On Mon, Jun 21, 2010 at 4:24 AM, marek piatek (BI) <marek.piatek@bbsrc.ac.uk
> 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).
>
>
If you can use heatmap.2, take a look at the rowsep (or colsep) arguments to
set off a block of genes.  Also, you could consider adding RowSideColors to
your gene of interest.

Sean


> Any other ideas?
>
> Thank you in advance,
> Marek
>
>
> -----Original Message-----
> From: Francois Pepin [mailto:francois@sus.mcgill.ca]
> Sent: 18 June 2010 20:41
> To: marek piatek (BI)
> Cc: bioconductor@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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