Agus,
Whether the background appears transparent or not depends on the device
where you plot the tree. On Linux, the default device (X11) is transparent:
par(bg)
[1] transparent
When plotting in a file, the default depends on the file format: pdf()
has transparent background, but png()
Many thanks Marcio and Emmanuel!
That solved my problems to plot the tree.
2012/8/22 Emmanuel Paradis emmanuel.para...@ird.fr
Agus,
Whether the background appears transparent or not depends on the device
where you plot the tree. On Linux, the default device (X11) is transparent:
par(bg)
That seems like it would be OK, at least if you think it is OK for
nonphylogenetic PCA.
An alternative is to simulate data along your phylogeny, analyze it the same
way, do it a couple thousand times, then make an empirical null distribution
of, say, the eigenvalues when the data have no
