R: Visualize phylogenetic lineages

plot.lineagePath {sitePath}

R Documentation

Visualize phylogenetic lineages

Description

Visualize lineagePath object. A tree diagram will be plotted and paths are black solid line while the trimmed nodes and tips will use grey dashed line.

Usage

## S3 method for class 'lineagePath'
plot(x, y = TRUE, ...)

Arguments

`x`	A `lineagePath` object
`y`	Whether plot the nodes from the `extendedSearch` in `fixationSites`
`...`	Arguments in `plot.phylo` functions.

Value

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

Examples

data("zikv_tree")
data("zikv_align")
tree <- addMSA(zikv_tree, alignment = zikv_align)
plot(lineagePath(tree, 0.996))

[Package sitePath version 1.0.3 Index]