Dear Karla,
First, I suggest you manage your alignment files in FASTA rather than in
NEXUS: this is much more efficient in practice.
You may read an alignment in a NEXUS file using read.nexus.data() in
ape, then convert it in "DNAbin" class with as.DNAbin(). The cbind()
funtion in ape
Hi Gabriel.
For future reference, phytools has a couple of functions that could be
useful. add.simmap.legend (e.g.,
http://www.phytools.org/blog/18Nov16-post.png), used on my blog here:
http://blog.phytools.org/2016/11/updates-to-permit-user-control-of-line.html
and add.color.bar (e.g.,
This is what finally worked for me for setting up the plot with the
legend how I wanted:
(result is in attached PDF)
Perhaps some of you will find it useful for your own work...
#Zeileis et al.'s function for drawing palettes
pal <- function(col, border = "light gray", ...)
{
n <- length(col)
Dear Karla,
what is exactly the problem and what did you try? There is a (generic)
function cbind for "phyDat" objects in phangorn, which should exactly do
this task.
library(phangorn)
data(Laurasiatherian)
(x1 <- subset(Laurasiatherian, 1:20))
(x2 <- subset(Laurasiatherian, 11:30))
cbind(x1,
Dear all,
I got alignments for many loci as nexus files and I've been trying to
concatenate them into a single alignment. However, some taxa are missing
from some of the loci, so that simple alternatives such as cbinding
individual files in phangorn doesn't work.
Any help with this will be
