Skip to contents

Autoplots for indiv_roh objects

Source: R/autoplot_indiv_roh.R
autoplot.indiv_roh.Rd

Plots of runs of homozygosity found by windows_indiv_roh(), equivalent to the plots of detectRUNS. Runs are coloured (or split) by group if the gen_tibble was grouped. The following types of plots are available:

  • runs: the runs of each individual along each chromosome (as detectRUNS::plot_Runs());

  • stacked: the runs of each group stacked along each chromosome, one run per line, ordered by start (as detectRUNS::plot_StackedRuns());

  • coverage: the percentage of individuals of each group in a run along each chromosome (as detectRUNS::plot_SnpsInRuns() and detectRUNS::plot_manhattanRuns(), computed from the runs rather than at each locus);

  • froh: the inbreeding coefficient F_ROH, the total length of the runs of an individual over the length of the genome (with froh_by = "individual", one point per individual, by group) or of each chromosome (with froh_by = "chromosome", the mean of each group) (as detectRUNS::plot_InbreedingChr()); the length of a chromosome is its largest position, as in detectRUNS;

  • violin: the distribution of the total (or mean, see method) length of the runs of each individual, by group (as detectRUNS::plot_ViolinRuns());

  • length_class: the percentage of runs in each class of length, by group (as detectRUNS::plot_DistributionRuns()).

Usage

# S3 method for class 'indiv_roh'
autoplot(
  object,
  type = c("runs", "stacked", "coverage", "froh", "violin", "length_class"),
  chromosome = NULL,
  froh_by = c("individual", "chromosome"),
  method = c("sum", "mean"),
  classes = c(0, 2, 4, 8, 16),
  ...
)

Arguments

object

an object of class indiv_roh, as returned by windows_indiv_roh()

type

the type of plot (runs, stacked, coverage, froh, violin or length_class)

chromosome

the chromosomes to plot (by default, all those with runs; for froh with froh_by = "individual", the genome is always used)

froh_by

for froh, whether to plot F_ROH of each individual over the genome (individual), or the mean F_ROH of each group on each chromosome (chromosome)

method

for violin, whether to plot the total (sum) or the mean (mean) length of the runs of each individual

classes

for length_class, the lower bounds of the classes of length of the runs, in Mb (the last class has no upper bound)

...

not currently used.

Value

a ggplot2 object

Details

Individuals with no runs count in coverage, froh and violin (with no runs, or a length of 0).

autoplot produces simple plots to quickly inspect an object. They are not customisable; we recommend that you use ggplot2 to produce publication ready plots.

Examples

# a simulated dataset of three populations with increasing inbreeding
bed_file <- system.file("extdata", "roh", "roh_sim.bed",
  package = "tidypopgen"
)
sim_gt <- gen_tibble(bed_file, backingfile = tempfile(), quiet = TRUE)
sim_roh <- windows_indiv_roh(sim_gt %>% group_by(population))

autoplot(sim_roh, type = "runs", chromosome = "3")

autoplot(sim_roh, type = "coverage")

autoplot(sim_roh, type = "froh")

autoplot(sim_roh, type = "length_class")