Plot GSEA enrichment results — plot_gsea_enrichment • bixverse.plots

Helper function to create the classical GSEA plots for a set of pathways of interest. You can also provide the underlying GSEA results to add the FDR and NES information to the plot.

Usage

plot_gsea_enrichment(
  stats,
  pathways,
  pathways_of_interest,
  gsea_results = NULL,
  gsea_param = 1,
  tick_size = 0.2,
  text_size = 5
)

Arguments

stats: Named numeric vector. The gene level statistic.
pathways: List. A named list with each element containing the genes for this pathway.
pathways_of_interest: String vector. Names of the pathways to plot. These strings need to be represented in the names of pathways.
gsea_results: Optional data.table with the bixverse GSEA results. If provided, the FDR and NES for the given pathway of interest will be also added to the plot.
gsea_param: Numeric. Defaults to 1.
tick_size: Numeric. The tick size. Defaults to 0.2.
text_size: Numeric. The text size. Defaults to 5. Only relevant when gsea_results is provided.

Value

A named list of ggplot objects, one per element of pathways_of_interest that survived the size filters.