[BioC] heatmap colours

[Byron Ellis]

It was originally done to mimic the Cy3/Cy5 labels. Everybody else used 
it because thats what the software did and there wasn't any way to 
change it.

Personally I like Blue->White->Red as fully saturated Blue and Red have 
roughly the same apparent brightness (as opposed to 
Blue->White->Yellow... I've never understood that color choice except 
that Blue and Yellow are, sort of, UCLA's school colors) and the plot 
background color is generally white, making white seem like the logical 
choice for "center." They maintain the "heat" paradigm as traditional 
indicators of hot and cold and unlike blackbody heat maps are more 
directly comparable in absolute value.

No, I don't have a function handy... I just keep a 1025 element vector 
of color values around in an RDA file.


On Monday, May 12, 2003, at 05:47  PM, 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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Byron Ellis (bellis at hsph.harvard.edu)
"Oook" - The Librarian