hapflk

An R script for representing cluster frequencies from hapflk output.

This script requires the following R packages installed:

RColorBrewer
ggplot2
grid

Usage:

first chmod +x hapflk-clusterplot.R

./hapflk-clusterplot.R output_file.bz2

Optionally, you can specify a range of position to plot with:

./hapflk-clusterplot.R output_file.bz2 xl xr

where xl (resp. xr) is the leftmost (resp. rightmost) position in base pairs. Scientific notation (e.g. 10e6 for ten million) is permitted.