[BioC] heatmap.2 coloring question

[James W. MacDonald]

Srinivas Iyyer wrote:
> Thank you ! It worked. 
> 
> apologies for not asking last time another question. 
> 
> 
> Is it possible to recreate a GSEA's Leading edge grid
> figure in R. 
> 
> I have a matrix of values based on NES(normalized
> enrichment scores) from various GSEA runs (not just
> one run). 
> 
> I combined all runs with rows as enriched gene sets
> and columns as my gene expression studies. 
> 
> I want to re-create a figure just like what GSEA
> leading edge plots look like. I tried using heatmap
> and heatmap.2 and they are not that appropriate for
> this representation. 
> 
> Is it possible to create grid and color each cells
> with a color code based on normalized enrichment
> scores. 

I have no idea what a GSEA leading edge plot might be, but if you want a 
grid of colors, you want the image() function (which is what the 
heatplot functions use).

Best,

Jim


> 
> thanks
> Srini
> 
> 
> 
> 
> --- "James W. MacDonald" <jmacdon at med.umich.edu>
> wrote:
> 
>>  From ?colorpanel in gplots:
>>
>> showpanel <- function(col)
>>       {
>>         image(z=matrix(1:100, ncol=1), col=col,
>> xaxt="n", yaxt="n" )
>>       }
>> showpanel(colorpanel(40, "blue","white","yellow"))
>>
>> Best,
>>
>> Jim
>>
>>
>>
>> Srinivas Iyyer wrote:
>>> Dear group, 
>>> I am using heatmap.2 for heatmaps. 
>>>
>>> heatmap.2(res1,cexRow = 0.28,cexCol=0.28
>>>
> ,col=rev(heat.colors(16)),keysize=1,na.color=par("bg"),densadj
>>> = 0.25,Colv=FALSE)
>>>
>>>
>>>
>>> I want to have a color key starting from blue to
>>> yellow through white.
>>>
>>> Say -7 is my min value and +4 is my max value. 
>>>
>>> Values around 0 should be totally white. 
>>>
>>> what kind of trick can do that for me. I will be
>> very
>>> happy if I can do that. 
>>>
>>> Any suggestions, please. 
>>> thank you. 
>>> srini
>>>
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>> -- 
>> James W. MacDonald, M.S.
>> Biostatistician
>> Affymetrix and cDNA Microarray Core
>> University of Michigan Cancer Center
>> 1500 E. Medical Center Drive
>> 7410 CCGC
>> Ann Arbor MI 48109
>> 734-647-5623
>>
> 
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623