Hi, I seek your help in converting my species cladogram to a dendrogram for use as an external column dendrogram for heirarchical clustering of a heatmap's Y axis.
My species cladogram *.te file looks as follows, but I wonder if you see any error(s) in it. (((((((((((((Mt3.5v5, Mt4.0v1), Car), (((Pvu186, Pvu218), (Gma109, Gma189)), Cca))), (((Ppe139, Mdo196), Fve226), Csa122)), ((((((((Ath167, Aly107), Cru183), (Bra197, Tha173)), Cpa113), (Gra221, Tca233)), (Csi154, (Ccl165, Ccl182))), ((Mes147, Rco119),(Lus200, (Ptr156, Ptr210)))), Egr201)), Vvi145), ((Stu206, Sly225), Mgu140)), Aco195), (((Sbi79, Zma181),(Sit164, Pvi202)), (Osa193, Bdi192))), Smo91), Ppa152), (((Cre169, Vca199), Csu227), ((Mpu228, Mpu229), Olu231))); I can open it without any error message using Dendroscope tree viewer software. But that does not mean that it is error proof. In R, I can use read.tree or read.newick to open this file However, plot(mytree) yields an error as follows: If I collapse the single nodes using > mytree=collapse.singles(mytree) plot(mytree) works, but looks totally bizarre with topology that is totally different from what I get using Dendrogram.... I am at a loss of how to make this species cladogam to dendrogram conversion working. I hope someone here can point out my mistake(s) and help me fix them. Thanks! -- Anand K.S. Rao PhD candidate, Plant Biology <http://www-plb.ucdavis.edu/> with a Designated Emphasis in Biotechnology <http://deb.ucdavis.edu/>, Doug Cook Laboratory for Legume Genetics and Genomics, Dept. of Plant Pathology <http://plantpathology.ucdavis.edu/>. UC- Davis <http://ucdavis.edu/>, CA - 95616 USA | [email protected] | (530) 574-5134 | LinkedIn <http://www.linkedin.com/in/anandksrao> _________________________________________________________________________ CTTATTGTTGAACTTOAATGGTGCTAATGATCCTCGTOTCTCCTGAACGT - translate THAT! [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
