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, showTips = FALSE, ...)

### Arguments

`x` | A `lineagePath` object
`y` | Whether plot the nodes from the `extendedSearch` in `fixationSites`
`showTips` | Whether to plot the tip labels. The default is `FALSE`.
`...` | 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))

[Package sitePath version 1.3.1 Index]