.drawString (nm[2], x+margin+width+6, rowstart-18);
}
else
{
g2d.drawString (name, x+margin, rowstart-20);
}
g2d.setFont(labelfont);
g2d.drawString("Enhances",x+66,rowstart);
g2d.drawString("Attenuates",x+134,rowstart);
g2d.drawString("Inverts",x+214,rowstart);
for (Cat cat : Cat.values())
{
List<Triplet> targets = mod.get(cat);
if (targets != null)
{
setBox(g2d, cat);
Rectangle bounds = cat.getBounds(mod.getHeight(cat) * 20, x, rowCenter);
g2d.fill(bounds);
setText(g2d);
int i=0;
for (Triplet t : targets)
{
i++;
// double ch = gene.calcPresenceOnTissue(posCancer);
double ch = gene2change.get(t.T);
g2d.setPaint(getColor(ch, UP_COLOR, DOWN_COLOR, NOTR_COLOR));
g2d.fillRect(bounds.x+1, bounds.y-20+i*20, 60, 20);
}
i=0;
for (Triplet t : targets)
{
i++;
// if (Difference.tissueSupportIsGreater(t))
if (isGoodTarget(t) || isBadTarget(t))
{
if (isGoodTarget(t))
{
g2d.setPaint(GOOD_TARGET_COLOR);
}
else
{
g2d.setPaint(BAD_TARGET_COLOR);
}
g2d.drawRect(bounds.x+1, bounds.y - 19 + (i * 20), 59, 18);
g2d.drawRect(bounds.x+2, bounds.y - 18 + (i * 20), 57, 16);
}
setText(g2d);
g2d.drawString(t.getTSym(), bounds.x+4, bounds.y-4+i*20);
}
}
}
}
private static boolean noChange(Gene g)
{
double dif = gene2change.get(g);
return dif > .4 && dif < .6;
}
private static boolean targetFollowing(Triplet t)
{
if (noChange(t.T)) return false;
double difT = gene2change.get(t.T) - .5;
double difM = gene2change.get(t.M) - .5;
double gamma = Difference.calcGamma(t);
return difT * difM * gamma > 0;
}
private static boolean targetConfirmsActivation(Triplet t)
{
if (noChange(t.T)) return false;
double difT = gene2change.get(t.T) - .5;
double gamma = Difference.calcGamma(t);
return difT * gamma > 0;
}
private static boolean isGoodTarget(Triplet t)
{
if (!targetFollowing(t)) return false;
double globalDifT = normalMap.get(t.T);
double difT = gene2change.get(t.T) - .5;
return globalDifT * difT < 0;
}
private static boolean isBadTarget(Triplet t)
{
if (!targetFollowing(t)) return false;
double globalDifT = normalMap.get(t.T);
double difT = gene2change.get(t.T) - .5;
return globalDifT * difT > 0;
}
private void setBox(Graphics2D g2d, Cat cat)
{
g2d.setPaint(Color.GRAY);
g2d.setComposite(box);
}
private void setText(Graphics2D g2d)
{
g2d.setPaint(Color.BLACK);
g2d.setComposite(text);
}
public static void generateSVG(List<Triplet> trips, String outFile) throws IOException
{
// Get a DOMImplementation.
DOMImplementation domImpl = GenericDOMImplementation.getDOMImplementation();
// Create an instance of org.w3c.dom.Document.
String svgNS = "http://www.w3.org/2000/svg";
Document document = domImpl.createDocument(svgNS, "svg", null);
// Create an instance of the SVG Generator.
SVGGraphics2D svgGenerator = new SVGGraphics2D(document);
PlotForTissue2 test = new PlotForTissue2();
Map<Gene, List<Triplet>> groupedTrips = groupToFactor(trips);
for (Gene factor : groupedTrips.keySet())
{
System.out.println("\nFactor = " + factor.getPrintable());
List<Triplet> tripGroup = groupedTrips.get(factor);
HashMap<String, Group> map = process(tripGroup);
System.out.println("mods before filtering = " + map.size());
filterMods(map);
System.out.println("mods after filtering = " + map.size());
if (!factor.id.startsWith("M"))
try{writeDownGroups(map.values(),
("result/group_vals/" + comtype + "-" + factor.id + ".txt").replace("|", "_"));
}catch (Throwable throwable){throwable.printStackTrace();}
if (!map.isEmpty())
{
test.paint(svgGenerator, new ArrayList<Group>(map.values()), factor);
}
}
// Finally, stream out SVG to the standard output using
// UTF-8 encoding.
boolean useCSS = true; // we want to use CSS style attributes
Writer out = new OutputStreamWriter(new FileOutputStream(outFile + ".svg"), "UTF-8");
svgGenerator.stream(out, useCSS);
}
public static void generatePNG(List<Triplet> trips, String outFile) throws IOException
{
PlotForTissue2 test = new PlotForTissue2();
Map<Gene, List<Triplet>> groupedTrips = groupToFactor(trips);
Map<Gene, List<Group>> groupsMap = new HashMap<Gene, List<Group>>();
for (Gene factor : groupedTrips.keySet())
{
if (factor.id.startsWith("M")) continue;
List<Triplet> tripGroup = groupedTrips.get(factor);
HashMap<String, Group> map = process(tripGroup);
System.out.println("mods before filtering: " + map.size());
filterMods(map);
System.out.println("mods after filtering: " + map.size());
if (!map.isEmpty())
{
groupsMap.put(factor, new ArrayList<Group>(map.values()));
}
}
List<Integer> heights = new ArrayList<Integer>();
for (Gene factor : groupsMap.keySet())
{
List<Group> groups = groupsMap.get(factor);
Collections.sort(groups);
for (int i = 0; i <= ((groups.size()-1) / 5); i++)
{
int up = 0;
int down = 0;
for (int j = i*5; j < Math.min((i*5) + 5, groups.size()); j++)
{
Group g = groups.get(j);
up = Math.max(up, g.getTop());
down = Math.max(down, g.getBottom());
}
heights.add(up + down);
}
}
int height = rowStart;
for (Integer h : heights)
{
height += (h * 20) + 96;
}
// Create a buffered image in which to draw
int width = 1310;
BufferedImage bufferedImage = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
// Create a graphics contents on the buffered image
Graphics2D g2d = bufferedImage.createGraphics();
g2d.setColor(Color.WHITE);
g2d.fillRect(0, 0, width, height);
for (Gene factor : groupsMap.keySet())
{
test.paint(g2d, groupsMap.get(factor), factor);
}
// Save as PNG
File file = new File(outFile + ".png");
ImageIO.write(bufferedImage, "png", file);
}
static void printScores(List<Triplet> trips) throws IOException
{
Map<Gene, List<Triplet>> groupedTrips = groupToFactor(trips);
for (Gene factor : groupedTrips.keySet())
{
List<Triplet> tripGroup = groupedTrips.get(factor);
HashMap<String, Group> map = process(tripGroup);
filterMods(map);
List<Group> grList = new ArrayList<Group>(map.values());
for (Group group : grList)
{
group.calcActivation();
}
Collections.sort(grList);
for (Group group : grList)
{
double difM = gene2change.get(
group.cats.values().iterator().next().iterator().next().M);
String changeM = difM > 0.5 ? "up" : "down";
System.out.println(factor.getPrintable() + "\t" + group.getName() + "\t" +
group.getSize() + "\t" + fmt.format(group.activScore) + "\t" + changeM);
}
}
}
private static HashMap<String, Group> process(List<Triplet> trips) throws IOException
{
HashMap<String, Group> model = new HashMap<String, Group>();
for (Triplet t : trips)
{
if (factorName == null)
{
factorName = t.getFSym();
}
String modul = t.M.getSymbol() + "|" + t.M.geneid + "|" + t.M.geneid;
if (!model.containsKey(modul)) model.put(modul, new Group(t.M));
Group mod = model.get(modul);
if (t.categ.startsWith("MoA")) continue;
Cat cat = Cat.valueOf(t.categ.replace(" ", "_"));
if (cat == null) continue;
if (mod.get(cat) == null) mod.put(cat, new ArrayList<Triplet>());
List<Triplet> tars = mod.get(cat);
tars.add(t);
}
return model;
}
private static void filterMods(HashMap<String, Group> map)
{
for (String key : new HashSet<String>(map.keySet()))
{
Group mod = map.get(key);
mod.calcActivation();
// if (mod.activScore > FOLLOW_PVAL_THR)
// {
// map.remove(key);
// }
}
}
private static Color getColor(double percent, Color c1, Color c0, Color c05)
{
if (percent < 0)
{
return ABSENT_COLOR;
}
if (percent > 0.5)
{
return getColor((percent - 0.5) * 2, c1, c05);
}
else
{
return getColor(percent * 2, c05, c0);
}
}
private static Color getColor(double percent, Color c1, Color c0)
{
assert percent >= 0 && percent <= 1 : "percent = " + percent;
return new Color((int) Math.round(c0.getRed() + ((c1.getRed() - c0.getRed()) * percent)),
(int) Math.round(c0.getGreen() + ((c1.getGreen() - c0.getGreen()) * percent)),
(int) Math.round(c0.getBlue() + ((c1.getBlue() - c0.getBlue()) * percent)));
}
private static void paintPresenceBox(Graphics2D g2d, List<Double> ratios,
int x, int y, int width, int height)
{
double range = width / (double) ratios.size();
for (int i = 0; i < ratios.size(); i++)
{
g2d.setPaint(getColor(ratios.get(i), UP_COLOR, DOWN_COLOR, NOTR_COLOR));
int startx = (int) Math.round(x + (i * range));
int stopx = (int) Math.round(x + ((i+1) * range));
g2d.fillRect(startx, y, stopx - startx, height);
}
}
private static Map<Gene, List<Triplet>> groupToFactor(List<Triplet> trips)
{
Map<Gene, List<Triplet>> map = new HashMap<Gene, List<Triplet>>();
for (Triplet t : trips)
{
if (!map.containsKey(t.F)) map.put(t.F, new ArrayList<Triplet>());
map.get(t.F).add(t);
}
return map;
}
static class Group implements Comparable
{
Gene mod;
private String name;
boolean following;
HashMap<Cat, List<Triplet>> cats = new HashMap<Cat, List<Triplet>>();
Double activScore;
public Group(Gene mod)
{
this.mod = mod;
name = mod.getSymbol();
}
public int compareTo(Object o)
{
Group g = (Group) o;
return g.getTop() + g.getBottom() - getTop() - getBottom();
// return ((Group) o).getSize()-this.getSize();
// return ((Group) o).score.compareTo(score);
}
public int getSize()
{
int i=0;
for (List<Triplet> trips : cats.values())
{
i+=trips==null?0:trips.size();
}
return i;
}
public Gene getFirstFac()
{
return cats.values().iterator().next().iterator().next().F;
}
public Gene getFirstMod()
{
return cats.values().iterator().next().iterator().next().M;
}
public int getTop()
{
return Math.max(getHeight(Cat.Enhances_Activation),
Math.max(getHeight(Cat.Attenuates_Activation),
getHeight(Cat.Inverts_Activation)));
}
public int getBottom()
{
return Math.max(getHeight(Cat.Enhances_Inhibition),
Math.max(getHeight(Cat.Attenuates_Inhibition),
getHeight(Cat.Inverts_Inhibition)));
}
public int getHeight(Cat cat)
{
return cats.get(cat)==null?0:cats.get(cat).size();
}
public String getName()
{
return name;
}
public List<Triplet> get(Cat cat)
{
return cats.get(cat);
}
public void put(Cat cat, List<Triplet> targets)
{
this.cats.put(cat, targets);
}
public List<Triplet> getTrips()
{
List<Triplet> trips = new ArrayList<Triplet>();
for (List<Triplet> list : cats.values())
{
trips.addAll(list);
}
return trips;
}
public List<Double> getChangeListOfMod()
{
List<Double> list = new ArrayList<Double>();
Set<Gene> geneSet = new HashSet<Gene>();
for (Cat cat : cats.keySet())
{
for (Triplet t : cats.get(cat))
{
if (!geneSet.contains(t.M))
{
// list.add(gene.calcPresenceOnTissue(cancer));
list.add(gene2change.get(t.M));
geneSet.add(t.M);
}
}
}
return list;
}
public void sortMembers()
{
for (List<Triplet> list : cats.values())
{
List<THolder> hl = new ArrayList<THolder>(list.size());
for (Triplet t : list)
{
hl.add(new THolder(t));
}
Collections.sort(hl);
list.clear();
for (THolder th : hl)
{
list.add(th.t);
}
}
}
public void calcActivation()
{
double activ = 0;
double total = 0;
for (Cat cat : cats.keySet())
{
List<Triplet> trips = cats.get(cat);
for (Triplet t : trips)
{
if (noChange(t.T)) continue;
double gamma = Difference.calcGamma(t);
String nm = t.getTSym() + (gamma > 0 ? "+" : "-");
activ += Math.signum(gamma) * gene2rankCh.get(t.T) / tar2modNum.get(nm);
// if (targetConfirmsActivation(t)) activ++;
// if (Math.random() < .5) good++;
total += 1D / tar2modNum.get(nm);
}
}
// double difM = gene2change.get(this.getFirstMod()) - .5;
// following = (activ - (total / 2D)) * difM > 0;
// if (total == 0) activScore = 0D;
// else
// {
// activScore = Binomial.getPval(activ, total);
// if (activScore == 0) activScore = 1E-10;
// activScore = Math.log(activScore);
// if (activ - (total / 2D) > 0) activScore *= -1;
// }
activScore = activ / total;
}
public String toString()
{
String s = name;
s += "\t";
boolean modUp = false;
boolean modDown = false;
for (Cat cat : cats.keySet())
{
for (Triplet t : cats.get(cat))
{
if (noChange(t.M)) continue;
if (gene2change.get(t.M) > .5) modUp = true;
if (gene2change.get(t.M) < .5) modDown = true;
}
}
s += modUp && modDown ? "U/D" : modUp ? "U" : modDown ? "D" : "-";
s += "\t" + fmt.format(activScore.doubleValue());
return s;
}
}
public static void writeDownGroups(Collection<Group> groups, String filename) throws Throwable
{
BufferedWriter writer = new BufferedWriter(new FileWriter(filename));
for (Group group : groups)
{
writer.write(group + "\n");
}
writer.close();
}
static class THolder implements Comparable
{
Triplet t;
String value;
THolder(Triplet t)
{
this.t = t;
value = Triplet.getGeneToSymbolMap().get(t.target) + t.tar_id;
}
public int compareTo(Object o)
{
return value.compareTo(((THolder)o).value);
}
}
enum Cat
{
Enhances_Activation(33, 137, 33, 1, 1),
Attenuates_Activation(144, 238, 144, 1, 2),
Inverts_Activation(253, 48, 48, 1, 3),
Enhances_Inhibition(106, 33, 137, 0, 1),
Attenuates_Inhibition(210, 143, 238, 0, 2),
Inverts_Inhibition(253, 207, 47, 0, 3);
private Color color;
private int v, h;
Cat(int r, int g, int b, int v, int h)
{
color = new Color(r, g, b);
this.v = v;
this.h = h;
}
public Color getColor()
{
return color;
}
public Rectangle getBounds(int height, int x, int y)
{
return new Rectangle(x + h * 68, y - v * (height + 8) + 4, 64, height);
}
}
protected static void printSignatureCommons(Collection<Group> groups)
{
for (Group g : groups)
{
System.out.print("\t" + g.name);
}
for (Group g1 : groups)
{
System.out.print("\n" + g1.name);
for (Group g2 : groups)
{
System.out.print("\t");
if (g1 != g2)
{
System.out.print(getCommonSignatureRatio(g1, g2, true));
}
}
}
System.out.println("");
}
protected static double getCommonSignatureRatio(Group g1, Group g2, boolean similar)
{
Map<String, Integer> map = new HashMap<String, Integer>();
List<Triplet> g1trips = g1.getTrips();
for (Triplet t : g1trips)
{
map.put(t.getTSym(), (int) Math.signum(Difference.calcGamma(t)));
}
int cnt = 0;
for (Triplet t : g2.getTrips())
{
if (map.containsKey(t.getTSym()))
{
if (similar)
if (((int) Math.signum(Difference.calcGamma(t))) == map.get(t.getTSym()))
{
cnt++;
}
else
if (((int) Math.signum(Difference.calcGamma(t))) != map.get(t.getTSym()))
{
cnt++;
}
}
}
return cnt / (double) g1trips.size();
}
static final Color UP_COLOR = new Color(255, 120, 100);
static final Color DOWN_COLOR = new Color(100, 150, 255);
static final Color NOTR_COLOR = new Color(255, 255, 255);
static final Color ABSENT_COLOR = new Color(255, 255, 200);
static final Color GOOD_TARGET_COLOR = new Color(255, 255, 0);
static final Color BAD_TARGET_COLOR = new Color(0, 0, 0);
}