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Old 03-14-2012, 12:38 PM   #1
Chuckytah
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Question 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/
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Old 03-15-2012, 02:58 AM   #2
mudshark
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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..
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Old 03-15-2012, 08:04 AM   #3
essvee
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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.
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Old 03-15-2012, 09:59 AM   #4
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I will try those suggestions. and i will post my script here thanks for answers
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Old 03-15-2012, 10:25 AM   #5
Chuckytah
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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)
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Old 03-15-2012, 10:25 AM   #6
Chuckytah
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Quote:
Originally Posted by essvee View Post
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?
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Old 03-15-2012, 10:26 AM   #7
Chuckytah
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Quote:
Originally Posted by mudshark View Post
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
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Old 03-15-2012, 11:03 AM   #8
Chuckytah
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Quote:
Originally Posted by essvee View Post
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
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Old 03-15-2012, 12:52 PM   #9
essvee
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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.
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Old 03-15-2012, 01:51 PM   #10
Chuckytah
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Quote:
Originally Posted by essvee View Post
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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