plot_densitree: Get a densiTree plot from a set of opentree_chronograms

View source: R/plots.R

plot_densitreeR Documentation

Get a densiTree plot from a set of opentree_chronograms

Description

Get a densiTree plot from a set of opentree_chronograms

Usage

plot_densitree(chronograms, include = TRUE, ...)

Arguments

chronograms

A list of chronograms as multiPhylo or as a plain list object.

include

Boolean or numeric vector. Default to TRUE, keep all chronograms in chronograms. If FALSE, exclude chronograms with only two tips. If numeric, it is used as indices to subset chronograms object.

...

Arguments passed on to phangorn::densiTree

type

a character string specifying the type of phylogeny, so far "cladogram" (default) or "phylogram" are supported.

alpha

parameter for semi-transparent colors.

direction

a character string specifying the direction of the tree. Four values are possible: "rightwards" (the default), "leftwards", "upwards", and "downwards".

optim

not yet used.

scaleX

scale trees to have identical heights.

col

a scalar or vector giving the colours used to draw the edges for each plotted phylogeny. These are taken to be in the same order than input trees x. If fewer colours are given than the number of trees, then the colours are recycled.

width

edge width.

lty

line type.

cex

a numeric value giving the factor scaling of the tip labels.

font

an integer specifying the type of font for the labels: 1 (plain text), 2 (bold), 3 (italic, the default), or 4 (bold italic).

tip.color

color of the tip labels.

adj

a numeric specifying the justification of the text strings of the labels: 0 (left-justification), 0.5 (centering), or 1 (right-justification).

srt

a numeric giving how much the labels are rotated in degrees.

underscore

a logical specifying whether the underscores in tip labels should be written as spaces (the default) or left as are (if TRUE).

label.offset

a numeric giving the space between the nodes and the tips of the phylogeny and their corresponding labels.

scale.bar

a logical specifying whether add scale.bar to the plot.

jitter

allows to shift trees. a list with two arguments: the amount of jitter and random or equally spaced (see details below)

Details

If [phangorn::densiTree()] throws an error, [plot_densitree()] chooses the chronogram with the most tips as consensus (using [datelife::get_biggest_phylo()]) we found that [phangorn::densiTree()] errors commonly from failing to do a consensus tree.


phylotastic/datelifeplot documentation built on July 14, 2022, 12:35 p.m.