itol_externalshape: create itol external shape file

In leylabmpi/LeyLabRMisc: Ley Lab misc R functions, rmd templates, etc.

create itol external shape file

Description

https://itol.embl.de/help.cgi#shapes

Usage

itol_externalshape(
  df,
  dataset_label,
  out_file = "itol_externalshape.txt",
  out_dir = getwd(),
  legend = NULL,
  WIDTH = 200
)

Arguments

df	A data.frame, tibble, or data.table (see above)
dataset_label	What to label the itol dataset
out_file	Name of the output file
out_dir	Where to write the output
legend	Specify particular legend (see itol_colorstrip)

Details

If a data.frame is provided, the row names must exactly match the tree node labels. The 1st column with be used for plotting. If a data.table or tibble is provided, the first column values must exactly match the tree node labels. The 2nd column will be used for plotting.

Examples

# data.frame input
df = data.frame(shape = c(1,1,2), row.names = LETTERS[1:3])
itol_externalshape(df, 'test_label')
# data.table
dt = data.table(taxa = LETTERS[1:3], shape = c(1,1,2))
itol_externalshape(dt, 'test_label')

leylabmpi/LeyLabRMisc documentation built on Nov. 3, 2022, 3:45 p.m.