Heatmaps from cuffdiff output
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Entering edit mode
8.8 years ago

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

cuffdiff heatmap RNA-Seq • 10k views
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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 with labRow=T though.

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Entering edit mode

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.

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Entering edit mode
8.7 years ago

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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Entering edit mode
8.8 years ago
nevev ▴ 110

In heatmaps in point 6. They say how to change the dimensions so that the gene names/ids don't overlap.

Good luck!

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8.7 years ago
alaincoletta ▴ 160

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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Entering edit mode
8.7 years ago

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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Entering edit mode

by using this comment I get heat map generated for log10foldchange, please can u help me with log 2 fold change