Create a ridgeplot to display the results of GSEA analysis

This function creates a ridgeplot that is useful for showing the results of GSEA analyses. The output of this function is a plot where enriched terms/pathways found with enrichGenes() function are visualized on the basis of the ranking metric used for the analysis. The resulting areas represent the density of signed p-values, log2 fold changes, or log.p-values belonging to genes annotated to that category.

Usage

gseaRidgeplot(
  enrichment,
  showTerms = 10,
  showTermsParam = "padj",
  title = NULL
)

Arguments

enrichment: An object of class FunctionalEnrichment containing enrichment results
showTerms: It is the number of terms to be shown, based on the order determined by the parameter showTermsParam; or, alternatively, a character vector indicating the terms to plot. Default is 10
showTermsParam: The order in which the top terms are selected as specified by the showTerms parameter. It must be one of ratio, padj (default), pval and overlap
title: The title of the plot. Default is NULL not to include a plot title

Value

An object of class ggplot containing the ridgeplot of GSEA results.

Author

Jacopo Ronchi, jacopo.ronchi@unimib.it

Examples

# load example FunctionalEnrichment object
obj <- loadExamples("FunctionalEnrichment")

# plot results
gseaRidgeplot(obj)
#> Picking joint bandwidth of 0.561