itol_boxplot: create itol boxplot file

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

create itol boxplot file

Description

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

Usage

itol_boxplot(
  df,
  dataset_label,
  out_file = "itol_boxplot.txt",
  out_dir = getwd(),
  key_color = "#ff0000",
  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
key_color	The color for the legend key
WIDTH	Maximum width

Details

If a data.frame is provided, the row names must exactly match the tree node labels. If a data.table or tibble is provided, the first column values must exactly match the tree node labels. Columns in the table must include: minimum,q1,median,q3,maximum,(extreme_value1),(extreme_value2)

Examples

# data.frame
df = data.frame(minimum = c(1,2,1), q1 = c(2,3,3), median = c(3,5,4), q3 = c(4,6,5), maximum = c(5,8,6), row.names = LETTERS[1:3])
itol_boxplot(df, 'test_label')
# data.table
dt = data.table(taxa = LETTERS[1:3], minimum = c(1,2,1), q1 = c(2,3,3), median = c(3,5,4), q3 = c(4,6,5), maximum = c(5,8,6))
itol_boxplot(dt, 'test_label')

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