Autoplots for qc_report_loci objects

For qc_report_loci, the following types of plots are available:

• overview: an UpSet plot, giving counts of snps over the threshold for missingness, minor allele frequency, and Hardy-Weinberg equilibrium P-value, and visualising the interaction between these

• all: a four panel plot, containing missing high maf, missing low maf, hwe, and significant hwe plots

• missing: a histogram of proportion of missing data

• missing low maf: a histogram of the proportion of missing data for snps with low minor allele freqency

• missing high maf:a histogram of the proportion of missing data for snps with high minor allele freqency

• maf: a histogram of minor allele frequency

• hwe: a histogram of HWE exact test p-values

• significant hwe: a histogram of significant HWE exact test p-values

Usage

# S3 method for class 'qc_report_loci'
autoplot(
  object,
  type = c("overview", "all", "missing", "missing low maf", "missing high maf", "maf",
    "hwe", "significant hwe"),
  maf_threshold = NULL,
  miss_threshold = NULL,
  hwe_p = NULL,
  ...
)

Arguments

object

an object of class qc_report_loci

type

the type of plot (one of overview, all, missing, missing low maf, missing high maf, maf, hwe, and significant hwe)

maf_threshold

a threshold for the accepted rate of minor allele frequency of loci

miss_threshold

a threshold for the accepted rate of missingness per loci

hwe_p

a threshold of significance for Hardy-Weinberg exact p-values

...

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.