r_script_rnaseq_heatmap.txt

setwd("/Volumes/cim/CIM-EPIGENOME-ORDOG/SHARED/Sabriya/Stem-Cell paper/Expression heatmap/2xscs70 and (MY up; DMP not up)")
 
library(gplots)
 
library(RColorBrewer)
 
library(colorRamps)
 
my_palette<-colorRampPalette(c("blue", "black", "yellow"))(n=299)
 
 
filename<-read.csv("2xscs70 MY up; DMP not up.csv", sep=",")
 
row.names(ICC)<-filename$Gene
 
ICC<-ICC[,2:5]
 
ICC_matrix<-data.matrix(ICC)
 
png("MY up DMP not up_02.png", width= 768, height = 1024, unit="px")
 
heatmap.2((ICC_matrix),col=my_palette, scale="none", key=TRUE, symkey=FALSE, Rowv="true", Colv="false", density.info="none", trace="none", keysize="1", cexRow="0.5", cexCol="1.2")
 
Warning messages:
1: In heatmap.2((ICC_matrix), col = my_palette, scale = "none", key = TRUE,  :
  Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
2: In heatmap.2((ICC_matrix), col = my_palette, scale = "none", key = TRUE,  :
  Discrepancy: Colv is FALSE, while dendrogram is `none'. Omitting column dendogram.
 
dev.off()