A small R script for generating pangenome accumulation curves
This R script will compute three type of pangenome-related accumulation curves (gene cluster accumulation, core genome and accumulation unique gene clusters) for a number of randomly sampled genomes based on a user defined number of permutations. The output is a table summerizing the permutation results using "matrixStats" R package (https://github.com/HenrikBengtsson/matrixStats).
Usage
source(“panplots.R”)
panplots(data, curve, iterations)
Arguments
data = a matrix with gene cluster presence-absence data with genomes as rows and gene clusters as columns.
curve = type of curve data to generate: "pan" for gene cluster accumulation curve, "core" for core genome accumulation curve, and "uniq" for unique gene clusters accumulation curve (default "pan").
iterations = the number of random genome permutations (default 100).