Code:2019-9-23-1: Difference between revisions
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####################################################################################################################### | ### Title : Heatmap plot based on raw methylation signals which shared with high GSI MHL regions | ||
### Title : Heatmap plot based on raw methylation signals which shared with high GSI MHL regions | ### Author: Shicheng Guo, Ph.D. Email: Shicheng.Guo@hotmail.com | ||
### Author: Shicheng Guo, Ph.D. Email: Shicheng.Guo@hotmail.com | ### Time : Sep/23/2015 | ||
### Time : Sep/23/2015 | ### New: Extract the methylation signals with MethylFreq2Matrix.pl | ||
### New: Extract the methylation signals with MethylFreq2Matrix.pl | ####################################################################################################################### | ||
####################################################################################################################### | |||
data<-read.table("MethylMatrix.Filelist.txt.freq",row.names=1,head=T,sep="\t",as.is=T,check.names=F) | data<-read.table("MethylMatrix.Filelist.txt.freq",row.names=1,head=T,sep="\t",as.is=T,check.names=F) | ||
s1<-grep("KZ",colnames(data)) | s1<-grep("KZ",colnames(data)) | ||
s2<-grep("STL",colnames(data)) | s2<-grep("STL",colnames(data)) | ||
length(s1) | length(s1) | ||
length(s2) | length(s2) | ||
newdata=data[,c(s1,s2)] | newdata=data[,c(s1,s2)] | ||
dim(na.omit(newdata)) | dim(na.omit(newdata)) | ||
newdata<-RawNARemove(newdata) | newdata<-RawNARemove(newdata) | ||
library("impute") | library("impute") | ||
newdata<-impute.knn(data.matrix(newdata))$data | newdata<-impute.knn(data.matrix(newdata))$data | ||
newdata[1:3,1:3] | newdata[1:3,1:3] | ||
saminfo<-read.table("saminfo.txt",head=F,sep="\t",as.is=T) | saminfo<-read.table("saminfo.txt",head=F,sep="\t",as.is=T) | ||
colnames(newdata)=saminfo[match(colnames(newdata),saminfo[,1]),2] | colnames(newdata)=saminfo[match(colnames(newdata),saminfo[,1]),2] | ||
newdata<-newdata[,order(colnames(newdata))] | newdata<-newdata[,order(colnames(newdata))] | ||
save(newdata,file="Raw.methy.GSI.RData") | |||
# source("http://www.bioconductor.org/biocLite.R") | save(newdata,file="Raw.methy.GSI.RData") | ||
# biocLite("grDevices") | |||
# biocLite("gplots") | # source("http://www.bioconductor.org/biocLite.R") | ||
library("grDevices") | # biocLite("grDevices") | ||
library("gplots") | # biocLite("gplots") | ||
pdf("Figure-20-raw-signal.pdf") | |||
col=colorRampPalette(c("yellow", "blue"))(20) | library("grDevices") | ||
heatmap.2(newdata,col=col,trace="none",density.info="none",Colv=F,Rowv=F,key=NA,keysize=1,cexCol=0.8,labRow=NA) | library("gplots") | ||
dev.off() | pdf("Figure-20-raw-signal.pdf") | ||
newdata<-newdata[match(corsort(rownames(newdata)),rownames(newdata)),] | col=colorRampPalette(c("yellow", "blue"))(20) | ||
corsort<-function(cor){ | heatmap.2(newdata,col=col,trace="none",density.info="none",Colv=F,Rowv=F,key=NA,keysize=1,cexCol=0.8,labRow=NA) | ||
dev.off() | |||
newdata<-newdata[match(corsort(rownames(newdata)),rownames(newdata)),] | |||
corsort<-function(cor){ | |||
} | a<-unlist(lapply(strsplit(as.character(cor),split=c(":")),function(x) x)) | ||
bed<-matrix(a,ncol=2,byrow=T) | |||
bed<-bed[order(bed[,1],as.numeric(bed[,2])),] | |||
cor<-apply(bed,1,function(x){paste(unlist(strsplit(x,"\t"))[1],":",unlist(strsplit(x,"\t"))[2],sep="")}) | |||
return(cor) | |||
} |
Revision as of 22:29, 23 September 2015
####################################################################################################################### ### Title : Heatmap plot based on raw methylation signals which shared with high GSI MHL regions ### Author: Shicheng Guo, Ph.D. Email: Shicheng.Guo@hotmail.com ### Time : Sep/23/2015 ### New: Extract the methylation signals with MethylFreq2Matrix.pl #######################################################################################################################
data<-read.table("MethylMatrix.Filelist.txt.freq",row.names=1,head=T,sep="\t",as.is=T,check.names=F) s1<-grep("KZ",colnames(data)) s2<-grep("STL",colnames(data)) length(s1) length(s2) newdata=data[,c(s1,s2)] dim(na.omit(newdata)) newdata<-RawNARemove(newdata) library("impute") newdata<-impute.knn(data.matrix(newdata))$data newdata[1:3,1:3] saminfo<-read.table("saminfo.txt",head=F,sep="\t",as.is=T) colnames(newdata)=saminfo[match(colnames(newdata),saminfo[,1]),2] newdata<-newdata[,order(colnames(newdata))]
save(newdata,file="Raw.methy.GSI.RData")
# source("http://www.bioconductor.org/biocLite.R") # biocLite("grDevices") # biocLite("gplots")
library("grDevices") library("gplots") pdf("Figure-20-raw-signal.pdf") col=colorRampPalette(c("yellow", "blue"))(20) heatmap.2(newdata,col=col,trace="none",density.info="none",Colv=F,Rowv=F,key=NA,keysize=1,cexCol=0.8,labRow=NA) dev.off() newdata<-newdata[match(corsort(rownames(newdata)),rownames(newdata)),]
corsort<-function(cor){
a<-unlist(lapply(strsplit(as.character(cor),split=c(":")),function(x) x))
bed<-matrix(a,ncol=2,byrow=T)
bed<-bed[order(bed[,1],as.numeric(bed[,2])),]
cor<-apply(bed,1,function(x){paste(unlist(strsplit(x,"\t"))[1],":",unlist(strsplit(x,"\t"))[2],sep="")})
return(cor)
}