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 1.3.1 Index]