core_plots: Plot the size of core-genome, accessory-genome and pan-genome

In irycisBioinfo/PATO: Pangenome Analysis Toolkit

Plot the size of core-genome, accessory-genome and pan-genome

Description

Takes the a mmseq object and plot the size of core, accessory and pan-genome data in the specified points and with the specified number of replicates.

Usage

core_plots(
  data,
  steps = 10,
  reps = 10,
  threshold = 0.98,
  type = "pato",
  n_cores
)

Arguments

data	A mmseq object.
steps	number or vector of points to calculate sizes.
reps	number of replicates for each point.
threshold	Minimun frequency (0-1) of the core-genome genes/proteins.
type	Output in format pato or roary style.
n_cores	Number of cores to use.

Value

A list with a ggplot2 object and a data.frame with the values of the final step.

Note

It's supossed the a gene/protein of the core-genome must be present in all the genomes of the dataset. Nevertheless, by random selection and/or errors in sequencing proccess (sequencing, assembly, ORF finding etc..) some genes/proteins could be missing. pato define the genome as, pangenome (the sum of all genomes), core-genome.

irycisBioinfo/PATO documentation built on Oct. 19, 2023, 3:07 p.m.