[BioC] Adjusting contrast in a heatmap

[Sean Davis]

On Tue, Apr 13, 2010 at 8:52 AM, Anthony Ferrari <ferraria at gmail.com> wrote:
> Hi all,
>
> I am working on a gene expression analysis.
> I want to plot the heatmap resulting from the clustering (for both arrays
> and genes)
>
> I am generating this plot with image() function with a red-black-green color
> palette but the resulting image has a really poor contrast (because of the
> extreme expression values most of the image is dark)
>
> Is there a known graphical parameter or a simple idea which I can use to
> obtain an image with good contrast ? (As we usually do in the pixels
> settings with treeview software )

Have a look at the breaks argument.

> ps : I don't wanna use existing packages like heatmap or heatmap.plus as I
> am customizing distances and linkage.

You can also customize these properties in heatmap, heatmap.2, etc.
See the help.

Sean