plot_pangenome_cumulative: plot_pangenome_cumulative

In gtonkinhill/panstripe: Pangenome Plots

plot_pangenome_cumulative

Description

Plots the cumulative branch length versus the cumulative number of gene gain and loss events. This is similar to the style of plot produced by TempEst. This function plots only the data points as the fit can not be included as Panstripe models the individual branches rather than the cumulative total.

Usage

plot_pangenome_cumulative(
  fit,
  plot = TRUE,
  legend = TRUE,
  text_size = 14,
  color_pallete = 6,
  facet = FALSE,
  smooth = FALSE
)

Arguments

fit	the result of running the 'panstripe' function. Multiple fits can be passed as a named list.
plot	whether to generate the plot (default) or return a data.frame
legend	toggles the display of the legend on and off
text_size	the base text size of the plot (default=14)
color_pallete	the pallete number passed to 'scale_fill_brewer'
facet	whether or not to generate separate plots for each pangenome (default=FALSE).
smooth	adds a linear line to aid the eye in seeing patters. This is NOT the model fit inferred by Panstripe. (default=FALSE)

Value

either a ggplot2 object or a 'data.frame' with the data needed to recreate the plot

Examples

sim <- simulate_pan(rate=1e-4)
fA <- panstripe(sim$pa, sim$tree, nboot=0)
plot_pangenome_cumulative(fA, color_pallete=6)
sim <- simulate_pan(rate=1e-3)
fB <-panstripe(sim$pa, sim$tree, nboot=0)
plot_pangenome_cumulative(list(a=fA,b=fB), color_pallete=6, smooth=TRUE)

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