[BioC] different color for a subset of points on heatmap

[marek piatek (BI)]

Hi Francois and all,

Thanks for your advice. However if I will give my subset different values they will get clustered in different way - which is not what I want. Your approach is good if I wouldn't be using clustering.
And also the subset I would like to use different colour for is a subset of larger population (its min and max values are within the larger set).

Any other ideas?

Thank you in advance,
Marek


-----Original Message-----
From: Francois Pepin [mailto:francois at sus.mcgill.ca] 
Sent: 18 June 2010 20:41
To: marek piatek (BI)
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] different color for a subset of points on heatmap

HI Marek,

The easiest way I can think of:

One would be give those genes a different set of values. So if all your data is between -5 to 5, have the special genes from say 10 to 20. Then you can send it a set of colors that covers everything.

Here's an example where half is positive and half is negative. You can see the transparent colors in half of the columns as opposed to the non-transparent ones otherwise.

> heatmap(matrix(c(1,runif(49),-1,-runif(49)),10),col=cbind(heat.colors(20,alpha=0.25),heat.colors(20,alpha=1)))

You'll need to be a bit careful to get the colors to match. I put the 1 and -1 to make sure that we cover the range and the colors and and values match.

HTH,

Francois

On Jun 18, 2010, at 6:38 AM, marek piatek (BI) wrote:

> Hi all,
> 
> Is there any way to use different color on a subset of points on a heatmap?
> I just would like see a particular set of genes standing out from the rest.
> 
> Thank you,
> Marek
> 
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