Question

Visualization of rownames in the heatmap.2 function for selected DE genes of a microarray dataset

0

Entering edit mode

svlachavas ▴ 830

@svlachavas-7225

Last seen 13 months ago

Germany/Heidelberg/German Cancer Resear…

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 ?

heatmap.2 gplots differential gene expression visualization • 5.3k views

ADD COMMENT • link 9.6 years ago svlachavas ▴ 830

0

Entering edit mode

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 REPLY • link 9.6 years ago b.nota ▴ 370

score 0 · Answer 1 · 2015-04-01

0

Entering edit mode

svlachavas ▴ 830

@svlachavas-7225

Last seen 13 months ago

Germany/Heidelberg/German Cancer Resear…

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 COMMENT • link 9.6 years ago svlachavas ▴ 830

0

Entering edit mode

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 REPLY • link 9.6 years ago b.nota ▴ 370

0

Entering edit mode

Dear b.nota,

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

ADD REPLY • link 9.6 years ago svlachavas ▴ 830

0

Entering edit mode

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

ADD REPLY • link 9.6 years ago b.nota ▴ 370

0

Entering edit mode

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 REPLY • link 9.6 years ago b.nota ▴ 370

0

Entering edit mode

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

ADD REPLY • link 9.6 years ago svlachavas ▴ 830