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,
  reference = NULL, gapChar = "-", ...)

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

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

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.

reference

Name of reference for site numbering. The name has to be one of the sequences' name. The default uses the intrinsic alignment numbering.

gapChar

The character to indicate gap. The numbering will skip the gapChar for the reference sequence.

...

Arguments in plot.phylo functions and other arguments.

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, 0.996)
plotSingleSite(paths, 139)
## Not run: 
fixations <- fixationSites(paths)
plotSingleSite(fixations, 139)

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

## End(Not run)
[Package sitePath version 1.0.3 Index]