In McTavishLab/physcraperex: Physcraper Workflow Examples

knitr::opts_chunk$set(
  echo = TRUE,
  collapse = TRUE,
  comment = "#>",
  root.dir= "/Users/luna/pj_physcraper/physcraperex"
)

source("../R/plots.R")

This function gets the tree file names saved in data-raw/trees/treebase/studyid folder, and returns the name of the file with all the tree file names:

treefiles_file <- get_file_names(studyid = "S1091")
treefiles_file

Now read that file into R to get the names of the tree files:

all_treefiles <- read.csv(treefiles_file, header = FALSE, colClasses = "character" )
is.character(all_treefiles[,1])

mkdir S1091-pdf

Let's plot everything

sapply(all_treefiles[,1], function(x) trenex2pdf(x))

mkdir data-raw/trees/treebase/S2137
mkdir data-raw/trees/treebase/S2137-pdf

wget "http://purl.org/phylo/treebase/phylows/tree/TB2:Tr5277?format=nexus"
mv TB2:Tr5277?format=nexus data-raw/trees/treebase/S2137/Tr5277.nex

wget "http://purl.org/phylo/treebase/phylows/tree/TB2:Tr5276?format=nexus"
mv TB2:Tr5276?format=nexus data-raw/trees/treebase/S2137/Tr5276.nex

treefiles_file <- get_file_names(studyid = "S2137")
treefiles_file
all_treefiles <- read.csv(treefiles_file, header = FALSE, colClasses = "character" )
is.character(all_treefiles[,1])
sapply(all_treefiles[,1], function(x) trenex2pdf(x, ))