plotSingleSite {sitePath} | R Documentation

## Color the tree by a single site

### Description

Plot and color the tree according to amino acid/nucleotide of the selected site. The color scheme depends on the `seqType` set in `addMSA` function.

For `lineagePath`, the tree will be colored according to the amino acid of the site. The color scheme tries to assign distinguishable color for each amino acid.

For `parallelSites`, the tree will be colored according to the amino acid of the site if the mutation is not fixed.

For `fixationSites`, it will color the ancestral tips in red, descendant tips in blue and excluded tips in grey.

### Usage

    plotSingleSite(x, site, ...)

    ## S3 method for class 'lineagePath'
    plotSingleSite(x, site, showPath = TRUE, showTips = FALSE, ...)

    ## S3 method for class 'sitesMinEntropy'
    plotSingleSite(x, site, ...)

    ## S3 method for class 'parallelSites'
    plotSingleSite(x, site, showPath = TRUE, ...)

    ## S3 method for class 'fixationSites'
    plotSingleSite(x, site, select = NULL, ...)

### Arguments

`x` | The object to plot.
`site` | For `lineagePath`, it can be any site within sequence length. For `fixationSites` and `parallelSites`, it is restrained to a predicted fixation site. The numbering is consistent with the reference defined by `setSiteNumbering`.
`...` | Other arguments. Since 1.5.4, the function uses `ggtree` as the base function to make plots so the arguments in `plot.phylo` will no longer work.
`showPath` | If plot the lineage result from `lineagePath`. The default is `TRUE`.
`showTips` | Whether to plot the tip labels. The default is `FALSE`.
`select` | Select which fixation path in to plot. The default is NULL which will plot all the fixations.

### Value

Since 1.5.4, the function returns a ggplot object so on longer behaviors like the generic `plot` function.

### See Also

`plot.sitePath`

### Examples

    data(zikv_tree)
    data(zikv_align)
    tree <- addMSA(zikv_tree, alignment = zikv_align)
    paths <- lineagePath(tree)
    plotSingleSite(paths, 139)
    fixations <- fixationSites(paths)
    plotSingleSite(fixations, 139)

[Package sitePath version 1.10.2 Index]