phsc.plot.phycollapsed.selected.individuals: Plot short read phylogenies and highlight individuals
In olli0601/Phyloscanner.R.utilities:

phsc.plot.phycollapsed.selected.individuals

R Documentation

Plot short read phylogenies and highlight individuals

Description

This function plots short read phylogenies and highlights the clades of two individuals in red and blue.

Usage

phsc.plot.phycollapsed.selected.individuals(
  phs,
  dfs,
  ids,
  plot.cols = rainbow(length(ids)),
  plot.cols.background = function(n) {     rainbow_hcl(n, start = 60, end = 240, c = 30,
    l = 80) },
  drop.blacklisted = TRUE,
  tip.regex = "(.*)_read_([0-9]+)_count_([0-9]+)",
  plot.file = NA,
  drop.less.than.n.ids = 2,
  pdf.h = 50,
  pdf.rw = 10,
  pdf.ntrees = 20,
  pdf.title.size = 40
)

Arguments

`phs`	List of trees in ape format
`dfs`	data.table with mandatory column 'IDX' and optional column 'TITLE'. IDX is the index of all phylogenies in 'phs' that are to be plotted. TITLE is a title for each sub-plot, for example specifying a window.
`ids`	Vector of regular expressions that identify individuals to be highlighted in colour.
`plot.cols`	Vector of colours for each individual
`drop.blacklisted`	Logical, indicating if all blacklisted taxa should be dropped prior to plotting.
`plot.file`	If not missing, the phylogenies will be printed to file.
`pdf.h`	Height of the pdf file in inches.
`pdf.rw`	Relative width of the pdf file, internally multiplied by the number of phylogenies to give the total width in inches.
`pdf.ntrees`	Number of trees per pdf.
`pdf.title.size`	Size of pdf title in inches.
`group.redo`	Logical, indicating if the colour groups should be recalculated from ids.