This is really a programming question but
ggtree might be too obscure for this question to be posted on StackOverFlow as a general R related question.
I am having trouble extrapolating this this tutorial and the
%<+% operator in
I have a Newick file and a table that has a number for every tip and node in the Newick file. I want to produce a final graphic that shows a tree where the numbers from the table are shown next to respective tips and nodes.
What I want to do is close to the tutorial, I want to take a tree object and use a data-frame where one column is node-names and the second column holds numerical information per node. I want to attach the information from the data-frame to the tree object.
The data-frame looks something like this:
|Node / tips||Count|
So, I want to ultimately display the number 12 next to node A and number 14 next to node B while keeping the names intact. Now I have the code working up to the following point:
(I am really only just working my way through learning R's grammar of graphics and R in general, so assume I am doing something wrong.)
library(ggplot2) library(ggtree) x <- read.tree("tree.txt") info <- read.csv("counts.csv",sep = '\t',header=TRUE) p <- ggtree(x) %<+% info + xlim(-.1, 5) p2 <- p + geom_tiplab(offset = 0.2) + geom_tippoint(aes(caption = Increase)) + theme_tree2()+geom_tiplab(align=TRUE, linesize=.5)+ xlim(0,25) ggsave("test_2.pdf", width = 60, height = 80, units = "cm", limitsize = FALSE) print(p2) ?geom_tippoint::aes() # is there a way to list all the option inside geom_tippoint::aes()
The above code overlays the
Newick_label column with the node names instead of attaching the value in the second column.
But specifically, I am at a loss as to how I can list the options available within
geom_tippoint(aes()). I can use
?geom_tippoint to access the documentation of
geom_tippoint but I think my task needs to manipulate options within the
aes() function and the the geom_tippoint() documentation does not list all the
aes() options available. And am stuck trying different keywords for
Can that be done in
ggtree or is this specific application of
ggtree obscure enough that there is no way to do this and produce a legible graphic? (eg issue: the graphic getting mushy overlays). I have hundred of (not uniform) genes trees so splitting data for each layer (node and tips) might be not the best way.
The files if anyone wants to try: counts and tree
Clarification on the labels for nodes and tips, I want to label both if possible. The data contains information for both.
Is annotating tips AND nodes out of the ordinary? Tips and nodes are technically different but I have quantitative data at both levels and am looking for the option to annotate at both levels.
geom_tiplab()if I get the chance this week I will post a response on a hypothetical data set, but can't do this today. Oh wait, maybe not, there is still the
nodeissue - those are different solutions - might be easier just to copy part of the tree file to see what 'A' and 'B' are. At present the table is called
node/tips: a tip is a subset of the nodes. $\endgroup$
geom_tiplab()for now, thanks! $\endgroup$