plot.phyMSAmatched {sitePath} | R Documentation

## Visualize the results

### Description

The plot function to visualize the return of functions in the package. The underlying function applies `ggplot2`. The function name `plot` is used to keep the compatibility with previous versions, but they do not behave like the generic `plot` function since 1.5.4.

A `phyMSAmatched` object will be plotted as a tree diagram.

A `lineagePath` object will be plotted as a tree diagram and paths are black solid line while the trimmed nodes and tips will use gray dashed line.

A `parallelSites` object will be plotted as original phylogenetic tree marked with parallel mutations attached as dot plot.

A `fixationSites` object will be plotted as original phylogenetic tree marked with fixation substitutions.

A `sitePath` object can be extracted by using `extractSite` on the return of `fixationSites`.

A `fixationIndels` object will be plotted as original phylogenetic tree marked with indel fixation.

A `fixationPath` object will be plotted as a `phylo` object. 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.

### Usage

    ## S3 method for class 'phyMSAmatched'
    plot(x, y = TRUE, ...)

    ## S3 method for class 'lineagePath'
    plot(x, y = TRUE, showTips = FALSE, ...)

    ## S3 method for class 'parallelSites'
    plot(x, y = TRUE, ...)

    ## S3 method for class 'fixationSites'
    plot(x, y = TRUE, tipsGrouping = NULL, ...)

    ## S3 method for class 'sitePath'
    plot(x, y = NULL, select = NULL, showTips = FALSE, ...)

    ## S3 method for class 'fixationIndels'
    plot(x, y = TRUE, ...)

    ## S3 method for class 'fixationPath'
    plot(x, y = TRUE, ...)

### Arguments

`x` | The object to plot.
`y` | Whether to show the fixation mutation between clusters. For `lineagePath` object and `sitePath` object, it is deprecated and no longer have effect since 1.5.4.
`...` | 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.
`showTips` | Whether to plot the tip labels. The default is `FALSE`.
`tipsGrouping` | A `list` to hold the grouping of tips for how the tree will be colored.
`select` | For a `sitePath` object, it can have result on more than one evolution pathway. This is to select which path to plot. The default is `NULL` which will plot all the paths. It is the same as `select` in `plotSingleSite`.

### Value

A ggplot object to make the plot.

### Examples

    data(zikv_tree)
    data(zikv_align)
    tree <- addMSA(zikv_tree, alignment = zikv_align)
    plot(tree)
    paths <- lineagePath(tree)
    plot(paths)
    parallel <- parallelSites(paths)
    plot(parallel)
    fixations <- fixationSites(paths)
    plot(fixations)
    sp <- extractSite(fixations, 139)
    plot(sp)
    x <- fixationPath(fixations)
    plot(x)

[Package sitePath version 1.8.4 Index]