tanglePlot: Plot the different nucleotides present in an alignment of...

In JosephCrispell/phyloHelpeR: Functions to help with plotting phylogenies in R

Description

Function uses coloured polygons to illustrate which nucleotides are present in each sequence at each position

Usage

tanglePlot(
  tree1,
  tree2,
  onlyIfDifferent = TRUE,
  connectingLine.col = "black",
  connectingLine.lwd = 1,
  connectingLine.lty = 1,
  offsetProp = NULL,
  leftMargins = c(0, 0, 0, 1),
  rightMargins = c(0, 1, 0, 0),
  ...
)

Arguments

tree1	an object of class "phylo" to compared to tree2
tree2	an object of class "phylo" to compared to tree1
onlyIfDifferent	a boolean variable, if TRUE only plots lines between tips that are in different locations on the phylogenies, otherwise lines between all tips are plotted. Defaults to TRUE
connectingLine.col	colour of the lines connecting tips. Defaults to black
connectingLine.lwd	width of the lines connecting tips. Defaults to 1
connectingLine.lty	type of the lines connecting tips. Defaults to 1 (solid)
offsetProp	offset value to displace starts of connecting lines from tips, set as the proportion of plotting window. Defaults to NULL (off)
leftMargins	margin parameters for the left tree plot. Defaults to c(0,0,0,1) to leave small space on right
rightMargins	margin parameters for the right tree plot. Defaults to c(0,1,0,0) to leave small space on left

Examples

# Set the seed
set.seed(76263)

# Create a random phylogeny
tree <- ape::rtree(n=50, rooted=TRUE)

# Rotate one of the nodes in the phylogeny - with tip labels it
rotated <- ape::rotate(tree, node=c("t35", "t34"))

# Compare the random and rotated phylogeny
tanglePlot(tree, rotated, connectingLine.col="red",
           connectingLine.lty=2, show.tip.label=TRUE, offsetProp=0.02)

JosephCrispell/phyloHelpeR documentation built on April 7, 2020, 8:28 a.m.