plot.sitePath {sitePath}R Documentation

Plot the fixation mutation

Description

Visualize the sitePath object which is the basic unit of the result of fixationSites and multiFixationSites.

Usage

## S3 method for class 'sitePath'
plot(x, y = NULL, showTips = FALSE, ...)

Arguments

x

A sitePath object

y

A sitePath object can have more than one fixation path. This is to select which path to plot. The default is NULL which will plot all the paths.

showTips

Whether to plot the tip labels. The default is FALSE.

...

Arguments in plot.phylo functions and other arguments.

Value

The function only makes plot and returns no value (It behaviors like the generic plot function).

See Also

plotSingleSite

Examples

data(zikv_align_reduced)
data(zikv_tree_reduced)
tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced)
paths <- lineagePath(tree)
fixations <- fixationSites(paths)
plot(fixations[[1]])

[Package sitePath version 1.4.2 Index]