plot_og_sizes: Plot orthogroup sizes per species

In almeidasilvaf/cogeqc: Systematic quality checks on comparative genomics analyses

Plot orthogroup sizes per species

Description

Plot orthogroup sizes per species

Usage

plot_og_sizes(orthogroups = NULL, log = FALSE, max_size = NULL)

Arguments

orthogroups	A 3-column data frame with columns Orthogroup, Species, and Gene. This data frame can be created from the 'Orthogroups.tsv' file generated by OrthoFinder with the function read_orthogroups().
log	Logical indicating whether to transform orthogroups sizes with natural logarithms. Default: FALSE.
max_size	Numeric indicating the maximum orthogroup size to consider. If this parameter is not NULL, orthogroups larger than max_size (e.g., 100) will not be considered. Default: NULL.

Value

A ggplot object with a violin plot.

Examples

data(og)
plot_og_sizes(og, log = TRUE)
plot_og_sizes(og, max_size = 100)
plot_og_sizes(og, log = TRUE, max_size = 100)

almeidasilvaf/cogeqc documentation built on Jan. 29, 2024, 7:20 a.m.