astralProjection: AstralProjection

In chutter/AstralPlane: R Package For Preparing, Running, Analyzing and Plotting for the Species Tree Program ASTRAL-III

AstralProjection

Description

Function for plotting data from the astralPlane format

Usage

astralProjection(
  astral.plane = NULL,
  local.posterior = TRUE,
  pie.plot = TRUE,
  pie.data = c("qscore", "genetree"),
  save.file = NULL,
  pie.colors = c("black", "grey", "white"),
  node.color.text = c("white"),
  node.color.bg = c("black"),
  node.label.size = 0.5,
  tip.label.size = 1,
  pie.chart.size = 1
)

Arguments

astral.plane	AstralPlane S4 object of data generated from AstralPlane function
local.posterior	plot the local posterior support?
pie.plot	select one to plot: 'qscore' the quartet support or 'genetree' proportion of gene trees that support a branch
save.file	if you wish to save to file, put file name. Saves as PDF
pie.colors	select three colors to plot your pie.plot
node.color.text	if local.posterior = TRUE, select the color of posterior support text
node.color.bg	if local.posterior = TRUE, select the color of posterior support background
tip.label.size	size of the tip labels, passed to cex in plotting function
pie.chart.size	size of pie chart, passed to edgelabel plotting function

Value

plots the phylogenetic tree and selected data associated with an AstralPlane object. Can optionally be saved to file as a PDF by giving save.file a file name.

Examples

your.tree = ape::read.tree(file = "file-path-to-tree.tre")
astral.data = astralPlane(astral.tree = your.tree,
                          outgroups = c("species_one", "species_two"),
                          tip.length = 1)

astralProjection(astral.plane = astral.data,
                 local.posterior = TRUE,
                 pie.plot = "qscore",
                 save.file = "test-dataset.pdf",
                 pie.colors = c("purple", "blue", "green"),
                 node.color.text = c("white"),
                 node.color.bg = c("black"),
                 tip.label.size = 0.75,
                 pie.chart.size = 1)

chutter/AstralPlane documentation built on Aug. 29, 2024, 5:21 p.m.