[BioC] different color for a subset of points on heatmap
michael watson (IAH-C)
michael.watson at bbsrc.ac.uk
Mon Jun 21 23:10:03 CEST 2010
I wouldn't necessarily change the colours (which mean something, scientifically).
Not sure if anyone has mentioned it yet, but how about:
mat <- matrix(rnorm(5000), ncol=10)
heatmap.2(mat, key=FALSE, trace="none", col=greenred.colors(70), rowsep=c(50,100), sepcolor="yellow")
From: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] On Behalf Of David Schruth [dschruth at u.washington.edu]
Sent: 21 June 2010 19:07
To: marek piatek (BI)
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] different color for a subset of points on heatmap
You could try using densCols:
my.colors <- c('red','blue','purple','orange')
x =lapply(seq(2,10,by=2), function(j) rnorm(1000,j))
y =lapply(seq(2,10,by=2), function(k) rnorm(1000,k))
lapply(1:4, function(i) points(x[[i]],y[[i]],
marek piatek (BI) wrote:
> 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,
> -----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.
> 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.
> 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,
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