plot_gain_loss: plot_gain_loss

In gtonkinhill/panstripe: Pangenome Plots

plot_gain_loss

Description

Plots a expected gain and loss events onto the branches of the phylogeny.

Usage

plot_gain_loss(fit, tip_label = TRUE, text_size = 14, color_pallete = 7)

Arguments

fit	a fitted pangenome model output by running 'panstripe'
tip_label	whether or not to show tree tip labels (default=TRUE)
text_size	adjusts the size of text in the plot
color_pallete	the colour pallete to use. A number between 1 & 9. See 'scale_colour_brewer' for more details

Value

a plot of the phylogeny coloured by the inferred total gene gain/loss events per branch

Examples

sim <- simulate_pan(rate=1e-3)
fA <- panstripe(sim$pa, sim$tree, nboot=0)
plot_gain_loss(fA, color_pallete=7)

gtonkinhill/panstripe documentation built on Feb. 27, 2025, 9:01 p.m.