plotMutSites {sitePath} | R Documentation

## Plot tree and mutation sites

### Description

The mutated sites for each tip in a phylogenetic tree will be represented as colored dots positioned by their site number.

### Usage

    plotMutSites(x, ...)

    ## S3 method for class 'SNPsites'
    plotMutSites(x, showTips = FALSE, ...)

    ## S3 method for class 'lineagePath'
    plotMutSites(x, ...)

    ## S3 method for class 'parallelSites'
    plotMutSites(x, ...)

    ## S3 method for class 'fixationSites'
    plotMutSites(x, ...)

    ## S3 method for class 'paraFixSites'
    plotMutSites(
      x,
      widthRatio = 0.75,
      fontSize = 3.88,
      dotSize = 1,
      lineSize = 0.5,
      ...
    )

### Arguments

`x` | An `SNPsites` object.
`...` | Other arguments
`showTips` | Whether to plot the tip labels. The default is `FALSE`.
`widthRatio` | The width ratio between tree plot and SNP plot
`fontSize` | The font size of the mutation label in tree plot
`dotSize` | The dot size of SNP in SNP plot
`lineSize` | The background line size in SNP plot

### Value

A tree plot with SNP as dots for each tip.

### Examples

    data(zikv_tree_reduced)
    data(zikv_align_reduced)
    tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced)
    plotMutSites(SNPsites(tree))

[Package sitePath version 1.8.4 Index]