Re: [R] heatmap.2 - change column & row locations; angle / rotate

From: Karl Brand <k.brand_at_erasmusmc.nl>
Date: Mon, 18 Apr 2011 18:23:12 +0200

Hi Chakravarthy,

[dont forget to Cc the list for useRs with the same Q.]

If you're trying to reuduce the isze of your row or column labels, i think the following arguments of heatmap.2 {gplots} is what you want to adjust- 'cexCol' and 'cexRow'.

Specifically on my question that you ask about, i found the BioC forum helpful:

http://permalink.gmane.org/gmane.science.biology.informatics.conductor/30112

And in fact the phylotemp() function by default pretty much did exactly what i needed, available here:

http://phylotemp.microeco.org/

However, it was pointed out to me that some times the best way to get it just right is using more basic functions, which for heatmaps would be image(). See:

https://www.stat.math.ethz.ch/pipermail/bioconductor/2010-August/034995.html

hth,

karl

On 04/18/2011 10:38 AM, chakri2sai_at_yahoo.co.in wrote:
> Dear Karl Brand,
>
> I am facing same problem as you have faced before (see appended mail below). I am writing to you to find out whether you have found a solution !
>
> I asked a similar question in R-forum (http://r.789695.n4.nabble.com/How-to-save-heatmap-as-image-or-pdf-td3412542.html#a3413871).
>
> Any pointers would be greatly appreciated
>
> Thanks
> Chakravarthy
> Junior Research Fellow
> Tata Institute of Fundamental Research
> Bangalore, India
>
> <quote author='Karl Brand'>
> Esteemed R user's,
>
> I'm struggling to achieve some details of a heatmap using heatmap.2():
>
> 1. Change label locations, for both rows& columns from the default
> right& bottom, to left and top.
> Can this be done within heatmap.2()? Or do i need to suppress this
> default behavior (how) and call a new function to relabel (what)
> specifying locations?
>
> 2. Change the angle of the labels.
> By default column labels are 90deg anti-clock-wise from horizontal. How
> to bring them back to horizontal? Or better, rotate 45deg clock-wise
> from horizontal (ie., rotate 135deg a.clock.wise from default)?
>
> Any suggestions or pointers to helpful resources greatly appreciated,
>
> Karl
>

-- 
Karl Brand <k.brand_at_erasmusmc.nl>
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
P +31 (0)10 704 3455 | F +31 (0)10 704 4743 | M +31 (0)642 777 268

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