[R-sig-phylo] Colouring node pies according to a discrete character.
Dear list I am trying to plot the results of an ancestral state reconstruction of 4 discrete traits onto a single phylogeny. What I would like to do is have a pie on each node split into 4 equal segments, and then have the colour of each segment correspond to the probable trait value at that node (black for present, white for absent, for example). Would anyone be able to offer me some guidance as to how to colour the segment based on a dataframe or matrix of trait values rather than the position of the segment in the pie (which is how the piechart legend seems to do it)? An alternative approach to representing 4 discrete traits at each node would be equally welcome! Cheers Henry [[alternative HTML version deleted]] ___ 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/
[R-sig-phylo] What order are the tips of a tree plotted in?
Dear List I am trying to plot two trees facing each other with pie charts at the nodes indicating marginal likelihoods of an ancestral state. I have broken the plotting frame into 3 sections, with one in the centre for the tip labels. I am using text(rep()) to plot the tip labels into this section, but they do not match up with the tips plotted by the ladderised tree. It seems like the plot() function is not plotting the tips in the edge order, and so when the tip labels are written in 1:n order, they do not match up. How can I reorder the tip labels to match the order in which the tips are plotted by plot()? I am happy with the tip order on the plotted tree, so I would rather work out how to reorder the tip labels in the text() command, rather than reorder the tips on the tree. I hope that makes sense! Henry Ferguson-Gow [[alternative HTML version deleted]] ___ 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/
[R-sig-phylo] utilise more data by making polytomies
Hi All I have a large dataset and a large tree, however the intersection between them both is quite low. As a supplement to analyses solely on the species that appear in both the dataset and the tree I thought I could take the species that are present in the dataset and not the tree, and add those tips in as a polytomy with their congenerics present on the tree. Is there a method in R that would help me to do this? Many thanks Henry [[alternative HTML version deleted]] ___ 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/
[R-sig-phylo] PGLS on a sample of trees
Hi I used the method of Kuhn et al (2011) to resolve polytomies in my tree leaving me with a posterior of thousands of trees. I was wondering how I would go about using PGLS on a sample of these trees so that the uncertainty in the resolution of the polytomies is incorporated into my analysis (i.e. some kind of combined coefficients and confidence intervals taken from multiple PGLS tests). This seems preferable to using either a tree summarised from the posterior or the initial tree complete with polytomies/arbitrarily resolved polytomies. Thanks Henry [[alternative HTML version deleted]] ___ 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/
