fixationPath {sitePath} | R Documentation

## Accumulation of fixed mutation as a tree

### Description

The tips are clustered according to the fixation sites. The transition of fixation sites will be plotted as a phylogenetic tree. The length of each branch represents the number of fixation mutation between two clusters. The name of the tree tips indicate the number of sequences in the cluster.

### Usage

    fixationPath(x, ...)

    ## S3 method for class 'sitesMinEntropy'
    fixationPath(x, minEffectiveSize = NULL, ...)

    ## S3 method for class 'fixationSites'
    fixationPath(x, minEffectiveSize = NULL, ...)

### Arguments

`x` | The return from `fixationSites` function.
`...` | Further arguments passed to or from other methods.
`minEffectiveSize` | The minimum size for a tip cluster.

### Value

An `fixationPath` object

### Examples

    data(zikv_tree_reduced)
    data(zikv_align_reduced)
    tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced)
    paths <- lineagePath(tree)
    mutations <- fixationSites(paths)
    fixationPath(mutations)

[Package sitePath version 1.6.6 Index]