plotMutSites: Plot tree and mutation sites

In wuaipinglab/sitePath: Phylogeny-based sequence clustering with site polymorphism

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))

wuaipinglab/sitePath documentation built on Sept. 26, 2022, 10:16 p.m.