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Stairway_output_summary_plot2.java
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Stairway_output_summary_plot2.java
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/**
*
* Copyright (c) @author Xiaoming Liu, Ph.D.
* Associate Professor,
* USF Genomics,
* College of Public Health,
* University of South Florida at Tampa
*
* This source code is distributed under the Artistic License 2.0
*
* The license can be found at
* https://opensource.org/licenses/Artistic-2.0
*/
import de.erichseifert.gral.data.DataTable;
import de.erichseifert.gral.io.plots.*;
import de.erichseifert.gral.plots.XYPlot;
import de.erichseifert.gral.plots.axes.LogarithmicRenderer2D;
import de.erichseifert.gral.plots.lines.DefaultLineRenderer2D;
import de.erichseifert.gral.plots.lines.LineRenderer;
import de.erichseifert.gral.graphics.Insets2D;
import de.erichseifert.gral.graphics.Label;
import de.erichseifert.gral.plots.axes.Axis;
import de.erichseifert.gral.plots.axes.LinearRenderer2D;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Font;
import java.io.*;
import java.io.IOException;
import java.util.*;
public class Stairway_output_summary_plot2 {
public static void main(String[] args)throws Exception{
if(args.length!=1&&args.length!=2){
System.out.println("Usage: java Stairway_output_summary_plot2 blueprint_file <output_dir>");
System.exit(1);
}
String blueprint_file=args[0];
BufferedReader in=new BufferedReader(new FileReader(blueprint_file));
String project_dir="";
String title="";
String xrange="0,0";
String yrange="0,0";
double xspacing=2;
double yspacing=2;
int fontsize=14;
double mu=1.2e-8;
double year_per_generation=24;
double missing_rate=0;
int nseq=0;
double L=0;
while(in.ready()){
String line=in.readLine();
if(line.indexOf("#")!=-1)line=line.substring(0,line.indexOf("#"));//remove comments
StringTokenizer t=new StringTokenizer(line,":#");
int nt=t.countTokens();
if(nt!=2)continue;
String tmp=t.nextToken().trim();
if(tmp.equalsIgnoreCase("project_dir"))project_dir=t.nextToken().trim();
else if(tmp.equalsIgnoreCase("plot_title"))title=t.nextToken().trim();
else if(tmp.equalsIgnoreCase("nseq"))nseq=Integer.parseInt(t.nextToken().trim());
else if(tmp.equalsIgnoreCase("L"))L=Double.parseDouble(t.nextToken().trim());
else if(tmp.equalsIgnoreCase("xrange"))xrange=t.nextToken().trim();
else if(tmp.equalsIgnoreCase("yrange"))yrange=t.nextToken().trim();
else if(tmp.equalsIgnoreCase("xspacing"))xspacing=Integer.parseInt(t.nextToken().trim());
else if(tmp.equalsIgnoreCase("yspacing"))yspacing=Integer.parseInt(t.nextToken().trim());
else if(tmp.equalsIgnoreCase("fontsize"))fontsize=Integer.parseInt(t.nextToken().trim());
else if(tmp.equalsIgnoreCase("mu"))mu=Double.parseDouble(t.nextToken().trim());
else if(tmp.equalsIgnoreCase("year_per_generation"))year_per_generation=Double.parseDouble(t.nextToken().trim());
}
in.close();
String outfile =correctDirectory(project_dir)+title+".final.summary";
String sep=File.separator;
String dir=correctDirectory(project_dir+sep+"final");
if(args.length==2){
dir=correctDirectory(project_dir+sep+args[1]);
outfile =correctDirectory(project_dir)+title+"."+args[1]+".summary";
title=title+" "+args[1];
}
if(!confirm_dir(dir)) System.exit(1);
File folder = new File(dir);
File[] listOfFiles = folder.listFiles();
String[] infiles=folder.list();
ArrayList list=new ArrayList();
for(int ii=0;ii<infiles.length;ii++){
if(infiles[ii].endsWith(".addTheta"))list.add(infiles[ii]);
}
int n1=list.size();
infiles=(String[])list.toArray(new String[n1]);
double xmin=-1;
double xmax=-1;
double ymin=-1;
double ymax=-1;
if(!xrange.equals("0,0")){
StringTokenizer t=new StringTokenizer(xrange,", ");
xmin=Double.parseDouble(t.nextToken());
xmax=Double.parseDouble(t.nextToken());
}
if(!yrange.equals("0,0")){
StringTokenizer t=new StringTokenizer(yrange,", ");
ymin=Double.parseDouble(t.nextToken());
ymax=Double.parseDouble(t.nextToken());
}
PrintWriter out=new PrintWriter(new FileWriter(outfile),true);
int nrep=infiles.length;
System.out.println("nrep="+nrep);
double[][] allest=new double[nseq-1][nrep];
for(int ii=0;ii<nrep;ii++){
in=new BufferedReader(new FileReader(dir+infiles[ii]));
System.out.println(ii+"\t"+infiles[ii]);
String line=in.readLine();
double fitness=0;
while(line.indexOf("final model:")==-1){
line=in.readLine();
}
StringTokenizer t=new StringTokenizer(line,"\t");
t.nextToken();
fitness=Double.parseDouble(t.nextToken());
line=in.readLine();
t=new StringTokenizer(line);
int dim=t.countTokens();
int[][] group=new int[dim][];
for(int i=0;i<dim;i++){
String tmp=t.nextToken();
StringTokenizer t2=new StringTokenizer(tmp,",");
int nxi=t2.countTokens();
group[i]=new int[nxi];
for(int j=0;j<nxi;j++)group[i][j]=Integer.parseInt(t2.nextToken());
}
line=in.readLine();
t=new StringTokenizer(line);
for(int i=0;i<dim;i++){
double theta=Double.parseDouble(t.nextToken());
for(int j=0;j<group[i].length;j++) {
allest[group[i][j]-2][ii]=theta;
}
}
in.close();
}
int dim=nseq-1;
double[][] time2=new double[dim][nrep];//record estimated time for each replication
double[] time3=new double[dim*nrep];//record all time points
int count=0;
for(int j=0;j<nrep;j++) {
for(int i=0;i<dim;i++)time2[i][j]=allest[i][j]/L/(i+2)/(i+1);
time3[count]=time2[dim-1][j];
count++;
for(int i=dim-2;i>=0;i--) {
time2[i][j]=time2[i][j]+time2[i+1][j];//cummulative time
time3[count]=time2[i][j];
count++;
}
}
System.out.println("data finished dim="+dim);
DataTable median=new DataTable(Double.class,Double.class);
DataTable P125=new DataTable(Double.class,Double.class);
DataTable P875=new DataTable(Double.class,Double.class);
DataTable P025=new DataTable(Double.class,Double.class);
DataTable P975=new DataTable(Double.class,Double.class);
DataTable median2=new DataTable(Double.class,Double.class);
float[][] work=new float[dim*nrep][nrep];//record theta at each time points for each replication
for(int k=0;k<dim*nrep;k++)Arrays.fill(work[k],-1);
Arrays.sort(time3);
for(int j=0;j<nrep;j++){
//System.out.println(j);
int kbegin=0;
for(int i=dim-1;i>=0;i--){
for(int k=kbegin;k<dim*nrep;k++){
if(work[k][j]<0&&time2[i][j]>time3[k])work[k][j]=(float)allest[i][j];
else if(work[k][j]<0){
kbegin=k;
break;
}
}
}
}
out.println("mutation_per_site\tn_estimation\ttheta_per_site_median\ttheta_per_site_2.5%\ttheta_per_site_97.5%\tyear\tNe_median\tNe_2.5%\tNe_97.5%\tNe_12.5%\tNe_87.5%");
for(int k=0;k<=dim*nrep-1;k++){
Arrays.sort(work[k]);
int npos=0;
for(int i=0;i<nrep;i++){
if(work[k][i]>0)npos++;
}
if(npos<nrep*(1-missing_rate))break;
double[] tmp=new double[npos];
int pos=0;
int pos2=0;
int pos3=0;
for(int i=0;i<nrep;i++){
if(work[k][i]>0){
tmp[pos]=work[k][i];
pos++;
}
}
if(k==dim*nrep-1){
}
else{
if(k==0){
median.add((1e-100/mu*year_per_generation)/1000,(tmp[npos/2]/L/mu/4)/1000);
median2.add((1e-100/mu)/1000,(tmp[npos/2]/L/mu/4)/1000);
P025.add((1e-100/mu*year_per_generation)/1000,(tmp[(int)(npos*0.025)]/L/mu/4)/1000);
P975.add((1e-100/mu*year_per_generation)/1000,(tmp[(int)(npos*0.975)]/L/mu/4)/1000);
P125.add((1e-100/mu*year_per_generation)/1000,(tmp[(int)(npos*0.125)]/L/mu/4)/1000);
P875.add((1e-100/mu*year_per_generation)/1000,(tmp[(int)(npos*0.875)]/L/mu/4)/1000);
out.println((1e-100)+"\t"+npos+"\t"+(tmp[npos/2]/L)+"\t"+(tmp[(int)(npos*0.025)]/L)+"\t"+(tmp[(int)(npos*0.975)]/L)+"\t"+1e-100/mu*year_per_generation+"\t"+(tmp[npos/2]/L/mu/4)+"\t"+(tmp[(int)(npos*0.025)]/L/mu/4)+"\t"+(tmp[(int)(npos*0.975)]/L/mu/4)+"\t"+(tmp[(int)(npos*0.125)]/L/mu/4)+"\t"+(tmp[(int)(npos*0.875)]/L/mu/4));
}
median.add((time3[k]/mu*year_per_generation)/1000,(tmp[npos/2]/L/mu/4)/1000);
median.add((time3[k+1]/mu*year_per_generation)/1000,(tmp[npos/2]/L/mu/4)/1000);
median2.add((time3[k]/mu)/1000,(tmp[npos/2]/L/mu/4)/1000);
median2.add((time3[k+1]/mu)/1000,(tmp[npos/2]/L/mu/4)/1000);
P025.add((time3[k]/mu*year_per_generation)/1000,(tmp[(int)(npos*0.025)]/L/mu/4)/1000);
P025.add((time3[k+1]/mu*year_per_generation)/1000,(tmp[(int)(npos*0.025)]/L/mu/4)/1000);
P975.add((time3[k]/mu*year_per_generation)/1000,(tmp[(int)(npos*0.975)]/L/mu/4)/1000);
P975.add((time3[k+1]/mu*year_per_generation)/1000,(tmp[(int)(npos*0.975)]/L/mu/4)/1000);
P125.add((time3[k]/mu*year_per_generation)/1000,(tmp[(int)(npos*0.125)]/L/mu/4)/1000);
P125.add((time3[k+1]/mu*year_per_generation)/1000,(tmp[(int)(npos*0.125)]/L/mu/4)/1000);
P875.add((time3[k]/mu*year_per_generation)/1000,(tmp[(int)(npos*0.875)]/L/mu/4)/1000);
P875.add((time3[k+1]/mu*year_per_generation)/1000,(tmp[(int)(npos*0.875)]/L/mu/4)/1000);
out.println((time3[k])+"\t"+npos+"\t"+(tmp[npos/2]/L)+"\t"+(tmp[(int)(npos*0.025)]/L)+"\t"+(tmp[(int)(npos*0.975)]/L)+"\t"+time3[k]/mu*year_per_generation+"\t"+(tmp[npos/2]/L/mu/4)+"\t"+(tmp[(int)(npos*0.025)]/L/mu/4)+"\t"+(tmp[(int)(npos*0.975)]/L/mu/4)+"\t"+(tmp[(int)(npos*0.125)]/L/mu/4)+"\t"+(tmp[(int)(npos*0.875)]/L/mu/4));
out.println((time3[k+1])+"\t"+npos+"\t"+(tmp[npos/2]/L)+"\t"+(tmp[(int)(npos*0.025)]/L)+"\t"+(tmp[(int)(npos*0.975)]/L)+"\t"+time3[k+1]/mu*year_per_generation+"\t"+(tmp[npos/2]/L/mu/4)+"\t"+(tmp[(int)(npos*0.025)]/L/mu/4)+"\t"+(tmp[(int)(npos*0.975)]/L/mu/4)+"\t"+(tmp[(int)(npos*0.125)]/L/mu/4)+"\t"+(tmp[(int)(npos*0.875)]/L/mu/4));
}
}
out.close();
System.out.println("write finished");
work=new float[0][0];
time2=new double[0][0];
time3=new double[0];
allest=new double[0][0];
XYPlot plot = new XYPlot();
nrep=0;
plot.add(nrep,median,true);
plot.add(nrep+1,P125,true);
plot.add(nrep+2,P875,true);
plot.add(nrep+3,P025,true);
plot.add(nrep+4,P975,true);
plot.add(nrep+5,median2,true);
double insetsTop = 80.0,
insetsLeft = 90,
insetsBottom = 80.0,
insetsRight = 40.0;
plot.setInsets(new Insets2D.Double(insetsTop, insetsLeft, insetsBottom, insetsRight));
plot.getTitle().setText(title);
plot.getTitle().setFont(new Font("SansSerif", Font.BOLD, fontsize+4));
plot.getTitle().setAlignmentY(-50);
// Style the plot area
plot.getPlotArea().setBorderColor(new Color(0.0f, 0.3f, 1.0f));
plot.getPlotArea().setBorderStroke(new BasicStroke(2f));
Axis x2 = new Axis();
plot.setAxis(XYPlot.AXIS_X2, x2);
if(!xrange.equals("0,0")){
plot.getAxis(XYPlot.AXIS_X).setRange(xmin, xmax);
plot.getAxis(XYPlot.AXIS_X2).setRange(xmin/year_per_generation, xmax/year_per_generation);
}
else {
double xmin2=plot.getAxis(XYPlot.AXIS_X).getMin().doubleValue();
double xmax2=plot.getAxis(XYPlot.AXIS_X).getMax().doubleValue();
plot.getAxis(XYPlot.AXIS_X2).setMin(xmin2/year_per_generation);
plot.getAxis(XYPlot.AXIS_X2).setMax(xmax2/year_per_generation);
}
if(!yrange.equals("0,0"))plot.getAxis(XYPlot.AXIS_Y).setRange(ymin, ymax);
// Style data series
LineRenderer lines1 = new DefaultLineRenderer2D();
lines1.setColor(new Color(Color.BLACK.getRed(),Color.BLACK.getGreen(),Color.BLACK.getBlue(),255));
LineRenderer lines2 = new DefaultLineRenderer2D();
LineRenderer lines3 = new DefaultLineRenderer2D();
lines3.setColor(new Color(Color.CYAN.getRed(),Color.CYAN.getGreen(),Color.CYAN.getBlue(),85));
LineRenderer lines4 = new DefaultLineRenderer2D();
lines4.setColor(new Color(Color.DARK_GRAY.getRed(),Color.DARK_GRAY.getGreen(),Color.DARK_GRAY.getBlue(),125));
LineRenderer lines5 = new DefaultLineRenderer2D();
lines5.setColor(new Color(Color.GRAY.getRed(),Color.GRAY.getGreen(),Color.GRAY.getBlue(),85));
LineRenderer lines6 = new DefaultLineRenderer2D();
lines6.setColor(new Color(Color.GREEN.getRed(),Color.GREEN.getGreen(),Color.GREEN.getBlue(),85));
LineRenderer lines7 = new DefaultLineRenderer2D();
lines7.setColor(new Color(Color.LIGHT_GRAY.getRed(),Color.LIGHT_GRAY.getGreen(),Color.LIGHT_GRAY.getBlue(),85));
LineRenderer lines8 = new DefaultLineRenderer2D();
lines8.setColor(new Color(Color.MAGENTA.getRed(),Color.MAGENTA.getGreen(),Color.MAGENTA.getBlue(),255));
LineRenderer lines9 = new DefaultLineRenderer2D();
lines9.setColor(new Color(Color.ORANGE.getRed(),Color.ORANGE.getGreen(),Color.ORANGE.getBlue(),255));
LineRenderer lines10 = new DefaultLineRenderer2D();
lines10.setColor(new Color(Color.PINK.getRed(),Color.PINK.getGreen(),Color.PINK.getBlue(),85));
LineRenderer lines11 = new DefaultLineRenderer2D();
lines11.setColor(new Color(Color.RED.getRed(),Color.RED.getGreen(),Color.RED.getBlue(),255));
LineRenderer lines12 = new DefaultLineRenderer2D();
lines12.setColor(new Color( Color.YELLOW.getRed(), Color.YELLOW.getGreen(), Color.YELLOW.getBlue(),85));
LineRenderer lines112 = new DefaultLineRenderer2D();
lines112.setColor(new Color(Color.RED.getRed(),Color.RED.getGreen(),Color.RED.getBlue(),0));
plot.setLineRenderers(median, lines11);//red
plot.setPointRenderers(median, null);
plot.setLineRenderers(median2, lines112);//transparent
plot.setPointRenderers(median2, null);
plot.setLineRenderers(P125, lines4);//dark grey
plot.setPointRenderers(P125, null);
plot.setLineRenderers(P875, lines4);//dark grey
plot.setPointRenderers(P875, null);
plot.setLineRenderers(P025, lines5);//grey
plot.setPointRenderers(P025, null);
plot.setLineRenderers(P975, lines5);//grey
plot.setPointRenderers(P975, null);
// Style axes
plot.setAxisRenderer(XYPlot.AXIS_X, new LogarithmicRenderer2D());
plot.setAxisRenderer(XYPlot.AXIS_Y, new LogarithmicRenderer2D());
plot.setAxisRenderer(XYPlot.AXIS_X2, new LogarithmicRenderer2D());
plot.setMapping(median2, XYPlot.AXIS_X2, XYPlot.AXIS_Y);
Label Xlabel=new Label("Time (1k years ago)");
Xlabel.setFont(new Font("SansSerif", Font.BOLD, fontsize));
plot.getAxisRenderer(XYPlot.AXIS_X).setLabel(Xlabel);
Label Xlabel2=new Label("Time (1k generations ago)");
Xlabel2.setFont(new Font("SansSerif", Font.BOLD, fontsize));
plot.getAxisRenderer(XYPlot.AXIS_X2).setLabel(Xlabel2);
Label Ylabel=new Label("Ne (1k individual)");
Ylabel.setFont(new Font("SansSerif", Font.BOLD, fontsize));
Ylabel.setRotation(90.0);
Ylabel.setAlignmentX(0.3);
plot.getAxisRenderer(XYPlot.AXIS_Y).setLabel(Ylabel);
plot.getAxisRenderer(XYPlot.AXIS_X).setIntersection(-Double.MAX_VALUE);
plot.getAxisRenderer(XYPlot.AXIS_Y).setIntersection( -Double.MAX_VALUE);
plot.getAxisRenderer(XYPlot.AXIS_X2).setIntersection(Double.MAX_VALUE);
plot.getAxisRenderer(XYPlot.AXIS_X).setTickFont(new Font("SansSerif", Font.PLAIN, fontsize));
plot.getAxisRenderer(XYPlot.AXIS_Y).setTickFont(new Font("SansSerif", Font.PLAIN, fontsize));
plot.getAxisRenderer(XYPlot.AXIS_X2).setTickFont(new Font("SansSerif", Font.PLAIN, fontsize));
plot.getAxisRenderer(XYPlot.AXIS_X).setTicksAutoSpaced(false);
plot.getAxisRenderer(XYPlot.AXIS_X).setTickSpacing(xspacing);
plot.getAxisRenderer(XYPlot.AXIS_X2).setTickSpacing(xspacing);
plot.getAxisRenderer(XYPlot.AXIS_Y).setTicksAutoSpaced(false);
plot.getAxisRenderer(XYPlot.AXIS_Y).setTickSpacing(yspacing);
plot.getAxisRenderer(XYPlot.AXIS_X).setMinorTicksVisible(false);
plot.getAxisRenderer(XYPlot.AXIS_X2).setMinorTicksVisible(false);
plot.getAxisRenderer(XYPlot.AXIS_Y).setMinorTicksVisible(false);
if(true){
File file = new File(outfile+".png");
try {
DrawableWriter writer = DrawableWriterFactory.getInstance().get("image/png");
writer.write(plot, new FileOutputStream(file), 1500, 750);
} catch (IOException e) {
}
}
if(true){
File file2 = new File(outfile+".pdf");
try {
DrawableWriter writer = DrawableWriterFactory.getInstance().get("application/pdf");
writer.write(plot, new FileOutputStream(file2), 1500, 750);
} catch (IOException e) {
}
}
}
private static boolean confirm_dir(String dir){
File f = new File(dir);
if (!f.exists()){
System.out.println("Error: Directory: "+ dir + "does not exists");
return false;
}
else if(!f.isDirectory()){
System.out.println("Error: "+dir + "exists but is not a directory");
return false;
}
return true;
}
private static String correctDirectory(String dir){
StringTokenizer t=new StringTokenizer (dir,"/\\\"\'");
int nt=t.countTokens();
String sep=File.separator;
String dir2="";
for(int i=0;i<nt;i++)dir2+=t.nextToken()+sep;
if((dir.charAt(0)=='\"'||dir.charAt(0)=='\'')&&(dir.charAt(1)=='/'||dir.charAt(1)=='\\'))dir2=sep+dir2;
else if(dir.charAt(0)=='/'||dir.charAt(0)=='\\')dir2=sep+dir2;
return dir2;
}
}