Plots GSEA data as bubble plot. Mainly useful to compare multiple gsea comparisons.

Usage

plot_gsea_bubbleplot(
  gsea,
  ...,
  sample_names = NULL,
  padj_cutoff = 0.05,
  top_n = Inf,
  remove_prefix = F,
  max_name_length = Inf
)

Arguments

gsea: Output from perform_GSEA.
...: Additional gsea outputs to be included in visualization.
sample_names: Character vector specifying the comparisons that were made in the GSEA. Optional.
padj_cutoff: padj_cutoff The maximum p.adjust value allowed for inclusion of the pathway.
top_n: he 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 object

Examples

if (FALSE) { # \dontrun{

gsea1 <- perform_GSEA(res1, genesets)
gsea2 <- perform_GSEA(res2, genesets)

#Show data of a single gsea as one column
bubbleplot <- plot_gsea_bubbleplot(gsea1, top_n = 10, sample_names = 'Comparison_1')

# Show data of multiple GSEAs as multiple columns.
bubbleplot <- plot_gsea_bubbleplot(gsea1, gsea2, top_n = 10, sample_names = c('test1', 'test2'))
} # }