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Old 07-28-2013, 05:23 PM   #7
jp.
Senior Member
 
Location: NikoNarita.jp

Join Date: Jul 2013
Posts: 142
Question

Hi cpleis
First of all, thank you for your kind reply here about Heatmap.
I want to know about .csv files, how did you make it ?
I have cufflinks output and used to make csHeatmap and also useg gplots after normalization of cuffdiff, but your Heatmap looks great, however, I can not find .csv ?
May you please reply on how to make .csv file which can be used for generating Heatmap.
Thank you

Quote:
Originally Posted by cpleis View Post
Hi SHeaph,
Unfortunately I was not able to resolve the issue. I think that the heat map function in R isn't able to resolved such a large number of data labels. I simply switched to showing the functional groups instead of individual genes and the heat map turned out fine. I've attached the final image I created and the code I used to create it (below).

**Using logFC data for only sig genes (FDR < 0.05)

install.packages("gplots")
library(gplots)
source("http://bioconductor.org/biocLite.R")
biocLite("ALL")

heatdata <- read.csv("Avg_log2FC_allbins_sig.csv", sep=",")
heatdata <- heatdata[,2:5]
heatdata_matrix <- data.matrix(heatdata)
pdf("Heatmap_all.pdf", width=10, height=5, paper="a4r")
data_heatmap <- heatmap.2(heatdata_matrix, col=redblue(75), scale="row",
key=TRUE, symkey=FALSE, density.info="none", trace="none", margins=c(10,10), labRow =rownames(heatdata_matrix),cexRow=0.5)
axis(4,
at=2:NROW(heatdata_matrix),
labels=rownames(heatdata_matrix[data_heatmap$rowInd] ),
cex=0.5)
dev.off()

If you do find another solution let me know!

Courtney
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