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Question: Visualization of rownames in the heatmap.2 function for selected DE genes of a microarray dataset
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gravatar for svlachavas
3.6 years ago by
svlachavas610
Greece/Athens/National Hellenic Research Foundation
svlachavas610 wrote:

Dear Bioconductor Community,

i tried the function heatmap.2 to produce a heatmap plot of 129 DE probesets based on an analysis on an affymetrix microarray dataset between cancer vs control samples. My final arguments for my function are:

heatmap.2(exprs(esetsel), col=greenred(75), scale="none", ColSideColors=patientcolors,
key=TRUE, symkey=FALSE, density.info="none", trace="none", cexRow=0.9, cexCol=0.8, margins=c(8,16))

# esetsel my expressionset with the selected probesets.

My main problem is that the rownames(probesets) arent shown clearly, and although i tried to change the argument cexRow nothing is improved. Any ideas how to impove the visualization of these probesets in the heatmap plot and change the size of the rows ?

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by svlachavas610

Hi,

It is not completely clear what you mean by not shown clear. Can you be more specific? Are they too long to fit within the margins?

You might wan to play around with "offsetRow" and with the margins a little, if that's the problem?

Good luck.

Ben

 

ADD REPLYlink written 3.6 years ago by b.nota300
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gravatar for svlachavas
3.6 years ago by
svlachavas610
Greece/Athens/National Hellenic Research Foundation
svlachavas610 wrote:

Dear b.nota,

i mean that the rownames of the corresponding probesets-genes look very fuzzy and i cannot even see clearly a single probeID

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by svlachavas610

Okay, you mean that the probe names still overlap each other, because there is not enough space (rows are not large enough for text).

You can try to change the size of the figure. If you make the figure in a pdf you can try:

pdf( "heatmap.pdf", width = 12, height = 10 )

heatmap.2(...)

dev.off()

Of course you'll have to find the right width and height for you heatmap by trying.

The space in the pdf can be changed with mfrow, e.g.,

par( mfrow = c(2,2) )

Hope this helps!

 

ADD REPLYlink written 3.6 years ago by b.nota300

Dear b.nota, 

thank you for your idea !! i will try it and give feedback

ADD REPLYlink written 3.6 years ago by svlachavas610

par( mfrow = c(2,2) ) should be par( mar = c(2,2) ), sorry for the confusion.

ADD REPLYlink written 3.6 years ago by b.nota300

Hi svlachavas,

I found out that changing the size of the pdf does not change the size of the heatmap, sorry my answer was too quick.

 

You'll need to change the layout. lmat, lwid, an especially lhei are the parameters you're looking for.

Good luck!

Ben

 

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by b.nota300

Yes Ben i checked it just earlier and it didnt worked !! So i will check the other arguments you mentioned

ADD REPLYlink written 3.6 years ago by svlachavas610
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