qc_report_loci
objectsautoplot.qc_report_loci.Rd
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
an object of class qc_report_loci
the type of plot (one of overview
, all
, missing
,
missing low maf
, missing high maf
, maf
, hwe
, and significant hwe
)
a threshold for the accepted rate of minor allele frequency of loci
a threshold for the accepted rate of missingness per loci
a threshold of significance for Hardy-Weinberg exact p-values
not currently used.
a ggplot2
object
autoplot
produces simple plots to quickly inspect an object. They are
not customisable; we recommend that you use ggplot2
to produce publication
ready plots.