plot_sfs: Plot 1 or 2d site frequency spectra.

In hemstrow/snpR: Whole-Genome Analysis Tools for Use with Single Nucleotide Polymorphism Data

Plot 1 or 2d site frequency spectra.

Description

Plot 1 or 2d site frequency spectra such as those created by make_SFS. Plots are made using ggplot2, and can be freely modified as is usual for ggplot objects.

Usage

plot_sfs(
  x = NULL,
  facet = NULL,
  viridis.option = "inferno",
  log = TRUE,
  pops = NULL,
  projection = NULL,
  fold = TRUE,
  update_bib = FALSE
)

Arguments

x	snpRdata object, matrix, or numeric vector. If a snpRdata object, The SNP metadata should contain "ref" and "anc" data. If it does not, the major allele will be assumed to be the ancestral. Alternatively, either a 2d site frequency spectra stored in a matrix, with an additional "pops" attribute containing population IDs, such as c("POP1", "POP2"), where the first pop is the matrix columns and the second is the matrix rows, or a 1d site frequency spectra stored as a numeric vector with a similar pops attribute giving the population name. These objects can be produced from a dadi input file using make_SFS.
facet	character, default NULL. Name of the sample metadata column which specifies the source population of individuals. For now, allows only a single simple facet (one column).If NULL, runs the entire dataset.
viridis.option	character, default "inferno". Viridis color scale option. See scale_gradient for details.
log	logical, default TRUE. If TRUE, the number of SNPs in each SFS cell is log transformed.
pops	character, default NULL. A vector of population names of up to length 2 containing the names of populations for which the an SFS is to be created. If NULL, runs the entire dataset.
projection	numeric. A vector of sample sizes to project the SFS to, in number of gene copies. Sizes too large will result in a SFS containing few or no SNPs. Must match the length of the provided pops vector.
fold	logical, default FALSE. Determines if the SFS should be folded or left polarized. If FALSE, snp metadata columns named "ref" and "anc" containing the identity of the derived and ancestral alleles, respectively, should be present for polarization to be meaningful.
update_bib	character or FALSE, default FALSE. If a file path to an existing .bib library or to a valid path for a new one, will update or create a .bib file including any new citations for methods used. Useful given that this function does not return a snpRdata object, so a citations cannot be used to fetch references. Ignored if a SFS is provided.

Details

The input SFS is either a 2d site frequency spectra stored in a matrix, with an additional "pops" attribute containing population IDs, such as c("POP1", "POP2"), where the first pop is the matrix columns and the second is the matrix rows, or a 1d site frequency spectra stored as a numeric vector with a similar pops attribute giving the population name. These objects can be produced from a dadi input file using make_SFS.

Generates a 1 or 2 dimensional site frequency spectrum using the projection methods and folding methods of Marth et al (2004) and Gutenkunst et al (2009). This code is essentially an R re-implementation of the SFS construction methods implemented in the program dadi (see Gutenkunst et al (2009)).

Value

A ggplot2 plot object of the provided SFS.

Examples

## Not run: 
# folded, 1D
plot_sfs(stickSNPs, projection = 20)

# unfolded, 1D, one specific population
plot_sfs(stickSNPs, facet = "pop", pops = "ASP", projection = 10, fold = FALSE)

# unfolded, two poplations
plot_sfs(stickSNPs, facet = "pop", pops = c("ASP", "CLF"), projection = c(10, 10))

# via a sfs matrix, useful for pulling in spectra from elsewhere
sfs <- calc_sfs(stickSNPs, facet = "pop", pops = c("ASP", "CLF"), projection = c(10, 10))
plot_sfs(sfs)

## End(Not run)

hemstrow/snpR documentation built on March 20, 2024, 7:03 a.m.