plotLeafTrace

Create a leafTrace plot

Description

The leaftrace draws a horizontal line for every leaf across the ARG, such that the distance between adjacent lines reflects the distance between the leaves corresponding to those lines. There is an randomness to the leaf order and the distance between non-adjacent lines cannot be ascertained

Usage

plotLeafTrace(file = NULL, x = NULL, col = "black", xlim = NULL,
  ylim = NULL, xlab = "Coordinate", ylab = "", add = FALSE,
  subset = NULL, lwd = 1, ...)

Arguments

Argument	Description
file	A leaf trace file (produced by the script arg-layout)
x	(alternative to file) A leaf trace data frame read in by readLeafTrace
col	Either a character string giving the color of the plot, or a list indexed by leaf or diploid individual names giving the color for each leaf/individual. Will assume that leafs are named with the convention _1 and _2 for the two diploid lineages
xlim	The range for x coordinates
ylim	The range for y coordinates
xlab	Label for the x-axis
ylab	Label for the y-axis
add	If TRUE, add plot to current plot
subset	If NULL, plot all leafs. Otherwise only plot individuals/leafs in this character vector
lwd	Line width
...	Additional objects passed to the plot function