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

[Thomas Girke]

The R code for co-plotting two trees with association lines is:

library(ape)
#two random trees
tree1<-rtree(40) #random tree with 40 leaves
tree2<-rtree(20) #random tree with 20 leaves

#creation of the association matrix
association<-matrix(ncol=2, nrow=40)
association[,1]<-association[,2]<-tree2$tip.label

# standard plot
cophyloplot(tree1, tree2, assoc=association, length.line=4, space=28, gap=3)

# interactive plot with rotations
cophyloplot(tree1, tree2, assoc=association, length.line=4, space=28, gap=3, rotate=TRUE)

Thomas

On Wed, Nov 03, 2010 at 02:33:17PM -0400, Sean Davis wrote:
> On Wed, Nov 3, 2010 at 2:26 PM, Saurin D. Jani <saurin_jani at yahoo.com>wrote:
> 
> > Hi Sean,
> >
> > thanks for your email and PDF ..that looks fantastic..The Image with
> > Heatmap...of two tissues...That exactly I am looking for..!!
> >
> > In my case..two tissues..I have one Normalized set of TWO classes Control
> > and Experimental..will that work?
> >
> > Do you have R code for that or should I ask author for this?
> >
> >
> There is no R code.  This thread began by a user asking for a way to create
> that PDF.  Thomas Girke just replied that there might be a similar
> functionality in the ape package.
> 
> Sean
> 
> 
> 
> > Thank you so much,
> > Saurin
> >
> >
> >
> > --- On Tue, 11/2/10, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> >
> > > From: Sean Davis <sdavis2 at mail.nih.gov>
> > > Subject: [BioC] Fwd:  how to plot corr between two tissues/dendrograms
> > > To: abosco at email.arizona.edu
> > > Cc: "Bioconductor Newsgroup" <bioconductor at stat.math.ethz.ch>
> > > Date: Tuesday, November 2, 2010, 9:38 PM
> > > ---------- 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
> > >
> > > -----Inline Attachment Follows-----
> > >
> > > _______________________________________________
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> >
> >
> >
> >
> 
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