[Patchwork-commits] r105 - pkg/patchworkCG/R

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

Author: sebastian_d
Date: 2012-03-01 10:23:17 +0100 (Thu, 01 Mar 2012)
New Revision: 105

Modified:
   pkg/patchworkCG/R/CG_KaChCN.r
   pkg/patchworkCG/R/patchwork.CG.r
   pkg/patchworkCG/R/patchwork.CGCNV.r
Log:
fixed one of the plotting functions

Modified: pkg/patchworkCG/R/CG_KaChCN.r
===================================================================
--- pkg/patchworkCG/R/CG_KaChCN.r	2012-02-29 10:29:39 UTC (rev 104)
+++ pkg/patchworkCG/R/CG_KaChCN.r	2012-03-01 09:23:17 UTC (rev 105)
@@ -45,6 +45,7 @@
             #Create a list of colors length of chromosome.
             #Assign color by middle of segment. (pos as an int).
 
+            ix <- chr==this$chr
             ix_p = ix & (pos < this$start)
             ix_q = ix & (pos > this$end)
             col <- rep('#B0B0B070',length(chr))

Modified: pkg/patchworkCG/R/patchwork.CG.r
===================================================================
--- pkg/patchworkCG/R/patchwork.CG.r	2012-02-29 10:29:39 UTC (rev 104)
+++ pkg/patchworkCG/R/patchwork.CG.r	2012-03-01 09:23:17 UTC (rev 105)
@@ -1,4 +1,4 @@
-patchwork.CG <- function(path=NULL,name='CG_sample_',manual_file_input = FALSE,masterVarBeta=NULL,somaticCnvSegments=NULL,depthOfCoverage=NULL)
+patchwork.CG <- function(path=NULL,name='CG_sample',manual_file_input = FALSE,masterVarBeta=NULL,somaticCnvSegments=NULL,depthOfCoverage=NULL)
 	{
 	
 	#------------------------------------------------#
@@ -274,7 +274,9 @@
 	#------------------------------------------------#
 	# Plot
 	#------------------------------------------------#
-	#patchwork.CGCNV(cn2=0.75,delta=0.36,het=0.5,hom=0.97) #HCC1187
+	#patchwork.CGCNV(cn2=0.75,delta=0.36,het=0.26,hom=0.97) #HCC1187 100%
+	#patchwork.CGCNV(cn2=0.8,delta=0.29,het=0.21,hom=0.8) #HCC1187 70%
+	#patchwork.CGCNV(cn2=,delta=,het=,hom=) #HCC2218 100%
 	
 	cat("Initiating Plotting \n")
 	CG_karyotype(segm$chr,segm$start,segm$end,segm$ratio,segm$ai,

Modified: pkg/patchworkCG/R/patchwork.CGCNV.r
===================================================================
--- pkg/patchworkCG/R/patchwork.CGCNV.r	2012-02-29 10:29:39 UTC (rev 104)
+++ pkg/patchworkCG/R/patchwork.CGCNV.r	2012-03-01 09:23:17 UTC (rev 105)
@@ -1,4 +1,4 @@
-patchwork.CGCNV = function(cn2,delta,het,hom,maxCn=8,ceiling=1,name="CGCNV_",CGfile=NULL,forcedelta=F)
+patchwork.CGCNV = function(cn2,delta,het,hom,maxCn=8,ceiling=1,name="CGCNV",CGfile=NULL,forcedelta=F)
 	{
 	data(ideogram,package="patchworkCG")