Autoplots for qc_report_indiv objects — autoplot.qc_report

For qc_report_indiv, the following types of plots are available:

scatter: a plot of missingness and observed heterozygosity within individuals.
relatedness: a histogram of paired kinship coefficients

Usage

# S3 method for class 'qc_report_indiv'
autoplot(
  object,
  type = c("scatter", "relatedness"),
  miss_threshold = 0.05,
  kings_threshold = NULL,
  ...
)

Arguments

object: an object of class qc_report_indiv
type: the type of plot (scatter,relatedness)
miss_threshold: a threshold for the accepted rate of missingness within individuals
kings_threshold: an optional numeric, a threshold of relatedness for the sample
...: not currently used.

Value

a ggplot2 object

Details

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

# Create a gen_tibble of lobster genotypes
bed_file <-
  system.file("extdata", "lobster", "lobster.bed", package = "tidypopgen")
example_gt <- gen_tibble(bed_file,
  backingfile = tempfile("lobsters"),
  quiet = TRUE
)

# Create QC report for individuals
indiv_report <- example_gt %>% qc_report_indiv()

# Autoplot missingness and observed heterozygosity
autoplot(indiv_report, type = "scatter", miss_threshold = 0.1)


# Create QC report with kinship filtering
indiv_report_rel <-
  example_gt %>% qc_report_indiv(kings_threshold = "second")

# Autoplot relatedness
autoplot(indiv_report_rel, type = "relatedness", kings_threshold = "second")
#> Warning: Removed 178 rows containing non-finite outside the scale range (`stat_bin()`).