R: Color the tree by a single site

plotSingleSite {sitePath}

R Documentation

Color the tree by a single site

Description

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

For multiFixationSites, it will color the tips which have their site fixed. The color will use the same amino acid color scheme as plotSingleSite.lineagePath

Usage

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

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

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

Arguments

`x`	A `fixationSites` object from `fixationSites` or the return from `addMSA` function.
`site`	One of the mutations in the `fixationSites` object. It should be from the `names` of the object. Or an integer to indicate a site could be provide. The numbering is consistent with the reference defined at `fixationSites`.
`showPath`	If plot the lineage result from lineagePath.
`showTips`	Whether to plot the tip labels. The default is `FALSE`.
`...`	Arguments in `plot.phylo` functions and other arguments.
`select`	Select which fixation path in to plot. The default is NULL which will plot all the fixations.

Value

The function only makes plot and returns no value (It behaviors like the generic plot function).

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)
## Not run: 
multiFixations <- multiFixationSites(paths)
plotSingleSite(multiFixations, 1542)

## End(Not run)