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-   -   R - problem in heatmap reading (http://seqanswers.com/forums/showthread.php?t=18420)

Chuckytah 03-14-2012 11:38 AM

R - problem in heatmap reading
 
Hi all, i'm using R to draw heatmaps... but I have a huge amount of data, around 600 genes... Did anyone could suggest me a better way to draw it? this image is to show you that the gene descritption can not be read at all... I've tryed to draw 3 separated heatmaps, with 200 genes each but it also dont work, i cant read the gene descritption it is all on top of other... I found this on the internet, search in google images.... it would be great for me to do a image like this: http://www.biomedcentral.com/content...9-9-92-s12.bmp anyone knows a solution?

sorry if my question is "too stupid" but i'm kind a basic user of R... this was the heatmap i get: http://postimage.org/image/asnzdlk9h/

mudshark 03-15-2012 01:58 AM

you simply need to either:
- increase the height of your device
AND/OR
- reduce the size of your characters

if you post your R script it is probably easier to suggest sth..

essvee 03-15-2012 07:04 AM

Personally, I would experiment with the cexRow value (start around 0.5 and go from there) and then save the heatmap as a pdf that I could modify further in illustrator or inkscape.
Hope that helps.

Chuckytah 03-15-2012 08:59 AM

I will try those suggestions. and i will post my script here :) thanks for answers

Chuckytah 03-15-2012 09:25 AM

Code:

genes <- read.csv("genes.csv", sep=",")
row.names(genes) <- genes$Descritpion
genes <- genes[,2:4]
genes_matrix <- data.matrix(genes)
genes_heatmap <- heatmap(genes_matrix, Rowv=NA, Colv=NA,col = heat.colors(256), scale="column", margins=c(5,10))

######or#########

library(gplots)
genes_heatmap2 <- heatmap.2(genes_matrix,trace="none",col=greenred(10))

#######or##########

genes_heatmap <- heatmap.2(genes_matrix, col=redgreen(75), scale="row", key=TRUE, symkey=FALSE, density.info="none", trace="none", cexRow=0.5)


Chuckytah 03-15-2012 09:25 AM

Quote:

Originally Posted by essvee (Post 67824)
Personally, I would experiment with the cexRow value (start around 0.5 and go from there) and then save the heatmap as a pdf that I could modify further in illustrator or inkscape.
Hope that helps.


I've put 0.5... you advise me to put what? :)

Chuckytah 03-15-2012 09:26 AM

Quote:

Originally Posted by mudshark (Post 67800)
you simply need to either:
- increase the height of your device
AND/OR
- reduce the size of your characters

if you post your R script it is probably easier to suggest sth..

Already here my R codes :)

Chuckytah 03-15-2012 10:03 AM

Quote:

Originally Posted by essvee (Post 67824)
Personally, I would experiment with the cexRow value (start around 0.5 and go from there) and then save the heatmap as a pdf that I could modify further in illustrator or inkscape.
Hope that helps.

changing the cexRow did not worked... :S cant read at all ... :S :(

essvee 03-15-2012 11:52 AM

Did not work? Can you please elaborate? Is it still too big/small? It should work with both heatmap and heatmap2. If it is too large still, decrease the number. Also, try looking at help(heatmap) and help(heatmap.2), you can learn a lot from the documentation.

Chuckytah 03-15-2012 12:51 PM

Quote:

Originally Posted by essvee (Post 67858)
Did not work? Can you please elaborate? Is it still too big/small? It should work with both heatmap and heatmap2. If it is too large still, decrease the number. Also, try looking at help(heatmap) and help(heatmap.2), you can learn a lot from the documentation.

still too small, i choose 0.06 and the words are above other/on top again... and if I choose 0.03 for example, when I save to .pdf the words dont apear at all :S


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