changeset 44:fa8dc7f00b43 draft

Uploaded

--- a/ideas_genome_tracks.R	Thu Dec 14 09:58:27 2017 -0500
+++ b/ideas_genome_tracks.R	Thu Dec 14 09:58:35 2017 -0500
@@ -2,6 +2,7 @@
 
 suppressPackageStartupMessages(library("data.table"))
 suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("viridislite"))
 
 option_list <- list(
             make_option(c("--build"), action="store", dest="build", help="Genome build"),
@@ -129,19 +130,19 @@
 }
 
 get_rgb<-function(statemean, markcolor=NULL)
-{    
+{
     if(length(markcolor) == 0) {
         markcolor = rep("",dim(statemean)[2]);
         markcolor[order(apply(statemean,2,sd),decreasing=T)]=hsv((1:dim(statemean)[2]-1)/dim(statemean)[2],1,1)
         markcolor = t(col2rgb(markcolor));
     }
-    
+
     rg = apply(statemean, 1, range);
     mm = NULL;
     for(i in 1:dim(statemean)[1]) {
         mm = rbind(mm, (statemean[i,]-rg[1, i]+1e-10)/(rg[2, i]-rg[1, i]+1e-10));
     }
-    mm = mm^5; 
+    mm = mm^5;
     if (dim(mm)[2]>1) {
         mm = mm / (apply(mm, 1, sum)+1e-10);
     }
@@ -155,7 +156,7 @@
     h = apply(h, 1, function(x){hsv(x[1], x[2], x[3])});
     rt = cbind(rt, h);
     return(rt);
-    
+
     h = t(apply(mycol, 1, function(x){rgb2hsv(x[1], x[2], x[3])}));
     h[,2] = h[,2]*s;
     h = apply(h, 1, function(x){hsv(x[1], x[2], x[3])});
@@ -181,7 +182,7 @@
     axis(1,at=1:p-0.5,labels=colnames(m),las=2);
     axis(4,at=1:l-0.5,labels=rownames(m),las=2);
     rect(rep(1:p-1,l),rep(1:l-1,each=p),rep(1:p,l),rep(1:l,each=p),col=round((t(m)-rg[1])/(rg[2]-rg[1])*100));
-    markcolor = t(col2rgb(terrain.colors(ceiling(p))[1:p]));    
+    markcolor = t(col2rgb(terrain.colors(ceiling(p))[1:p]));
     for(i in 1:length(marks)) {
         if (regexpr("h3k4me3",tolower(marks[i]))>0) {
             markcolor[i,]=c(255,0,0);