[R] color palette heatmap

Achim Zeileis Achim.Zeileis at uibk.ac.at
Wed Feb 10 22:39:38 CET 2010

On Wed, 10 Feb 2010, joonR wrote:

> Hi,
> I'm kinda new of the R world.
> I need to use the heatmap or heatmap.2 function to plot correlation values.
> 2 questions:
> - how can I specify a color palette? (would like to have a transition from
> blue(-1) to white(0) to red(1))

In example(heatmap.2), there is an example for a blue-white-red scale 
using the bluered() function from gplots.

bluered() does its transitions in RGB space which is typically suboptimal. 
A better approach is to do it in HCL space, e.g., as the diverge_hcl() 
function from "colorspace" does. For example:

   heatmap.2(as.matrix(mtcars), col = diverge_hcl(11),
     scale="column", tracecol = NULL)

> - how can I use heatmap.2 imposing a specific order (like hclust.order)?
>  I mean, I don't want heatmap.2 to re-cluster/re-order my data but just to
> plot them according to a specified (by me) order (I tried Rowv = hc$order
> where hc is an hclust object, but without success)

Someone else will have to help here...sorry.


> can you help me?
> Thanks a lot!
> J
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