[Patchwork-commits] r74 - in pkg: patchwork/R patchworkCG/R patchworkCG/man patchworkData
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 25 14:53:13 CET 2012
Author: sebastian_d
Date: 2012-01-25 14:53:13 +0100 (Wed, 25 Jan 2012)
New Revision: 74
Added:
pkg/patchwork/R/zzz.R
Modified:
pkg/patchwork/R/patchwork.CNA.r
pkg/patchworkCG/R/CG_KaCh.r
pkg/patchworkCG/R/CG_KaChCN.r
pkg/patchworkCG/R/CG_Ka_check.r
pkg/patchworkCG/R/CG_karyotype.r
pkg/patchworkCG/R/patchwork.CG.r
pkg/patchworkCG/R/patchwork.CGCNV.r
pkg/patchworkCG/man/CG_KaCh.Rd
pkg/patchworkCG/man/CG_KaChCN.Rd
pkg/patchworkCG/man/patchwork.CG.Rd
pkg/patchworkCG/man/patchwork.CGCNV.Rd
pkg/patchworkData/DESCRIPTION
Log:
Changed input to include depthOfCoverage file for better values in plotting. Changed many parameters in plotting regarding Segment size to plot size in whole genome view. Added line for segments in AI part of plotting.
Modified: pkg/patchwork/R/patchwork.CNA.r
===================================================================
--- pkg/patchwork/R/patchwork.CNA.r 2012-01-24 12:35:46 UTC (rev 73)
+++ pkg/patchwork/R/patchwork.CNA.r 2012-01-25 13:53:13 UTC (rev 74)
@@ -57,8 +57,6 @@
#after this, no further normalization was done on reference sequences.
#Apply normal reference to data.
- #If solid is true it will runa gainst a SOLiD reference, else
- # it will go with Illumina.
if(length(data) < 9)
{
cat("Initiating Application of Reference \n")
Added: pkg/patchwork/R/zzz.R
===================================================================
--- pkg/patchwork/R/zzz.R (rev 0)
+++ pkg/patchwork/R/zzz.R 2012-01-25 13:53:13 UTC (rev 74)
@@ -0,0 +1,7 @@
+.onLoad <- function(...){
+ packageStartupMessage(
+ "Welcome to patchwork for CompleteGenomics data! \n
+ cite us! \n
+ How to run this \n"
+ )
+ }
\ No newline at end of file
Modified: pkg/patchworkCG/R/CG_KaCh.r
===================================================================
--- pkg/patchworkCG/R/CG_KaCh.r 2012-01-24 12:35:46 UTC (rev 73)
+++ pkg/patchworkCG/R/CG_KaCh.r 2012-01-25 13:53:13 UTC (rev 74)
@@ -1,5 +1,5 @@
CG_KaCh <- function(chr,start,end,int,ai,mchr,mpos,mval,
- sval,name='',xlim=c(0,2.4),ylim=c(0.3,1))
+ sval,schr,spos,name='',xlim=c(0,2.4),ylim=c(0.3,1))
{
#packagepath = system.file(package="patchwork")
@@ -24,9 +24,11 @@
length=end-start
size=rep(1,length(chr))
- size[length>2000000]=2
- size[length>5000000]=3
- size[length>10000000]=4
+ size[length>1000000]=2
+ size[length>3000000]=3
+ size[length>5000000]=4
+ size[length>10000000]=5
+ size[length>20000000]=6
for (c in 1:24)
{
@@ -91,8 +93,8 @@
lwd=4,)
par(new=F)
- six <- mchr==as.character(this$chr)
- plot(mpos[six],sval[six],
+ six <- schr==as.character(this$chr)
+ plot(spos[six],sval[six],
pch=16,
cex=2,
cex.lab=3,
@@ -107,6 +109,15 @@
xaxt="n")
axis(1,cex.axis=2)
axis(2,cex.axis=2)
+
+ segments(x0=start[ix],x1=end[ix],
+ y0=ai[ix],y1=ai[ix],
+ col=col,
+ lwd=4,)
+
dev.off()
}
- }
\ No newline at end of file
+ }
+#library(patchworkCG)
+#load("CG.Rdata")
+#name = "C2_"
\ No newline at end of file
Modified: pkg/patchworkCG/R/CG_KaChCN.r
===================================================================
--- pkg/patchworkCG/R/CG_KaChCN.r 2012-01-24 12:35:46 UTC (rev 73)
+++ pkg/patchworkCG/R/CG_KaChCN.r 2012-01-25 13:53:13 UTC (rev 74)
@@ -1,6 +1,5 @@
CG_KaChCN <- function(chr,start,end,int,ai,Cn,mCn,mchr,mpos,mval,
- sval,name='',xlim=c(0,2.4),ylim=c(0,1),
- maxCn=8)
+ sval,schr,spos,name='',xlim=c(0,2.4),ylim=c(0,1),maxCn=8)
{
#packagepath = system.file(package="patchwork")
@@ -25,9 +24,11 @@
length=end-start
size=rep(1,length(chr))
- size[length>2000000]=2
- size[length>5000000]=3
- size[length>10000000]=4
+ size[length>1000000]=2
+ size[length>3000000]=3
+ size[length>5000000]=4
+ size[length>10000000]=5
+ size[length>20000000]=6
for (c in 1:24)
{
@@ -112,9 +113,9 @@
lwd=4,)
par(new=F)
- six <- as.character(mchr)==this$chr
+ six <- as.character(schr)==this$chr
- plot(mpos[six],sval[six],
+ plot(spos[six],sval[six],
pch=16,
cex=2,
cex.lab=3,
Modified: pkg/patchworkCG/R/CG_Ka_check.r
===================================================================
--- pkg/patchworkCG/R/CG_Ka_check.r 2012-01-24 12:35:46 UTC (rev 73)
+++ pkg/patchworkCG/R/CG_Ka_check.r 2012-01-25 13:53:13 UTC (rev 74)
@@ -21,10 +21,12 @@
length=end-start
labels=paste(Cn,mCn,sep='m')
- size=rep(1,length(chr))
- size[length>2000000]=2
- size[length>5000000]=3
- size[length>10000000]=4
+ size=rep(1,length(chr))
+ size[length>1000000]=2
+ size[length>3000000]=3
+ size[length>5000000]=4
+ size[length>10000000]=5
+ size[length>20000000]=6
## The variants present in this data
variants <- unique(labels)
Modified: pkg/patchworkCG/R/CG_karyotype.r
===================================================================
--- pkg/patchworkCG/R/CG_karyotype.r 2012-01-24 12:35:46 UTC (rev 73)
+++ pkg/patchworkCG/R/CG_karyotype.r 2012-01-25 13:53:13 UTC (rev 74)
@@ -23,10 +23,12 @@
pos <- (start+end)/2
length=end-start
- size=rep(0.5,length(chr))
- size[length>2000000]=1
- size[length>5000000]=2
- size[length>10000000]=3
+ size=rep(0.5,length(chr))
+ size[length>1000000]=1
+ size[length>3000000]=2
+ size[length>5000000]=3
+ size[length>10000000]=4
+ size[length>20000000]=5
for (c in 1:24)
Modified: pkg/patchworkCG/R/patchwork.CG.r
===================================================================
--- pkg/patchworkCG/R/patchwork.CG.r 2012-01-24 12:35:46 UTC (rev 73)
+++ pkg/patchworkCG/R/patchwork.CG.r 2012-01-25 13:53:13 UTC (rev 74)
@@ -1,4 +1,4 @@
-patchwork.CG <- function(path,name='CG_sample_',manual_file_input = FALSE,masterVarBeta=NULL,somaticCnvSegments=NULL)
+patchwork.CG <- function(path,name='CG_sample_',manual_file_input = FALSE,masterVarBeta=NULL,somaticCnvSegments=NULL,depthOfCoverage=NULL)
{
#------------------------------------------------#
@@ -15,51 +15,129 @@
cat("\n","ex: ~/user/documents/projekt/somaticCnvSegmentsNondiploidBeta-123-456-ASM-T1-N1.tsv")
cat("\n","Enter complete path AND filename to your somaticCnvSegmentsNondiploidBeta file:","\n")
sm = scan(n=1,what=character())
+ cat("\n","ex: ~/user/documents/projekt/depthOfCoverage_100000-123-456-ASM-T1.tsv")
+ cat("\n","Enter complete path AND filename to your depthOfCoverage file:","\n")
+ dc = scan(n=1,what=character())
+ skip_mv = scan(file=mv,n=1,what=character(),quiet=T)
+ i = 1
+ j = grep(">locus",skip_mv)
+ while(length(j) != 1)
+ {
+ skip_mv = scan(file=mv,n=1,skip=i,what=character(),quiet=T)
+ j = grep(">locus",skip_mv)
+ i = i + 1
+ }
+ skip_mv = i + 1
+
+ skip_sm = scan(file=sm,n=1,what=character(),quiet=T)
+ i = 1
+ j = grep(">chr",skip_sm)
+ while(length(j) != 1)
+ {
+ skip_sm = scan(file=sm,n=1,skip=i,what=character(),quiet=T)
+ j = grep(">chr",skip_sm)
+ i = i + 1
+ }
+ skip_sm = i + 1
+
+ skip_dc = scan(file=dc,n=1,what=character(),quiet=T)
+ i = 1
+ j = grep(">chr",skip_dc)
+ while(length(j) != 1)
+ {
+ skip_sm = scan(file=dc,n=1,skip=i,what=character(),quiet=T)
+ j = grep(">chr",skip_dc)
+ i = i + 1
+ }
+ skip_dc = i + 1
+
cat("\n","Reading files","\n")
#Read masterVarBeta
- mastervar = read.table(mv, sep="\t",skip=21,
+ mastervar = read.table(mv, sep="\t",skip=skip_mv,
colClasses=c("NULL","NULL","character","integer","integer",
"NULL","character",rep("NULL",16),"numeric","numeric",
rep("NULL",17),"integer","integer",rep("NULL",5)))
#Read somaticCnvSegmentsNondiploidBeta
- segm = read.table(sm,sep="\t",skip=21,
+ segm = read.table(sm,sep="\t",skip=skip_sm,
colClasses=c("character","integer","integer","numeric","numeric",
rep("NULL",7)))
- #save(segm,mastervar,file="QA.Rdata")
+ #Read depthOfCoverage
+ depcov = read.table(dc,sep="\t",skip=skip_dc,
+ colClasses=c("character","integer","integer",rep("NULL",3),"numeric"))
}
- else if(length(masterVarBeta) == 1 & length(somaticCnvSegments) == 1)
+ else if(length(masterVarBeta) == 1 & length(somaticCnvSegments) == 1 & length(depthOfCoverage) == 1)
{
mv_ = strsplit(masterVarBeta,"/")
sm_ = strsplit(somaticCnvSegments,"/")
+ dc_ = strsplit(depthOfCoverage,"/")
mv = grep("masterVar",mv_[[1]],value=T)
sm = grep("somaticCnv",sm_[[1]],value=T)
+ dc = grep("depthOfCoverage",dc_[[1]],value=T)
- cat("\n","Reading files:",mv," and ",sm,"\n")
+ skip_mv = scan(file=masterVarBeta,n=1,what=character(),quiet=T)
+ i = 1
+ j = grep(">locus",skip_mv)
+ while(length(j) != 1)
+ {
+ skip_mv = scan(file=masterVarBeta,n=1,skip=i,what=character(),quiet=T)
+ j = grep(">locus",skip_mv)
+ i = i + 1
+ }
+ skip_mv = i + 1
+
+ skip_sm = scan(file=somaticCnvSegments,n=1,what=character(),quiet=T)
+ i = 1
+ j = grep(">chr",skip_sm)
+ while(length(j) != 1)
+ {
+ skip_sm = scan(file=somaticCnvSegments,n=1,skip=i,what=character(),quiet=T)
+ j = grep(">chr",skip_sm)
+ i = i + 1
+ }
+ skip_sm = i + 1
+
+ skip_dc = scan(file=depthOfCoverage,n=1,what=character(),quiet=T)
+ i = 1
+ j = grep(">chr",skip_dc)
+ while(length(j) != 1)
+ {
+ skip_dc = scan(file=depthOfCoverage,n=1,skip=i,what=character(),quiet=T)
+ j = grep(">chr",skip_dc)
+ i = i + 1
+ }
+ skip_dc = i + 1
+
+ cat("\n","Reading files: \n",mv,"\n",sm,"\n",dc,"\n")
#Read mastervarbeta file in ASM folder
mastervar = read.table(masterVarBeta,
sep="\t",
colClasses=c("NULL","NULL","character","integer","integer",
"NULL","character",rep("NULL",16),"numeric","numeric",
rep("NULL",17),"integer","integer",rep("NULL",5)),
- skip=21)
+ skip=skip_mv)
+
#Read somaticCnvSegmentsNondiploidBeta in ASM/CNV folder
segm = read.table(somaticCnvSegments,
- sep="\t",skip=21,
+ sep="\t",skip=skip_sm,
colClasses=c("character","integer","integer","numeric","numeric",
rep("NULL",7)))
+
+ depcov = read.table(depthOfCoverage,sep="\t",skip=skip_dc,
+ colClasses=c("character","integer","integer",rep("NULL",3),"numeric"))
}
else
{
mastervar_ = list.files(path=path,pattern="masterVar")
path_segm = paste(path,"/CNV",sep="")
segm_ = list.files(path=path_segm,pattern="somaticCnvSegmentsNondiploid")
+ depcov_ = list.files(path=path_segm,pattern="depthOfCoverage")
skip_mv = scan(file=paste(path,"/",mastervar_,sep=""),n=1,what=character(),quiet=T)
i = 1
@@ -82,6 +160,17 @@
i = i + 1
}
skip_sm = i + 1
+
+ skip_dc = scan(file=paste(path_segm,"/",depcov_,sep=""),n=1,what=character(),quiet=T)
+ i = 1
+ j = grep(">chr",skip_dc)
+ while(length(j) != 1)
+ {
+ skip_dc = scan(file=paste(path_segm,"/",depcov_,sep=""),n=1,skip=i,what=character(),quiet=T)
+ j = grep(">chr",skip_dc)
+ i = i + 1
+ }
+ skip_dc = i + 1
cat("\n","Reading files from ASM folder \n")
@@ -99,14 +188,19 @@
sep="\t",skip=skip_sm,
colClasses=c("character","integer","integer","numeric","numeric",
rep("NULL",7)))
+
+ depcov = read.table(paste(path_segm,"/",depcov_,sep=""),sep="\t",skip=skip_dc,
+ colClasses=c("character","integer","integer",rep("NULL",3),"numeric"))
}
-
+
colnames(segm)=c("chr","start","end","avgnormcov","relcov")
colnames(mastervar)=c("chr","begin","end","vartype","ref_count","tot_count",
"ref_countN","tot_countN")
+ colnames(depcov)=c("chr","begin","end","avgnormcov")
+
cat("File input complete \n")
#------------------------------------------------#
@@ -147,6 +241,11 @@
cat("Performing calculations \n")
+ depcov$ratio <- NA
+
+ #Dubbelkolla, alla segment ej 100kb
+ depcov$ratio = depcov$avgnormcov / mean(depcov$avgnormcov)
+
mastervar$ratio <- mastervar$min <- mastervar$max <- mastervar$mut_count <- NA
#Calculate and fill min/max columns
@@ -165,7 +264,7 @@
cat("Saving objects to CG.Rdata \n")
- save(segs,mastervar,file="CG.Rdata")
+ save(segs,mastervar,depcov,file="CG.Rdata")
#------------------------------------------------#
# Plot
@@ -177,7 +276,8 @@
name=name,xlim=c(0,2.4),ylim=c(0,1))
CG_KaCh(segs$chr,segs$start,segs$end,segs$ratio,segs$ai,
- mastervar$chr,mastervar$begin,mastervar$ratio,(1 - mastervar$min/mastervar$max),
+ depcov$chr,depcov$begin,depcov$ratio,(1 - mastervar$min/mastervar$max),
+ mastervar$chr,mastervar$begin,
name=name,xlim=c(0,2.4),ylim=c(0,1))
cat("Plotting Complete \n")
cat("patchwork.CG Complete \n Please read documentation on running patchwork.CGCNV \n")
Modified: pkg/patchworkCG/R/patchwork.CGCNV.r
===================================================================
--- pkg/patchworkCG/R/patchwork.CGCNV.r 2012-01-24 12:35:46 UTC (rev 73)
+++ pkg/patchworkCG/R/patchwork.CGCNV.r 2012-01-25 13:53:13 UTC (rev 74)
@@ -1,11 +1,19 @@
-patchwork.CGCNV = function(cn2,delta,het,hom,maxCn=8,ceiling=1,name="CGCNV_")
+patchwork.CGCNV = function(cn2,delta,het,hom,maxCn=8,ceiling=1,name="CGCNV_",CGfile=NULL)
{
# patchwork.CGCNV(0.75,0.35,0.25,0.95)
#packagepath = system.file(package="patchwork")
#load(paste(packagepath,"/data/commonSnps132.RData",sep=""))
#load(paste(packagepath,"/data/ideogram.RData",sep=""))
data(ideogram,package="patchworkCG")
- load("CG.Rdata")
+
+ if(length(CGfile)==1)
+ {
+ load(CGfile)
+ }
+ else
+ {
+ load("CG.Rdata")
+ }
voidchrom <- c('chrX','chrY') # may add non-integer chroms here....
@@ -265,7 +273,7 @@
regions$mCn <- mCn
regions$fullCN <- fullCN
- save(regions,int,ai,file="Regions.RData")
+ save(regions,int,ai,file="CGCNV.Rdata")
write.csv(regions,file='Copynumbers.csv')
@@ -282,8 +290,9 @@
xlim=c(0,2.4),ylim=c(0,1))
CG_KaChCN(regions$chr,regions$start,regions$end,regions$ratio,regions$ai,
- regions$Cn,regions$mCn,mastervar$chr,
- mastervar$begin,mastervar$ratio,
- (1 - mastervar$min/mastervar$max),name=name,xlim=c(0,2.4),
- ylim=c(0,1))
+ regions$Cn,regions$mCn,depcov$chr,
+ depcov$begin,depcov$ratio,
+ (1 - mastervar$min/mastervar$max),
+ mastervar$chr,mastervar$begin,
+ name=name,xlim=c(0,2.4),ylim=c(0,1))
}
\ No newline at end of file
Modified: pkg/patchworkCG/man/CG_KaCh.Rd
===================================================================
--- pkg/patchworkCG/man/CG_KaCh.Rd 2012-01-24 12:35:46 UTC (rev 73)
+++ pkg/patchworkCG/man/CG_KaCh.Rd 2012-01-25 13:53:13 UTC (rev 74)
@@ -12,7 +12,7 @@
}
\usage{
-CG_KaCh(chr,start,end,int,ai,mchr,mpos,mval,sval,name,xlim,ylim)
+CG_KaCh(chr,start,end,int,ai,mchr,mpos,mval,sval,schr,spos,name,xlim,ylim)
}
\arguments{
@@ -32,17 +32,23 @@
Allelic imbalance as calculated from (1 - (lesser readcount / greater readcount)) per segment.
}
\item{mchr}{
- Chromosomes name of mastervar.
+ Chromosomes name of depcov (depthOfCoverage file).
}
\item{mpos}{
- Start position from mastervar.
+ Start position from depcov.
}
\item{mval}{
- Ratio between mastervars total allelecount divided by mean total allelecount.
+ Ratio between averagenormalizedcoverage and mean(averagenormalizedcoverage) from depthOfCoverage file.
}
\item{sval}{
Inverse ratio between allele maximum and allele minimum per position.
}
+ \item{schr}{
+ Chromosomes name of mastervar.
+ }
+ \item{spos}{
+ Start position from mastervar.
+ }
\item{name}{
Name that you want output to have. Default is '' which will yield files named as '_KaCh_chr#.png'.
When method is run by patchwork.CG() it will take that functions name parameter.
Modified: pkg/patchworkCG/man/CG_KaChCN.Rd
===================================================================
--- pkg/patchworkCG/man/CG_KaChCN.Rd 2012-01-24 12:35:46 UTC (rev 73)
+++ pkg/patchworkCG/man/CG_KaChCN.Rd 2012-01-25 13:53:13 UTC (rev 74)
@@ -13,7 +13,7 @@
}
\usage{
-CG_KaChCN(chr,start,end,int,ai,Cn,mCn,mchr,mpos,mval,sval,name='',xlim=c(0,2.4),ylim=c(0,1),maxCn=8)
+CG_KaChCN(chr,start,end,int,ai,Cn,mCn,mchr,mpos,mval,sval,schr,spos,name='',xlim=c(0,2.4),ylim=c(0,1),maxCn=8)
}
\arguments{
@@ -39,17 +39,23 @@
mCn.
}
\item{mchr}{
- Chromosomes name of mastervar.
+ Chromosomes name of depcov (depthOfCoverage file).
}
\item{mpos}{
- Start position from mastervar.
+ Start position from depcov.
}
\item{mval}{
- Ratio between mastervars total allelecount divided by mean total allelecount.
- }
+ Ratio between averagenormalizedcoverage and mean(averagenormalizedcoverage) from depthOfCoverage file.
+ }
\item{sval}{
Inverse ratio between allele maximum and allele minimum per position.
}
+ \item{schr}{
+ Chromosomes name of mastervar.
+ }
+ \item{spos}{
+ Start position from mastervar.
+ }
\item{name}{
Name that you want output to have. Default is '' which will yield files named as '_KaChCN_chr#.png'.
When method is run by patchwork.CGCNV() it will that functions name parameter.
Modified: pkg/patchworkCG/man/patchwork.CG.Rd
===================================================================
--- pkg/patchworkCG/man/patchwork.CG.Rd 2012-01-24 12:35:46 UTC (rev 73)
+++ pkg/patchworkCG/man/patchwork.CG.Rd 2012-01-25 13:53:13 UTC (rev 74)
@@ -14,7 +14,7 @@
}
\usage{
-patchwork.CG(path,name='CG_sample_',manual_file_input=FALSE,masterVarBeta=NULL,somaticCnvSegments=NULL)
+patchwork.CG(path,name='CG_sample_',manual_file_input=FALSE,masterVarBeta=NULL,somaticCnvSegments=NULL,depthOfCoverage=NULL)
}
\arguments{
@@ -40,6 +40,12 @@
from having to conserve the CompleteGenomics file structure.
Default is NULL.
}
+ \item{depthOfCoverage}{
+ Path to AND COMPLETE name of the depthOfCoverage file, should you wish to implement it directly. Useful if you want to run
+ the program on multiple samples and wish to create a script going from file to file. This saves you
+ from having to conserve the CompleteGenomics file structure.
+ Default is NULL.
+ }
}
\details{
Modified: pkg/patchworkCG/man/patchwork.CGCNV.Rd
===================================================================
--- pkg/patchworkCG/man/patchwork.CGCNV.Rd 2012-01-24 12:35:46 UTC (rev 73)
+++ pkg/patchworkCG/man/patchwork.CGCNV.Rd 2012-01-25 13:53:13 UTC (rev 74)
@@ -18,7 +18,7 @@
}
\usage{
-patchwork.CGCNV(cn2,delta,het,hom,maxCn=8,ceiling=1,name="CGCNV_")
+patchwork.CGCNV(cn2,delta,het,hom,maxCn=8,ceiling=1,name="CGCNV_",CGfile=NULL)
}
\arguments{
@@ -44,6 +44,11 @@
\item{name}{
Default is "CGCNV_". The name you want attached to generated plots.
}
+ \item{CGfile}{
+ Default is NULL. If your CG.Rdata file is not in your working directory, and you dont wish to move
+ it to your working directory, you can simply input the path here as CGfile = "path/to/file/CG.Rdata"
+ so patchwork.CGCNV can find its data.
+ }
}
\details{
Modified: pkg/patchworkData/DESCRIPTION
===================================================================
--- pkg/patchworkData/DESCRIPTION 2012-01-24 12:35:46 UTC (rev 73)
+++ pkg/patchworkData/DESCRIPTION 2012-01-25 13:53:13 UTC (rev 74)
@@ -4,7 +4,7 @@
Version: 2.0
Date: 2011-10-13
Author: Markus Rasmussen, Sebastian DiLorenzo
-Maintainer: Markus Rasmussen <Markus.Rasmussen at medsci.uu.se>
+Maintainer: Markus Rasmussen <Markus.Mayrhofer at medsci.uu.se>
Description: The data needed to perform patchwork functions.
License: GPL-2
#LazyLoad: no
More information about the Patchwork-commits
mailing list