package gem;
import org.w3c.dom.DOMImplementation;
import org.w3c.dom.Document;
import org.apache.batik.dom.GenericDOMImplementation;
import org.apache.batik.svggen.SVGGraphics2D;
import gem.util.Progress;
import java.awt.*;
import java.util.*;
import java.util.List;
import java.io.IOException;
import java.io.Writer;
import java.io.OutputStreamWriter;
import java.io.FileOutputStream;
/**
* 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 PlotForTissue
{
static boolean groupMod = true;
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, 12);
public static final Font targetfont = new Font("Verdana", Font.PLAIN, 8);
public static final Font labelfont = new Font("Verdana", Font.PLAIN, 6);
public static final Font idfont = new Font("Verdana", Font.PLAIN, 5);
static String factorName;
static boolean[] pos;
static int rowStart = 60;
//public static Font upFont;
//public static Font downFont;
public static void main(String[] args) throws Throwable
{
// String tissue = "Breast";
String file = "result/Big_all_fdr0.05_var1.0";
List<Triplet> trips = Triplet.readTripsAndAssociate(file + ".xls",
"resource/exp_big_1.txt", "resource/exp_big_2.txt", "resource/exp_big_3.txt", "resource/exp_big_4.txt");
// "resource/experiments_expO_1.txt", "resource/experiments_expO_2.txt");
// "resource/exp_Treg_1.exp", "resource/exp_Treg_2.exp", "resource/exp_Treg_3.exp");
// trips = Triplet.selectModulator(trips, "FABP1");
// trips = Triplet.selectTarget(trips, "LTF");
trips = Triplet.selectFactor(trips, "MYB", true);
// pos = CellTypeMatcher.getTissueHitArrayForExpO(tissue);
pos = CellTypeMatcher.getLeukemiaHitArrayForBigdata();
// System.out.println("Getting subtypes ...");
// boolean[][] subtypes = Subtype.getSubtypes(trips, pos, 2);
// for (boolean[] subtype : subtypes)
// {
// System.out.println("subtype : " + Subtype.count(subtype));
// }
// pos = subtypes[1];
CaseCounter.count(trips, pos);
// generateHistoplot(trips, pos, file + "_" + tissue + ".svg");
generateHistoplot(trips, pos, file + "_Leukemia.svg");
}
public void paint(Graphics2D g2d, java.util.List<Group> modlist, Gene factor)
{
Collections.sort(modlist);
boolean[] fp = factor.getPresentSubset(pos);
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 + 10 * top + 6;
int rowbottom = rowCenter + 10 * bottom + 42;
setText(g2d);
g2d.setFont(modfont);
String facName = Triplet.getGeneToSymbolMap().get(factor.geneid);
FontMetrics fm = g2d.getFontMetrics();
int width = fm.stringWidth(facName);
g2d.setPaint(getColor(factor.calcPresenceOnTissue(pos),
UP_COLOR, DOWN_COLOR, NOTR_COLOR));
g2d.fillRect(9, rowCenter - 6, width+2, 12);
setText(g2d);
g2d.drawString(facName, 10, rowCenter + 5);
g2d.setFont(idfont);
String[] id = factor.id.split("\\|");
g2d.drawString (id[0], 10 + width + 3, rowCenter - 1);
g2d.drawString (id[1], 10 + width + 3, rowCenter + 6);
g2d.drawString("activates",30,rowCenter-10);
g2d.setFont(labelfont);
g2d.drawString("inhibits",30,rowCenter+15);
for (int col = 0; col < row.length; col++)
{
Group mod = row[col];
if (mod!=null)
{
drawGroup(g2d, mod, 50 + 120 * col, rowStart, rowCenter, rowbottom, fp);
}
}
rowStart = rowbottom;
}
}
private void drawGroup(Graphics2D g2d, Group mod, int x,
int rowstart, int rowCenter, int rowbottom, boolean[] fp)
{
mod.sortMembers();
boolean showIsoforms = mod.getName().contains("|");
g2d.setColor(Color.LIGHT_GRAY);
g2d.drawRect(x+27,rowstart-25,110,rowbottom-rowstart-10);
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= ((120 - width) / 2) + (showIsoforms ? 7 : 27);
g2d.setComposite(text);
paintPresenceBox(g2d,
groupMod ? mod.getPresenceListOfMod(fp) : mod.getPresenceListOfTar(fp),
x+margin, rowstart - 22, width, 15);
setText(g2d);
if (showIsoforms)
{
String[] nm = mod.getName().split("\\|");
assert nm.length == 3 : "name = " + mod.getName();
g2d.drawString (nm[0], x+margin, rowstart-10);
g2d.setFont(idfont);
g2d.drawString (nm[1], x+margin+width+3, rowstart-16);
g2d.drawString (nm[2], x+margin+width+3, rowstart-9);
}
else
{
g2d.drawString (name, x+margin, rowstart-10);
}
g2d.setFont(labelfont);
g2d.drawString("Enhances",x+33,rowstart);
g2d.drawString("Attenuates",x+67,rowstart);
g2d.drawString("Inverts",x+107,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) * 10, x, rowCenter);
g2d.fill(bounds);
setText(g2d);
int i=0;
for (Triplet t : targets)
{
i++;
g2d.setPaint(getColor(
groupMod ? t.T.calcPresenceOnTissue(fp) : t.M.calcPresenceOnTissue(fp),
UP_COLOR, DOWN_COLOR, NOTR_COLOR));
g2d.fillRect(bounds.x+1, bounds.y-10+i*10, 30, 10);
}
setText(g2d);
i=0;
for (Triplet t : targets)
{
i++;
// if (Triplet.getGeneToSymbolMap().get(t.target).equals("TMPO"))
// {
// System.out.print("");
// }
if (TissueInterpreter.isModAffectable(t))
{
g2d.drawRect(bounds.x+1, bounds.y-10+i*10, 30, 10);
}
g2d.drawString(groupMod ? t.getTSym() : t.getMSym(),
bounds.x+2, bounds.y-2+i*10);
}
}
}
}
private void setBox(Graphics2D g2d, Cat cat)
{
// g2d.setPaint(cat.getColor());
g2d.setPaint(Color.GRAY);
g2d.setComposite(box);
}
private void setText(Graphics2D g2d)
{
g2d.setPaint(Color.BLACK);
g2d.setComposite(text);
}
public static void generateHistoplot(java.util.List<Triplet> trips, boolean[] pos, String outFile) throws IOException
{
PlotForTissue.pos = pos;
// 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);
PlotForTissue test = new PlotForTissue();
Map<Gene, List<Triplet>> groupedTrips = groupToFactor(trips);
for (Gene factor : groupedTrips.keySet())
{
// Triplet.keepMostSignif(trips);
List<Triplet> tripGroup = groupedTrips.get(factor);
HashMap<String, Group> map = process(tripGroup);
filterMods(map);
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), "UTF-8");
svgGenerator.stream(out, useCSS);
}
private static HashMap<String, Group> process(java.util.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 = groupMod ? t.getMSym() : t.getTSym();
modul += "|" + (groupMod ? t.mod_id : t.tar_id);
if (!model.containsKey(modul)) model.put(modul, new Group(modul, pos));
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);
if (mod.getSize() < 1)
{
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, java.util.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
{
private String name;
HashMap<Cat, List<Triplet>> cats = new HashMap<Cat, List<Triplet>>();
boolean[] pos;
public Group(String modName, boolean[] pos)
{
assert modName != null;
this.name=modName;
this.pos = pos;
}
public int compareTo(Object o)
{
return ((Group) o).getSize()-this.getSize();
}
public int getSize()
{
int i=0;
for (List<Triplet> trips : cats.values())
{
i+=trips==null?0:trips.size();
}
return i;
}
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 int getModStatusInTissue()
{
boolean up = false;
boolean down = false;
for (Cat cat : cats.keySet())
{
for (Triplet t : cats.get(cat))
{
if (t.M.calcPresenceOnTissue(pos) > 0.5) up = true;
else down = true;
}
}
if (up && down) return 0;
if (up) return 1;
else return -1;
}
public java.util.List<Double> getPresenceListOfMod(boolean[] pos)
{
java.util.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(t.M.calcPresenceOnTissue(pos));
geneSet.add(t.M);
}
}
}
return list;
}
public java.util.List<Double> getPresenceListOfTar(boolean[] pos)
{
java.util.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.T))
{
list.add(t.T.calcPresenceOnTissue(pos));
geneSet.add(t.T);
}
}
}
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);
}
}
}
}
static class THolder implements Comparable
{
Triplet t;
String value;
THolder(Triplet t)
{
this.t = t;
value = Triplet.getGeneToSymbolMap().get(groupMod ? t.target : t.modulator) +
(groupMod ? t.tar_id : t.mod_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 * 34, y - v * (height + 4) + 2, 32, height);
}
}
static final Color UP_COLOR = new Color(255, 110, 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);
}