Create a GSEA plot that displays the running enrichment score (ES) for a given pathway

This function creates a classic enrichment plot to show the results of gene set enrichment analyses (GSEA). In particular, this function takes as input GSEA results originating from the enrichGenes() function, and returns a ggplot2 object with GSEA plot. In this kind of plots, the running enrichment score (ES) for a given pathway is shown on the y-axis, whereas gene positions in the ranked list are reported on the x-axis.

Usage

gseaPlot(
  enrichment,
  pathway,
  showTitle = TRUE,
  rankingMetric = FALSE,
  lineColor = "green",
  lineSize = 1,
  vlineColor = "red",
  vlineSize = 0.6
)

Arguments

enrichment: An object of class FunctionalEnrichment containing enrichment results
pathway: It must be the name of a significantly enriched term/pathway for which we want to produce a GSEA plot (e.g. 'Thyroid hormone synthesis')
showTitle: Logical, whether to add the name of the pathway/term as plot title. Default is TRUE
rankingMetric: Logical, whether to show the variations of the ranking metric below the plot. Default is FALSE
lineColor: It must be an R color name that specifies the color of the running score line. Default is green. Available color formats include color names, such as 'blue' and 'red', and hexadecimal colors specified as #RRGGBB
lineSize: The line width of the running score line. Default is 1
vlineColor: It must be an R color name that specifies the color of the vertical line indicating the enrichment score (ES). Default is red. Available color formats include color names, such as 'blue' and 'red', and hexadecimal colors specified as #RRGGBB
vlineSize: The line width of the vertical line indicating the enrichment score (ES). Default is 0.6

Value

An object of class ggplot containing the GSEA plot.

Author

Jacopo Ronchi, jacopo.ronchi@unimib.it

Examples

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

# plot results
gseaPlot(obj, pathway = "Thyroid hormone synthesis")