phsc.plot.phy.selected.pairs: Plot all short read phylogenies including two individuals

In olli0601/phyloscan:

Plot all short read phylogenies including two individuals

Description

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

Usage

phsc.plot.phy.selected.pairs(
  phs,
  dfs,
  id1,
  id2,
  plot.file = NA,
  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.
id1	Regular expression that identifies the first individual, to be plotted in red.
id2	Regular expression that identifies the first individual, to be plotted in blue.
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.

Value

List of ggtree objects, ready for printing.

olli0601/phyloscan documentation built on April 25, 2024, 4:16 a.m.