plotGenotype - 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.

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")

See also¶

inferGenotype