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

[Saurin D. Jani]

Hi Thomas,

thank you so much..That ape code helps a lot. I really appreciate that. 

Thanks,
Saurin 

--- On Wed, 11/3/10, Thomas Girke <thomas.girke at ucr.edu> wrote:

> From: Thomas Girke <thomas.girke at ucr.edu>
> Subject: Re: [BioC] Fwd: how to plot corr between two tissues/dendrograms
> To: "Sean Davis" <sdavis2 at mail.nih.gov>
> Cc: "saurin_jani at yahoo.com" <saurin_jani at yahoo.com>, "abosco at email.arizona.edu" <abosco at email.arizona.edu>, "Bioconductor Newsgroup" <bioconductor at stat.math.ethz.ch>
> Date: Wednesday, November 3, 2010, 2:51 PM
> 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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