Dear All,
I'm a new user of R in phylogenetics and population genetics. So,
please, apologize me in advance if what I'm asking is a basic and banal
question. Briefly, I used the function mst of the package APE to produce
a minimun spanning tree startin from a distance matrix. I used the
default argument graph ("nsca" or "cirle"), or I plotted the samples by
using externally produced coordinates (i.e. PCA coordinates). In all the
cases, I didn't manage to apply colours to a set of defined categories
of samples. I tried by defining a categorical vector and using the
argument col of the function plot, like in this example:
colour<-as.character(PCAcor[,3])
plot(MSTtre, x1 = PCAcor[,1], x2 = PCAcor[,2], col=colour)
Or I directly use the argument col of the function plot, like this (one
among the various tempts):
plot(MSTtre, graph="nsca", col="blue", "black").
In any case, I didn't get back any error message, but the plot was
always black and white.
May you suggest me the right approach?
Many thanks!
Regards,
Fabrizio
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