plotGenotype: Show a colorful representation of a genotype

In tigger: Infers Novel Immunoglobulin Alleles from Sequencing Data

Show a colorful representation of a genotype

Description

plotGenotype plots a genotype table.

Usage

plotGenotype(
  genotype,
  facet_by = NULL,
  gene_sort = c("name", "position"),
  text_size = 12,
  silent = FALSE,
  ...
)

Arguments

genotype	data.frame of alleles denoting a genotype, as returned by inferGenotype.
facet_by	column name in genotype to facet the plot by. if NULL, then do not facet the plot.
gene_sort	string defining the method to use when sorting alleles. if "name" then sort in lexicographic order. If "position" then sort by position in the locus, as determined by the final two numbers in the gene name.
text_size	point size of the plotted text.
silent	if TRUE do not draw the plot and just return the ggplot object; if FALSE draw the plot.
...	additional arguments to pass to ggplot2::theme.

Value

A ggplot object defining the plot.

See Also

inferGenotype

Examples

# Plot genotype
plotGenotype(SampleGenotype)

# Facet by subject
genotype_a <- genotype_b <- SampleGenotype
genotype_a$SUBJECT <- "A"
genotype_b$SUBJECT <- "B"
geno_sub <- rbind(genotype_a, genotype_b)
plotGenotype(geno_sub, facet_by="SUBJECT", gene_sort="pos")

tigger documentation built on Oct. 10, 2023, 5:08 p.m.