Plots GSEA results as bar plot.

Usage

plot_gsea_barplot(
  gsea,
  pos_color = "gold1",
  neg_color = "darkblue",
  padj_cutoff = 0.05,
  top_n = Inf,
  remove_prefix = F,
  max_name_length = Inf
)

Arguments

gsea: Output from perform_GSEA.
pos_color: Character vector specifying which color to use for activated pathways.
neg_color: Character vector specifying which color to use for repressed pathways.
padj_cutoff: The maximum p.adjust value allowed for inclusion of the pathway.
top_n: The maximum number of pathways included. Takes the top_n pathways with the lowest p.adj values.
remove_prefix: Boolean specifying to remove the prefix from pathway names.
max_name_length: Numeric value specifying the max length of pathway names.

Value

A ggplot bar plot object

Examples

if (FALSE) { # \dontrun{
gsea <- perform_GSEA(res, genesets)

# Bar plot of 10 pathways with lowest padj values.
barplot <- plot_gsea_barplot(gsea, top_n = 10)

#Bar plot of 10 pathways with lowest values and different colors for bars.
barplot <- plot_gsea_barplot(gsea, pos_color = 'red3', neg_color = 'dodgerblue', top_n = 10)
} # }