Skip to contents

Plot site frequency spectra

Source: R/autoplot_sfs.R
autoplot_sfs.Rd

Plot the site frequency spectra computed by pop_sfs() (bar plots of the number of sites by allele count, one panel per population), pairwise_pop_sfs() (heatmaps of the joint spectra, one panel per pair of populations), or a single spectrum returned with type = "array" (a bar plot for one population, a heatmap for two). The output of pop_sfs_preview() is plotted as the number of segregating sites for each projection, one panel per population, with the projection chosen by default marked. Spectra of more than two populations (from nwise_pop_sfs()) cannot be plotted; use pairwise_pop_sfs() to plot the joint spectra of pairs of populations.

Usage

# S3 method for class 'sfs'
autoplot(object, masked = FALSE, log = NULL, min_sites = NULL, ...)

# S3 method for class 'pop_sfs_tbl'
autoplot(object, masked = FALSE, log = NULL, ...)

# S3 method for class 'pairwise_sfs_tbl'
autoplot(object, masked = FALSE, log = NULL, min_sites = NULL, ...)

# S3 method for class 'sfs_preview_tbl'
autoplot(object, ...)

Arguments

object

the output of pop_sfs() or pairwise_pop_sfs() (with type = "tidy", the default), an sfs object of one or two populations (returned with type = "array"), or the output of pop_sfs_preview().

masked

boolean, whether to show the masked cells of the spectra. Defaults to FALSE.

log

boolean, whether to show the numbers of sites on a log scale (the y axis of bar plots, the colour scale of heatmaps). If NULL (the default), a log scale is used for heatmaps only.

min_sites

the lower limit of the log colour scale of heatmaps: cells with fewer (but more than 0) sites are shown with the lightest colour. If NULL (the default), a thousandth of the largest number of sites in a cell.

...

currently unused.

Value

a ggplot2 object.

Details

The masked cells of the spectra (the corners, i.e. sites monomorphic in the projected sample, and the cells that were folded out in a folded spectrum; see pop_sfs()) are not shown by default. In heatmaps, the numbers of sites are shown on a log scale by default, and empty cells are left blank. As the projection spreads each locus over many cells, many cells have a tiny fraction of a site: on a log scale, the colour scale starts at min_sites (by default, a thousandth of the largest number of sites in a cell), and cells with fewer sites are shown with its lightest colour (as vmin in the plots of dadi).

See also

pop_sfs(), pairwise_pop_sfs(), pop_sfs_preview()

Examples

example_gt <- load_example_gt("grouped_gen_tbl")

# the 1D spectrum of each population
example_gt %>%
  pop_sfs(n_proj = 4) %>%
  autoplot()


# the joint spectrum of each pair of populations
example_gt %>%
  pairwise_pop_sfs(n_proj = 4, folded = FALSE) %>%
  autoplot()


# a single spectrum
sfs_2d <- example_gt %>%
  pairwise_pop_sfs(n_proj = 4, folded = FALSE, type = "array")
autoplot(sfs_2d$pop1.pop2)


# the number of segregating sites for each projection
example_gt %>%
  pop_sfs_preview() %>%
  autoplot()