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----- > > > > > > > > > _______________________________________________ > > > > 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 > > > > > > > > > > > > > > > > ??? [[alternative HTML version > deleted]] > > > > _______________________________________________ > > 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 > > >