Dear Klaus, Dear phylo-R users,
your code does work but is still not doing exactly what I want. I am hoping to get the number of the edge which leads to A automatically through sth similar to what I have for the colouring of the tips. (color[which(tree$tip.label=="A")]<-"red") Also, I would like to colour the other branches (from earlier "split-off- nodes") leading to A in red too. Let me try to clarify: I work on creating a tree for a protein family and want to colour branches based on a selection of protein names (by creating a vector which contains all the names of proteins which share properties), (for example using sth like this color[which(tree$tip.label%in%VECTORWITHNAMES)]<-"red") and these proteins cluster in the same part of the tree, thus I want to colour all the branches leading to these protein-tips red (or any other colour). To add some complexity, there are different properties that different proteins in that tree share, so in the end I would like to have different colours in the tree, with each colour reflecting another property... Any ideas if this is possible in R or with another tool? Thanks for the help G Gudrun Gygli, MSc PhD candidate Wageningen University Laboratory of Biochemistry Dreijenlaan 3 6703 HA Wageningen The Netherlands Phone 31 317483387 e-mail: gudrun.gy...@wur.nl - - - - - - - - - - - - - - - - - - Project information: http://www.wageningenur.nl/en/show/Bioinformatics-structural-biology-and-molecular-modeling-of-Vanillyl-Alcohol-Oxidases-VAOs.htm ________________________________ From: Klaus Schliep <klaus.schl...@gmail.com> Sent: Tuesday, January 26, 2016 10:34 AM To: Gygli, Gudrun Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] colouring tree branches like tips Dear Gudrun, almost right, try this code: set.seed(42) tree<-pbtree(n=10) tree$tip.label<-c("A","B","Q","M","C","D","F","X","Z","W") color<-rep("black",length(tree$tip.label)) color[which(tree$tip.label=="A")]<-"red" edgecolor<-rep("black",length(tree$edge)) plot(tree) edgelabels() # edge 3 leads to A edgecolor[3]<-"red" plot(tree, edge.color=edgecolor) Regards, Klaus On Tue, Jan 26, 2016 at 3:06 AM, Gygli, Gudrun <gudrun.gy...@wur.nl<mailto:gudrun.gy...@wur.nl>> wrote: Dear fellow phylo-R users, I am trying to colour tree (terminal and non terminal) branches in the same colour as the tip of said branch. To illustrate, see the code below, which is almost doing what I want. You can see that only colouring a specific tip, which is called A in this example, is no problem. However, I cannot colour the branches leading up to tip "A" in red with this code. I tried using tree$edge, but this is not working the way I thought. Does anyone know how to colour all the branches leading up to tip "A" in red? tree<-pbtree(n=10) tree$tip.label<-c("A","B","Q","M","C","D","F","X","Z","W") color<-rep("black",length(tree$tip.label)) color[which(tree$tip.label=="A")]<-"red" edgecolor<-rep("black",length(tree$edge)) edgecolor[which(tree$tip.label=="A")]<-"red" Thanks a lot for any help. Best regards G Gudrun Gygli, MSc PhD candidate Wageningen University Laboratory of Biochemistry Dreijenlaan 3 6703 HA Wageningen The Netherlands Phone 31 317483387 e-mail: gudrun.gy...@wur.nl<mailto:gudrun.gy...@wur.nl> - - - - - - - - - - - - - - - - - - Project information: http://www.wageningenur.nl/en/show/Bioinformatics-structural-biology-and-molecular-modeling-of-Vanillyl-Alcohol-Oxidases-VAOs.htm _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org<mailto:R-sig-phylo@r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
