plot.expansionsMCMC: Plot results

In dhelekal/CaveDive: Phylodynamics for Clonal Expansion

Plot results

Description

Plot results

Usage

## S3 method for class 'expansionsMCMC'
plot(
  x,
  ...,
  mode = c("summary", "modes", "persistence", "traces", "mtraces", "popfunc"),
  k_modes = NULL,
  correlates = list(),
  corr_axis_title = list(),
  corr_legend_title = list(),
  gt.K = NULL,
  gt.t_mid = NULL,
  gt.time = NULL,
  branch = NULL,
  t_max = NULL,
  tree_scale = NULL
)

Arguments

x	expansionsMCMC object
...	further arguments passed to plot
mode	one of "summary" - produces a summary plot for this chain, "modes" - plot marginals for top k posterior probability branches, "persistence" - plot posterior probability of expansion tip membership, "traces" - plot traces for N, number of expansions, and branches , "mtraces" - plot traces for expansion parameters for top k posterior probability branches, "popfunc" - plot posterior population functions.
k_modes	number of highest posterior probability branches to generate plots for used by "modes", "mtraces", "popfunc"
correlates	(Optional) correlates to plot alongside persistence matrix used by "persistence" plot
corr_axis_title	(Optional) axis title for correlate map used by "persistence" plot
corr_legend_title	(Optional) legend title for correlate map used by "persistence" plot
gt.K	true K values if plotting for diagnostic purposes
gt.t_mid	true t_mid values if plotting for diagnostic purposes
gt.time	true expansion time values if plotting for diagnostic purposes
branch	which branch to generate "popfunc" plot for
t_max	upper x-axis limit for "popfunc" plot
tree_scale	time unit axis label

dhelekal/CaveDive documentation built on June 11, 2024, 4:32 p.m.