plotFixationSites: Plot the result of fixation sites

In Takkoona/sitePath: Phylogeny-based sequence clustering with site polymorphism

Plot the result of fixation sites

Description

Visualize the results of paraFixSites

Usage

plotFixationSites(x, ...)

## S3 method for class 'fixationSites'
plotFixationSites(x, site = NULL, ...)

## S3 method for class 'paraFixSites'
plotFixationSites(x, site = NULL, ...)

Arguments

x	return from paraFixSites
...	further arguments passed to or from other methods.
site	the number of the site according to setSiteNumbering. If not provided, all sites will be plotted as labels on the tree

Value

A ggplot object.

Examples

data(zikv_tree_reduced)
data(zikv_align_reduced)
paraFix <- paraFixSites(zikv_tree_reduced, alignment = zikv_align_reduced)
plotFixationSites(paraFix)

Takkoona/sitePath documentation built on Sept. 28, 2022, 1:24 a.m.