Generate GSE dotplots — plot_gse_dotplot • bixverse.plots

This function can take in the output of bixverse::gse_hypergeometric() or bixverse::gse_hypergeometric_list() and generates in the former case a single plot and in the latter case a list of plots per target set.

Usage

plot_gse_dotplot(
  res,
  size_range = c(2, 5),
  viridis_option = "D",
  direction = -1,
  max_terms = NULL,
  .verbose = TRUE,
  ...
)

res: data.table with the enrichment results. Needs to have the columns c("hits", "target_set_lengths", "gene_set_name", "gene_set_lengths", "fdr").
size_range: Numerical vector of size 2. Defines the size range for the dots in the plot.
viridis_option: String. The option to forward to ggplot2::scale_fill_viridis_c().
direction: 1 or -1. The direction in the colour palette.
max_terms: Optional integer. Show only the this many most significant gene sets. Applied per target set when several were tested. Defaults to NULL, i.e. everything that passed the enrichment threshold.
.verbose: Boolean. Controls verbosity of the function.
...: Further parameters to forward to wrap_and_truncate(), which shortens the gene set labels.

If the output of bixverse::gse_hypergeometric_list() was provided, a list of dotplots per target gene set. Otherwise, a single GSE OAE dot plot.