fixationPath: Accumulation of fixed mutation as a tree

In Takkoona/sitePath: Phylogeny-based sequence clustering with site polymorphism

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)

Takkoona/sitePath documentation built on Sept. 28, 2022, 1:24 a.m.