[BioC] heatmap colours

[Robert Gentleman]

If you want to choose good colors please look at Cynthia Brewer's work
 (www.colorbrewer.org) or the R package RColorBrewer
 and yes there are examples of doing so in Bioconcductor and no we
 don't force people to make good choices :-)

 Robert

On Mon, May 12, 2003 at 11:47:33PM +0200, Johannes Hüsing wrote:
> Jean Yee Hwa Yang <jean at biostat.ucsf.edu> [Mon, May 12, 2003 at 07:31:59PM CEST]:
> [...]
> > 
> > ## Red -- Black -- Green
> [...]
> > ## Red -- white -- Green
> [...]
> > ## blue--yellow
> [...]
> 
> General discussion about the usefulness of heat maps aside, why is 
> everyone infatuated with the red/green contrast? Just because cDNA
> chips are marked with red and green dye? We are not looking at a
> chip image here, so generally we are free wrt choice of colours.
> 
> Red and green is less than optimal for several reasons:
> 
> - A non-neglectable proportion of the population, especially the
>   male sector of it, cannot distinguish between those colours.
> - It makes for poor contrast when transformed to grayscale.
> 
> The visualization guides I have read don't condone a red/green
> contrast scale (while Edward Tufte doesn't specifically list it as a
> deterring example, he doesn't recommend it either).  One suggestion is
> a palet along black -- red -- orange -- yellow -- white, mimicking the
> appearance of a black body heated up.  (That would cause "heat map" to
> be an apt term at last.
> 
> ok. I'm feeling better now.
> 
> 
> Johannes
> -- 
> Johannes Hüsing   There is something fascinating about science. One gets
> hannes at ruhrau.de  such wholesale returns of conjecture from such a 
>                   trifling investment of fact.                Mark Twain
> 
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-- 
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20                            |
| Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu        |
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