Hello,
I am working with cummeRbund package to generate heatmap from cuffdiff output.
I tried to run heatmap with the following command in R-
h<-csHeatmap(myGenes,cluster='both')
It displays a message -
Using tracking_id, rep_name as id variables
No id variables; using all as measure variables
The gene names are very cluttered in the heatmap.
Is there a way to specify which ID's to use or change the font size in the heatmap?
Thanks,
Tejaswi
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written
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tejaswikoganti
First you make a list of your genes:
myGeneIds<-c("gene1","gene2","gene3","gene4","gene5")
myGenes<-getGenes(cuff,myGeneIds)
Then you can create a heatmap of the gene-list.
pdf(file="myHeatgraph.pdf")
csHeatmap(myGenes,cluster='both')
dev.off()
Hope this helps!
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written
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Root Troubleshoot •
Here is a step-by-step tutorial. You can download public datasets with a report and step by step examples.
https://insilicodb.com/differential-gene-expression-heatmap-from-rnaseq-data-using-cummerbund/
In InSilico DB, use the filters, on the left, to narrow your search to RNA-Seq data.
Hope this helps.
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written
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alaincoletta
I figured there were too many genes in my heatmap. I just had to increase the threshold value and reduce the font.
I found this command to change font -
h <- csHeatmap(myGenes)
h <- h + theme(axis.text.x=element_text(size=14),axis.text.y=element_text(size=6))
Thanks!
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written
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tejaswikoganti
by using this comment I get heat map generated for log10foldchange, please can u help me with log 2 fold change
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Hi Tejaswi,
I see the same message, but I also see no heatmap as the result, it is very frustrating. If you found out an answer yet, please let know!
Best,
Monika
Update: when I set
labRow=F, then I see the heatmap. Because it skips the row labels. So I suppose my problem was not connected to the message! Not sure how to make it work withlabRow=Tthough.How is the data for heatmap looks like? There could be alternative solutions to your problem: show the data sample - we would help you to plot it.