plot_saturation: Draw a saturation plot of the oligotyping input file

In genomewalker/oligo4fun: Oligtyping diagnostics for functional genes

Description

Draw a saturation plot of the oligotyping input file

Usage

plot_saturation(aln = aln, nseqs = 1000, model = "K80", all = FALSE,
  verbose = TRUE, seed = 0, rsamp = FALSE, ...)

Arguments

aln	a matrix containing the DNA sequences; this must be of class "DNAbin"
nseqs	a value for the number of sequences to pick
model	a character string specifying the evolutionary model to be used by dist.dna
all	a logical indicating whether to use all codon positions; defaults to FALSE so only the third codon position is used.
verbose	a logical indicating whether to show in screen the progress; defaults to TRUE.
seed	a value for the random number generator. This will allow you to repeat the analysis

Details

Usually oligotyping datasets are very large and perform a full analysis would be computationally really expensive. We recommend to use up to 5000 random sequences in a desktop computer. You can calculate multiple saturation plots and its associated statistics using plot_saturation_n to get a better overview of your alignment.

Value

An object of class “oligodiag” is a list containing at least the following components:

plot

a ggplot object containing the saturation plot

seed

the seed used for picking the random sequences

aln

a matrix of the random selected sequences stored in binary format

stats

mean and standard deviation of transitions and transversions

all_codons

logical if all codon positions have been used

saturation

whether your alignemnt possible presents saturation

Examples

saturation_plot <- plot_saturation(aln, nseqs = 1000, all = FALSE)

genomewalker/oligo4fun documentation built on May 17, 2019, 1:11 a.m.