search

carolindahms / TreeMix

Scripts to analyze data using TreeMix. This pipeline runs TreeMix with bootstrapping, helps choose number of migration events and creates a consensus tree. It plots the maximum likelihood tree with bootstrap values, drift and residuals and calculates statistics for every migration event, such as migration support, standard error and p-values.
22 stars 1 forks source link

Issue with viualization of bootstraped tree #10

Open rezakhalkhali opened 10 months ago

rezakhalkhali commented 10 months ago

I run treemix with bootstraping using Treemix_bootstrap.sh (BITE R package) with one migration event. it worked without any error. Now when I want to draw the tree, the tree is drawn but without any migration event and I get the following warning message.

Warning message:
In max(e[e[, 5] == "MIG", 4]) :
  no non-missing arguments to max; returning -Inf

I have used the following commands for this analysis:

./Treemix_bootstrap.sh treemix.gz 1 8 1000 horse 100 ~/phylip-3.697/exe/consense out_bootstraped

source("treemix_boostrap.R")

source("newick.split.R")

source("plotting_funcs.R")

treemix.bootstrap(in.file = "infile_bootstraped",
                  out.file = "test",
                  phylip.file = "bootstraped_outtree.newick", nboot = 100,
                  cex=0.5, xmin = -0.005, disp = 0.001,
                  boot.legend.location = "top", xbar = 0.05)

Updated: For more clarify

The interesting thing is that after running the Treemix_bootstrap.sh program for each number of migration event (m), in the tree visualization stage, the number of observed migration events on constructed tree is one less than the number of migration event in the previous stage. For example, I run Treemix_bootstrap.sh program based on two migration events, but its visualized tree shows only one migration event, and when I run it with one event, its tree does not have any migration event. Please, those who have worked in this field, help me to solve this issue