This is my first post so please tell me if I am breaking your rules! My problem is described in the comments of this simplified version of my code. I ...
I have a file with the phylogenetic tree that is the output of doing RAxML. I want to plot this tree with the R package ggtree and show the bootstrap ...
Is it possible to highlight clade by tip labels in ggtree (A_ and B_ in the example below)? Finding node numbers is really annoying especially when yo ...
I am trying to to include my results of ancestral state estimation as pie charts at the nodes of a phylogenetic tree. It works fine for rectangular tr ...
I want to label a specific branch (e.g., "Group 1") on the tree, but I didn't found a specific function to do that. Any ideas? ...
I'm trying to read a Newick-format tree into R. My tree file looks like this: When I read this into R with ape::read.tree(), it appears to correctl ...
I am VERY new to R, so I am sorry if this question is obvious. I would like to add multiple labels to branches in a phylogenetic tree, but I can only ...
I'm trying to make a plot using ggtree - but I'm having some issues when I try to have both the tip points and branches colored. The tree works with b ...
Im trying to add a heatmap to my phylogenetic tree. The range of the heatmap should be from 0 to 100 instead it only covers the the min and max of the ...
Given a tree with tip labels colored by a group eg: The legend will contain a instead of the desired square. ggplot2 documentation says to use "ove ...
I am trying to visualize my ggtree and I seem to be stuck on the last final step; repositioning the tree labels from horizontal to verticle so that th ...
I would like to set x axis on a heatmap ggtree. This is my code , and I got this picture The problem is that when I showed the heatmap, the x axi ...
I am attempting to create a phylogeny tree that shows different coloured tip points for different dorsal patterns, when I first attempted this a few w ...
I have very limited experience coding so please bear with me! I have a newick tree and a .txt file with various cell numbers assigned to various clon ...
I'm creating a tree with a ggtree and gheatmap. I am trying to work out how to remove the space between the tip tiles and/or merge adjacent tiles with ...
I tried to install ggtree by using command >BiocManager::install("ggtree") but in the end in am getting error >Installation paths not writeable, ...
I am trying to plot an ancestral states tree generated in RevBayes using RevGadgets 1.0.0 and ggtree 2.4.2. The call is the following, and all of the ...
I have been trying to plot a tree with color-coded branches and tips using the ggtree package in R. Here is an example code using a tree of Anolis liz ...
I'm trying to remove the x-axis from one plot (the tree on the left should have no x-axis labels, ticks, line, etc.), while keeping the x-axis on the ...
I am trying to add range bars to nodes as described in the treedata book. Here is an example from the book of what I am trying to achieve: Note the ...