addSNPScale: Add a SNP scale to phylogeny

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

Description

Function that adds a SNP scale onto a plotted phylogeny

Usage

addSNPScale(
  x = NULL,
  y = NULL,
  position = NULL,
  size = 1,
  lineWidth = 1,
  cex = 1,
  offset = 0.5
)

Arguments

x	An optional numeric X coordinate for the scale
y	An optional numeric Y coordinate for the scale
lineWidth	A numeric scaling factor to change the width of the scale line. Defaults to 1. Equivalent to lwd
cex	A numeric scaling factor to chancge the size of the scale label. Defaults to 1.
offset	This value controls the distance (‘offset’) of the text label from the scale in fractions of a character width. Defaults to 0.5.
postion	An optional character vector detailing the location of the plot (top, middle, left, right, etc.)

Examples

# Set the plotting margins
par(mar=c(0,0,0,0))

# Set the seed
set.seed(76263)

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

# Rescale the branch lengths to simulate SNPs
tree$edge.length <- round(tree$edge.length*10, digits=0)

# Plot the phylogeny
ape::plot.phylo(tree)

# Add a SNP scale
addSNPScale(position="bottomright", size=5)

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