Plot tree and mutation sites

The mutated sites for each tip in a phylogenetic tree will be represented as colored dots positioned by their site number.

plotMutSites(x, ...)

# S3 method for SNPsites
plotMutSites(x, showTips = FALSE, ...)

# S3 method for lineagePath
plotMutSites(x, ...)

# S3 method for parallelSites
plotMutSites(x, ...)

# S3 method for fixationSites
plotMutSites(x, ...)

# S3 method for 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))