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Old 01-18-2013, 06:19 AM   #4
Location: Cork

Join Date: Nov 2012
Posts: 13

Originally Posted by cpleis View Post
I have a large data set from RNA sequencing and I am trying to make a heatmap of my data. I have am having issues formatting my heatmap figure. My data set is large with the log2 fold change for over 6oo genes across 4 treatments. My csv file is formatted as such:
Gene Drought Ozone Temp1 Temp2
Glyma# -0.130545875 -0.098349739 0.170508007 0.091996284
So far I have gotten an image, but I can't seem to get the gene names to
display properly. Here is my code:

heatdata <- read.csv("logFC_bin17.csv", sep=",")
heatdata <- heatdata[,2:5]
heatdata_matrix <- data.matrix(heatdata)
rownames(heatdata_matrix) = paste("Gene", 2:655)
jpeg("Heatmap_bin17.jpeg", width=8, height=8, units="in", res=300,
data_heatmap <- heatmap.2(heatdata_matrix, col=redgreen(75), scale="row",
key=TRUE, symkey=FALSE,"none", trace="none", margins=c(10,10), labRow =rownames(heatdata_matrix),cexRow=0.5)

Everything about my image is fine except the right axis with the gene ID labels is blurred together (I am having issues uploading the image). It looks like 4 thin rectangles covering up the data. I want it to look like this:

Any suggestions for how to modify the code would be great. I've done a lot of R searches and can't seem to find any modifications that fix my data.
Hi cpleis,

I was just wondering if you were able to resolve this issue? I am having similar difficulties at the moment, I have just over 200 hits and the gene ID label is also blurred. I am new to cummeRbund and R and I created the map with the following command:

> h.rep<-csHeatmap(myGenes,cluster='both',replicates=T)
> h.rep

Any help would be great!
Many thanks!
SHeaph is offline   Reply With Quote