Plot top Gene Set Enrichment Analysis (GSEA) results in a barplot.

This function condenses GSEA results by plotting the top significant gene sets.

Usage

GSEA_barplot(
  gsea.res,
  genesets.name = NULL,
  padj.th = 0.05,
  top = 35,
  color.by.direction = FALSE,
  up.color = "red",
  down.color = "blue"
)

Arguments

gsea.res

A data.frame of GSEA results as returned by fgsea::fgsea().

genesets.name

A name for the gene set collection or group, used to label plot.

padj.th

The significance threshold (adjusted p-value) for filtering gene sets Defaults to 0.05.

top

The number of top significant gene sets in each direction to consider. Defaults to 35.

color.by.direction

Logical. If TRUE, bars are colored by up/down direction instead of significance. Defaults to FALSE.

up.color

Color for upregulated pathways if color.by.direction is TRUE. Defaults to "red".

down.color

Color for downregulated pathways if color.by.direction is TRUE. Defaults to "blue".

Value

A ggplot object.

Author

Jared Andrews

Examples

if (FALSE) { # \dontrun{
GSEA_barplot(gsea.list = my_gsea_results, outdir = "./summary", padj.th = 0.01, top = 50)
} # }