plotGenotypeConfidence: Show a genotype with a confidence evidence panel

In tigger: Infers Novel Immunoglobulin Alleles from Sequencing Data

Show a genotype with a confidence evidence panel

Description

plotGenotypeConfidence draws a genotype with plotGenotype and adds a color panel beside it showing a per-gene confidence value, such as the k_diff produced by inferGenotypeBayesian.

Usage

plotGenotypeConfidence(
  genotype,
  confidence_col,
  allele_col = "alleles",
  gene_sort = c("name", "position"),
  text_size = 12,
  confidence_breaks = c(0, 1, 2, 3, 4, 5, 10, 20, 50, Inf),
  silent = FALSE,
  ...
)

Arguments

genotype	data.frame of alleles denoting a genotype, as returned by inferGenotypeBayesian.
confidence_col	name of the column in genotype holding the per-gene confidence value, e.g. "k_diff". The value is binned and shown on a blue color scale, with the column name as the legend title; white marks genes with no value.
allele_col	name of the column in genotype holding the alleles to plot, passed to plotGenotype. Set to "genotyped_alleles" to plot the most likely alleles.
gene_sort	string defining the method to use when sorting alleles, passed to plotGenotype.
text_size	point size of the plotted text.
confidence_breaks	numeric vector of breaks used to bin the confidence value into color groups. The default c(0, 1, 2, 3, 4, 5, 10, 20, 50, Inf) matches the binning used by RAbHIT for the haplotype lK panel.
silent	if TRUE do not draw the plot and just return the grob; if FALSE draw the plot.
...	additional arguments to pass to ggplot2::theme of the genotype panel.

Value

A gridExtra grob combining the genotype plot with the confidence panel.

See Also

plotGenotype, inferGenotypeBayesian

Examples

# The Bayesian genotype carries a per-gene confidence (k_diff) and, optionally,
# a genotyped_alleles column
geno_bayesian <- inferGenotypeBayesian(AIRRDb, germline_db=SampleGermlineIGHV,
                                       novel=SampleNovel, genotyped_alleles=TRUE)
plotGenotypeConfidence(geno_bayesian, confidence_col="k_diff",
                       allele_col="genotyped_alleles")

tigger documentation built on Oct. 7, 2026, 1:07 a.m.