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KlausVigo / phangorn

Phylogenetic analysis in R
http://klausvigo.github.io/phangorn/
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densiTree not working #146

Closed Cosmophasis closed 1 year ago

Cosmophasis commented 1 year ago

Hi Klaus,

I am trying to plot a DensiTree with my species tree output from StarBEAST2. I use read.nexus to read my trees and then use the trees as x in densiTree. The output shows the tip labels and the time axis but there's no trees.

I have attached a file for your reference. Geo_star_eupa2_species.txt

Thanks in advance, Colin

KlausVigo commented 1 year ago

Dear Colin, you have 1001 trees, so you might want to change the parameter alpha (opacity) to a larger value and also increase the line width so that the chance that are lines are plotted on top of each other. E.g. try densiTree(x, width = 5, alpha=.01) Kind regards, Klaus

Cosmophasis commented 1 year ago

Hi Klaus, Thanks for the quick response. For some reason it works perfectly fine now with the default parameters. Thanks again, Colin