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 = NULL,
  kings_threshold = kings_threshold,
  ...
)

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.