[BioC] Fwd: how to plot corr between two tissues/dendrograms

Thomas Girke thomas.girke at ucr.edu
Wed Nov 3 18:35:31 CET 2010


The phylogenetics package ape on CRAN has a variety of tree plottings facilities 
that come close to what you are looking for:
http://cran.at.r-project.org/web/packages/ape/index.html

For instance, take a look at the last image on their screenshot site: 
http://ape.mpl.ird.fr/ape_screenshots.html

In general, ape is a very nice resource for customizing trees for gene
expression, phylogenic or many other use cases.

Thomas


On Tue, Nov 02, 2010 at 09:38:25PM -0400, Sean Davis wrote:
> ---------- Forwarded message ----------
> From: abosco at email.arizona.edu <abosco at email.arizona.edu>
> Date: Tue, Nov 2, 2010 at 9:28 PM
> Subject: Re: [BioC] how to plot corr between two tissues/dendrograms
> To: "Davis, Sean (NIH/NCI) [E]" <sdavis2 at mail.nih.gov>
> 
> 
> Hi Sean,
> 
> 
> Thanks for your email.
> 
> I have attached the figure in PDF..
> 
> To clarify, each cluster dendrogram represents the gene coexpression pattern
> within each tissue, and the blue links represent gene-gene correlations
> between
> tissues (ie similar idea to Dobrin et al. Genome Biol. 2009;10(5):R55.
> Epub 2009
> May 22).
> 
> The idea is to construct gene coexpression modules for each tissue
> independently, then quantify molecular interactions between the two tissues.
> 
> 
> Best regards,
> 
> 
> Anthony Bosco
> 
> 
> 
> Quoting Sean Davis <sdavis2 at mail.nih.gov>:
> 
> > On Mon, Nov 1, 2010 at 7:35 PM, <abosco at email.arizona.edu> wrote:
> >
> >> Dear list,
> >>
> >>
> >> I have some microarray data in which gene expression was profiled in two
> >> different tissues, collected at the same time from the same subjects.
> >>
> >> I would like to use hierarchical clustering initially to cluster the gene
> >> expression patterns separately for each tissue.
> >>
> >> Then I would like to correlate gene expression traits between the two
> >> tissues,
> >> and plot the two cluster dendrograms together with links representing the
> >> between tissue correlations of the clustered genes in a single plot (see
> >> hypothetical example in the attached powerpoint slide).
> >>
> >> The problem is that I do not know how to go about plotting this in R.
> >>
> >> Can anyone please point me in the right direction?
> >>
> >>
> > Hi, Anthony.  Powerpoint get's scrubbed, I think.  You may have to put up
> a
> > link to the slide.  I have to admit, I'm not clear on what you want to do.
> >
> > Sean


> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor



More information about the Bioconductor mailing list