Heatmap plot: Difference between revisions

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>Shicheng
(Created page with "setwd("/media/NAS3_volume2/shg047/Alice") heatMap<-function(data){ # note: this function include correlation based heatmap (pearson or spearman) # data: row is gene and col...")
 
>Shicheng
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Line 1: Line 1:
setwd("/media/NAS3_volume2/shg047/Alice")
heatMap<-function(data){
# note: this function include correlation based heatmap (pearson or spearman)
# data: row is gene and column is sample
# colname and rowname cannot be NULL
# Usage example:
# test<- matrix(runif(100),nrow=20)
# colnames(test)=c("A","A","A","B","B")
# rownames(test)=paste("Gene",1:20,sep="")
# HeatMap(test)
library("gplots")
colors <- colorpanel(75,"midnightblue","mediumseagreen","yellow")
colors <-bluered(75)
sidecol<-function(x){
x<-as.numeric(as.factor(x))
col<-rainbow(length(table(x)))
sapply(x,function(x) col[x])
}
Hclust=function(x){hclust(x,method="complete")}
#Distfun=function(x){as.dist((1-cor(t(x),method = "pearson")^2))}
ColSideColors=sidecol(colnames(data))
Heatmap<-heatmap.2(data,trace="none",
hclust=Hclust,
cexRow = 1, cexCol = 1,
ColSideColors=ColSideColors,
density.info="none",col=colors,
Colv=T,Rowv = TRUE,
keysize=0.9, margins = c(10, 10)
)
return(Heatmap)
}
data1<-read.table("PluDiff_allsample.txt",head=T,sep = "\t",row.names=1)
colnames(data1)[grep("ips",colnames(data1))]="iPS"
colnames(data1)[grep("NT",colnames(data1))]="SCNT"
Heatmap<-heatMap(data.matrix(data1))
save.image(file = "heatmap.scRNA.alice.RData")
shg047@genomeMiner:~/work/Alice$ perl ~/bin/code2wiki.pl xx
  setwd("/media/NAS3_volume2/shg047/Alice")
  setwd("/media/NAS3_volume2/shg047/Alice")
  heatMap<-function(data){
  heatMap<-function(data){

Latest revision as of 23:21, 20 January 2017

setwd("/media/NAS3_volume2/shg047/Alice")
heatMap<-function(data){
# note: this function include correlation based heatmap (pearson or spearman)
# data: row is gene and column is sample
# colname and rowname cannot be NULL
# Usage example:
# test<- matrix(runif(100),nrow=20)
# colnames(test)=c("A","A","A","B","B")
# rownames(test)=paste("Gene",1:20,sep="")
# HeatMap(test)
library("gplots")
colors <- colorpanel(75,"midnightblue","mediumseagreen","yellow")
colors <-bluered(75)
sidecol<-function(x){
x<-as.numeric(as.factor(x))
col<-rainbow(length(table(x)))
sapply(x,function(x) col[x])
}
Hclust=function(x){hclust(x,method="complete")}
#Distfun=function(x){as.dist((1-cor(t(x),method = "pearson")^2))}
ColSideColors=sidecol(colnames(data))
Heatmap<-heatmap.2(data,trace="none",
hclust=Hclust,
cexRow = 1, cexCol = 1,
ColSideColors=ColSideColors,
density.info="none",col=colors,
Colv=T,Rowv = TRUE,
keysize=0.9, margins = c(10, 10)
)
return(Heatmap)
}
data1<-read.table("PluDiff_allsample.txt",head=T,sep = "\t",row.names=1)
colnames(data1)[grep("ips",colnames(data1))]="iPS"
colnames(data1)[grep("NT",colnames(data1))]="SCNT"
Heatmap<-heatMap(data.matrix(data1))
save.image(file = "heatmap.scRNA.alice.RData")