[Patchwork-commits] r42 - pkg/patchwork/R

[noreply at r-forge.r-project.org]

Author: sebastian_d
Date: 2011-12-08 10:59:09 +0100 (Thu, 08 Dec 2011)
New Revision: 42

Modified:
   pkg/patchwork/R/karyotype.r
   pkg/patchwork/R/karyotype_chroms.r
   pkg/patchwork/R/karyotype_chromsCN.r
   pkg/patchwork/R/patchwork.CNA.r
   pkg/patchwork/R/patchwork.alleledata.r
Log:
Did i just commit? cant remember :), lets do it again so i can test it on SSH



Modified: pkg/patchwork/R/karyotype.r
===================================================================
--- pkg/patchwork/R/karyotype.r	2011-12-07 16:47:12 UTC (rev 41)
+++ pkg/patchwork/R/karyotype.r	2011-12-08 09:59:09 UTC (rev 42)
@@ -1,4 +1,4 @@
-karyotype <- function(chr,start,end,int,ai,chroms,
+karyotype <- function(chr,start,end,int,ai,
 						name='',xlim=c(0,2.4),ylim=c(0.3,1)) 
 	{   
     png(paste(name,'.karyotype.png',sep=''),width=1300,height=1300)
@@ -9,10 +9,6 @@
     	
     	data(ideogram,package="patchworkData")
     	
-    	#substitute ideogram chr names with chroms-object chr names
-    	# so it will work independent of chr field name.
-    	#ideogram = merge(chroms,ideogram,all=F,by=1)
-    	
 		colors_p <- colorRampPalette(c("#6600FF","#9900CC"),space="rgb")
     	colors_q <- colorRampPalette(c("#CC0099","#CC0000"),space="rgb")
 

Modified: pkg/patchwork/R/karyotype_chroms.r
===================================================================
--- pkg/patchwork/R/karyotype_chroms.r	2011-12-07 16:47:12 UTC (rev 41)
+++ pkg/patchwork/R/karyotype_chroms.r	2011-12-08 09:59:09 UTC (rev 42)
@@ -1,4 +1,4 @@
-karyotype_chroms <- function(chr,start,end,int,ai,chroms,mchr,mpos,mval,
+karyotype_chroms <- function(chr,start,end,int,ai,mchr,mpos,mval,
 								schr,spos,sval,name='',xlim=c(0,2.4),ylim=c(0.3,1))  
 	{   
     
@@ -8,11 +8,6 @@
     
     data(ideogram,package="patchworkData")
     
-    #substitute ideogram chr names with chroms-object chr names
-    # so it will work independent of chr field name.
-    
-    #ideogram$chr = chroms
-    
     #create a color ramp palette to segue the color scheme for plot.
     
     colors_p <- colorRampPalette(c("#6600FF","#9900CC"),space="rgb")

Modified: pkg/patchwork/R/karyotype_chromsCN.r
===================================================================
--- pkg/patchwork/R/karyotype_chromsCN.r	2011-12-07 16:47:12 UTC (rev 41)
+++ pkg/patchwork/R/karyotype_chromsCN.r	2011-12-08 09:59:09 UTC (rev 42)
@@ -9,14 +9,6 @@
     
     data(ideogram,package="patchworkData")
     
-    #substitute ideogram chr names with chroms-object chr names
-    # so it will work independent of chr field name.
-    
-    #chroms = as.character(unique(schr))
-    #chroms = chroms[chroms != chroms[grep("M",chroms)]]
-    
-    #ideogram$chr = chroms
-    
     colors_p <- colorRampPalette(c("#6600FF","#9900CC"),space="rgb")
     colors_q <- colorRampPalette(c("#CC0099","#CC0000"),space="rgb")
 

Modified: pkg/patchwork/R/patchwork.CNA.r
===================================================================
--- pkg/patchwork/R/patchwork.CNA.r	2011-12-07 16:47:12 UTC (rev 41)
+++ pkg/patchwork/R/patchwork.CNA.r	2011-12-08 09:59:09 UTC (rev 42)
@@ -29,24 +29,9 @@
 	#either chr1...chr22,chrX,chrY or 1...22,X,Y
 	data(ideogram,package="patchworkData")
 	
-	if(grep("chr",as.character(alf$achr[1])) == 1)
-		{
-		chroms = as.character(unique(ideogram$chr))
-		}
-	else
-		{
-		alf$achr = as.character(alf$achr)
-		for(i in 1:22)
-			{
-			alf$achr[alf$achr == as.character(i)] = paste("chr",as.character(i),sep="")
-			}
-		i = "X"
-		alf$achr[alf$achr == as.character(i)] = paste("chr",as.character(i),sep="")
-		i = "Y"
-		alf$achr[alf$achr == as.character(i)] = paste("chr",as.character(i),sep="")
-		chroms = as.character(unique(ideogram$chr))
-		}
+	chroms = as.character(unique(ideogram$chr))	
 		
+		
 	#relic from using alf as chrom generator.
 	#chroms = chroms[chroms != chroms[grep("M",chroms)]]
 	
@@ -124,10 +109,10 @@
 	#Plot it
 	cat("Initiating Plotting \n")
 	karyotype(segs$chr,segs$start,segs$end,segs$median,segs$ai,
-			chroms,name=as.character(BamFile),
+			name=as.character(BamFile),
 			xlim=c(0,2.4),ylim=c(0.3,1))
 	karyotype_chroms(segs$chr,segs$start,segs$end,segs$median,segs$ai,
-			chroms,kbsegs$chr,kbsegs$pos,kbsegs$ratio,
+			kbsegs$chr,kbsegs$pos,kbsegs$ratio,
 			alf$achr,alf$apos,(1-alf$amin/alf$amax),
 			name=as.character(BamFile),xlim=c(0,2.4),
 			ylim=c(0.3,1))

Modified: pkg/patchwork/R/patchwork.alleledata.r
===================================================================
--- pkg/patchwork/R/patchwork.alleledata.r	2011-12-07 16:47:12 UTC (rev 41)
+++ pkg/patchwork/R/patchwork.alleledata.r	2011-12-08 09:59:09 UTC (rev 42)
@@ -32,5 +32,24 @@
 
 	alf=merge(alf,dbSnp[,c(1,3)], all=F, by=1:2)
 	
+	#Force compatability between naming of chromosomes to our chromosome names
+	#from ideogram file. chr1...chr22,chrX,chrY
+	data(ideogram,package="patchworkData")
+	alf = alf[-grep("M",alf$achr),]
+	alf$achr = as.character(alf$achr)
+	
+	x_x = strsplit(alf$achr[1],"chr")
+	if(length(x_x[[1]]) == 1)
+		{
+		for(i in 1:22)
+			{
+			alf$achr[alf$achr == as.character(i)] = paste("chr",as.character(i),sep="")
+			}
+		i = "X"
+		alf$achr[alf$achr == as.character(i)] = paste("chr",as.character(i),sep="")
+		i = "Y"
+		alf$achr[alf$achr == as.character(i)] = paste("chr",as.character(i),sep="")
+		}
+		
 	return(alf)
 	}