R help - Nov 2008 - row labels in heatmap.2(package gplots)

Dear R users,

I have a question regarding how to make row labels readable in a heat map.

I have successfully made a heat map using function "heatmap.2" in the
package "gplots". However, as there are many rows in the heat map, I
have difficulties labeling them (heatmap.2 provides a parameter
"labRow" to label the row names, but as I have too many rows, I can
not make them readable). Do you have any suggestions to improve the labeling?

I am thinking about using multiple columns to label the row names instead of one
column(the default in heatmap.2). I have tried to use "mtext" to write
texts on the margin of the heat map, but it could not work either. Do you think
this can work? How can I know the coordinates of each row in a heat map?

Thank you very much!

Jun

I could not tell from the help file whether rotation of the x labels  
is supported in heatmap.2. I did read (perhaps in one of the linked to  
help files)  that rotation  was only allowed with "text" and I was  
left wondering if it might be possible to use text(x) and list(rot=90)  
as arguments to a scales call.

At any rate, the results of this worked levelplot example from  
Sarkar's text is worth considering:

data(Cars93, package="MASS")
library(lattice)
  cor.Cars93 <- cor(Cars93[, !sapply(Cars93, is.factor)], use
="pair")
  levelplot(cor.Cars93,  scales =list(x=list(rot=90)))

-- 
David Winsemius

On Nov 25, 2008, at 2:19 PM, Jun Ding wrote:
> Dear R users,
>
> I have a question regarding how to make row labels readable in a  
> heat map.
>
> I have successfully made a heat map using function "heatmap.2" in
> the package "gplots". However, as there are many rows in the heat
> map, I have difficulties labeling them (heatmap.2 provides a  
> parameter "labRow" to label the row names, but as I have too many
> rows, I can not make them readable). Do you have any suggestions to  
> improve the labeling?
>
> I am thinking about using multiple columns to label the row names  
> instead of one column(the default in heatmap.2). I have tried to use  
> "mtext" to write texts on the margin of the heat map, but it
could
> not work either. Do you think this can work? How can I know the  
> coordinates of each row in a heat map?
>
> Thank you very much!
>
> Jun
>
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