Sean Davis | 25 Jul 21:07 2010
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Re: heatmap.2 - change column & row locations; angle / rotate

On Sun, Jul 25, 2010 at 9:04 AM, Karl Brand <k.brand@...> wrote:

> Cheers Amos,
>
> From this post response its clear there's no simple way to do this with
> available R heatmap functions. And with your example in hand can plow on and
> hopefully get a workable solution. Thanks alot for this!
>
> Karl
>
>
>
For a totally different approach:

library(latticeExtra)
 ?dendrogramGrob

Sean

>
> On 7/23/2010 3:16 PM, Amos Folarin wrote:
>
>> Hi Karl,
>> The only way I know to rotate the labels is pretty crude. You will have to
>> reconstitute the labels using the text() function.
>> The caveat here is you'll have to play around to get this right.
>>
>> Try something like this:
>>
>> Library(gplots)
>> x<- matrix(rnorm(25), 5)
>> heatmap.2(x, labRow="", labCol="") #remove the labels
>> # plot the text, perhaps someone can think of a smarter way of getting the
>> labels in position...
>> text(seq(par("xaxp")[1]+par("xaxp")[2]/par("xaxp")[3], par("xaxp")[2],
>> by=0.8*(par("xaxp")[2]/par("xaxp")[3])),par("usr")[3], par("usr")[3] - 0.2,
>> labels = c("first", "second", "third", "fourth", "fifth"), srt = 45, pos =
>> 1, xpd = TRUE)
>>
>> Unfortunatetly the heatmap is laid out in a 2x2 matrix with the
>> dendrograms and key in the first 3 cells and the heatmap in the bottom right
>> -- I'm not sure if it is possible to access the axes of this element
>> independently. If one could then it might make positioning the labels for
>> the heatmap moiety of the plot simple.
>>
>>
>>
>> Amos
>>
>>
>>
>> -----Original Message-----
>> From: bioconductor-bounces@... [mailto:
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>> bioconductor-request@...
>> Sent: 23 July 2010 11:00
>> To: bioconductor@...
>> Subject: Bioconductor Digest, Vol 89, Issue 22
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>> Today's Topics:
>>
>>    1. heatmap.2 - change column&  row locations; angle  / rotate
>>       (Karl Brand)
>>    2. In limma, how to set quility weight for each spot. (Jinyan Huang)
>>    3. Re: In limma, how to set quility weight for each spot.
>>       (Sean Davis)
>>    4. Re: exonmap/xmapcore error (Crispin Miller)
>>    5. Heatmap.2 scale problems: Sacling inside the function gives
>>       different results than scaling outside!!! (Elmer Fern?ndez)
>>    6. Re: exonmap/xmapcore error (Crispin Miller)
>>    7. Re: Heatmap.2 scale problems: Sacling inside the function
>>       gives different results than scaling outside!!! (Sean Davis)
>>    8. ShortRead QA (Alex Gutteridge)
>>    9. Re: Heatmap.2 scale problems: Sacling inside the function
>>       gives different results than scaling outside!!! (Bazeley, Peter)
>>   10. Re: Heatmap.2 scale problems: Sacling inside the function
>>       gives different results than scaling outside!!! (Benjamin Otto)
>>   11. Biostrings - vcountPattern optimization (Erik Wright)
>>   12. Re: Biostrings - vcountPattern optimization (Steve Lianoglou)
>>   13. problem about hgu133plus2 annotation (Gina Liao)
>>   14. Re: Heatmap.2 scale problems: Sacling inside the function
>>       gives different results than scaling outside!!! (Elmer Fern?ndez)
>>   15. Re: problem about hgu133plus2 annotation (Marc Carlson)
>>   16. Re: problem about hgu133plus2 annotation (James W. MacDonald)
>>   17. Re: Biostrings - vcountPattern optimization (Patrick Aboyoun)
>>   18. Re: feature request - pairwiseAlignment() in Biostrings
>>       (Patrick Aboyoun)
>>   19. Re: Biostrings - vcountPattern optimization (Erik Wright)
>>   20. Re: feature request - pairwiseAlignment() in Biostrings
>>       (Michael Lawrence)
>>   21. Re: Heatmap.2 scale problems: Sacling inside the function
>>       gives different results than scaling outside!!! (Steve Lianoglou)
>>   22. Re: Biostrings - vcountPattern optimization (Herv? Pag?s)
>>   23. Re: Heatmap.2 scale problems: Sacling inside the function
>>       gives different results than scaling outside!!! (Elmer Fern?ndez)
>>   24. Re: Heatmap.2 scale problems: Sacling inside the function
>>       gives different results than scaling outside!!! (Sean Davis)
>>   25.  the design matrix again (Gordon K Smyth)
>>   26. Open Postdoc Positions (Thomas Girke)
>>   27. Re: htQPCR (Heidi Dvinge)
>>   28. Re: Problem with function limmaCtData in HTqPCR package:
>>       "leading minor of order 2 is not positive definite" (Heidi Dvinge)
>>   29. building a refseq-based transcriptDb: warnings of interest?
>>       (Vincent Carey)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 22 Jul 2010 12:18:16 +0200
>> From: Karl Brand<k.brand@...>
>> To: bioconductor@...
>> Subject: [BioC] heatmap.2 - change column&  row locations; angle  /
>>        rotate
>> Message-ID:<4C481AE8.7060701@...>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> <Reposting from "r-help@...">
>>
>> Esteemed BioC 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
> Department of Genetics
> Erasmus MC
> Dr Molewaterplein 50
> 3015 GE Rotterdam
> T +31 (0)10 704 3457 |F +31 (0)10 704 4743 |M +31 (0)642 777 268
>
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