addInconsistentPositionAlignment: Adds nucleotide alignment to right of plotted phylogenetic...

In JosephCrispell/homoplasyFinder: Tools to identify and plot homoplasies on a phylogenetic tree

Description

Function used by plotAnnotatedTree()

Usage

addInconsistentPositionAlignment(
  tree,
  fastaFile,
  inconsistentPositions,
  cex,
  addSeparatorLines,
  actualPositions
)

Arguments

tree	An object of class "phylo" produced by readAnnotatedTree()
fastaFile	The full path to the FASTA formatted nucleotide sequence alignment
inconsistentPositions	An integer array of the inconsistent positions identified by HomoplasyFinder. Produced by runHomoplasyFinderInJava()
cex	A multiplier value to change the size of position labels
addSeparatorLines	A boolean variable to determine whether white separator lines are plotted on alignment. Defaults to true
actualPositions	An integer array of length=length(inconsistentPositions) that reports the actual positions on the genome of inconsistent positions. Useful when homoplasyFinder was run on concatenated sites. Defaults to NULL meaning it is ignored.

JosephCrispell/homoplasyFinder documentation built on June 7, 2021, 11 a.m.