[BioC] heatplot() 1. red-*black*-green palette, 2.suppress drawing of the row dendrogram (but NOT row reordering)

Karl Brand k.brand at erasmusmc.nl
Sun Aug 8 21:07:56 CEST 2010

Hi Amos,

Thank you for your comments & suggestions. Unfortunately i still haven't 
found a simple way to get black *INTO* my heatplot() palette (not remove 
as was mis-communicated in my previous email).

#This is the actual code i attempted to get black into the palette
#Attempt  red/black/green palette with heatmap.2() "col=" argument:
my.mat <- matrix(rnorm(250), nrow=50, ncol=5)
heatplot(my.mat, dend="both", cols.default=FALSE, col = c(redgreen(256)))

#Using correct heatplot() "lowcol=" argument also fails.
#Just get red/green palette:
heatplot(my.mat, dend="both", cols.default=FALSE, 
lowcol=c(colorpanel(256, low="green", mid="black", high="red")))

Unless you/some one can demonstrate how, it seems to me heatplot() can 
only accept a 2 color gradient. So no red-BLACK-green, or any other 
3-shade palette with out modifying the heatplot() function. Again any 
pointers on this appreciated.

Re. dendrogram plotting- again, *unlike* heatmap.2, i can not achieve 
row ordering *without* drawing a row dendrogram. Only choices visible to 
me- 1. use heatmap.2(), 2. delete post-R eg. with GIMP, or 3. modify 
heatplot(). Suggestions on this last option also greatly appreciated.

With thanks in advance for comments,


On 8/7/2010 8:41 PM, Amos Folarin wrote:
> Hi Karl,
> You can plot your palet based on whatever colorscheme you want i.e.
> redgreen() or greenred(). If you want black omitted then maybe try building
> a custom colorpanel(n, low, mid, high), where you specify your own mid point
> color.
> I see you already have some ordering set for your Rows and Cols.
> Error in heatmap.2(data, Colv = Colv, Rowv = Rowv, col = plotcols, scale =
> scale,  :
> the dendrogram plotting is controled by the dendrogram arg. dendrogram =
> c("both","row","column","none"), I'm not sure why this is not matching the
> arguement correctly (suggest you post the actual code you are using).
> but dendrogram="column" should work.
> There is a good tutorial here -- see end of:
> http://www2.warwick.ac.uk/fac/sci/moac/students/peter_cock/r/heatmap/
> Regards,
> Amos Folarin
> 	[[alternative HTML version deleted]]
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Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
T +31 (0)10 704 3457 |F +31 (0)10 704 4743 |M +31 (0)642 777 268

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