Question: Heatmaps from cuffdiff output
2
gravatar for tejaswikoganti
5.0 years ago by
United States
tejaswikoganti60 wrote:

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

heatmap rna-seq cuffdiff • 8.2k views
ADD COMMENTlink modified 4.9 years ago • written 5.0 years ago by tejaswikoganti60

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.

ADD REPLYlink written 4.9 years ago by Pavel Senin1.9k
2
gravatar for Root Troubleshoot
4.9 years ago by
Nijmegen, Netherlands
Root Troubleshoot20 wrote:

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!

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by Root Troubleshoot20
1
gravatar for nevev
4.9 years ago by
nevev90
Germany
nevev90 wrote:

I think an answer to your question might be here:

https://pods.iplantcollaborative.org/wiki/display/eot/RNA-Seq_tutorial#RNA-Seq_tutorial-CuffDiffOutputs

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

 

Good luck!

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by nevev90
1
gravatar for alaincoletta
4.9 years ago by
alaincoletta110
Belgium
alaincoletta110 wrote:

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.


 

ADD COMMENTlink written 4.9 years ago by alaincoletta110
1
gravatar for tejaswikoganti
4.9 years ago by
United States
tejaswikoganti60 wrote:

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!

ADD COMMENTlink written 4.9 years ago by tejaswikoganti60
0
gravatar for nevev
4.9 years ago by
nevev90
Germany
nevev90 wrote:

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.

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by nevev90
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