GSEA enrichment plot — plot_enrichment • coriell

Drop-in replacement for fgsea::plotEnrichment() which allows more plot customization and annotation. The source code for this function was lifted from: https://github.com/alserglab/fgsea/blob/master/R/plot.R.

Usage

plot_enrichment(
  pathway,
  stats,
  gseaParam = 1,
  ticksSize = 0.5,
  annotate = FALSE,
  FDR = NULL,
  ES = NULL,
  NES = NULL,
  tickAlpha = 1,
  tickColor = "black",
  lineWidth = 1,
  lineColor = NULL,
  lineAlpha = 1,
  hlinesColor = "black",
  hlinesType = 2,
  anno_x_pos = 0.8,
  anno_y_pos = 0.7,
  anno_size = 10,
  fdr_digits = 3,
  es_digits = 2,
  nes_digits = 2,
  plotTitle = NULL,
  xlab = "Rank",
  ylab = "Enrichment Score"
)

Arguments

pathway: Gene set to plot
stats: Gene-level statistics
gseaParam: GSEA parameter
ticksSize: size of the rank tick mark
annotate: Should the supplied FDR, ES, and NES values be annotated on the plot? default (FALSE)
FDR: numeric. manually supplied FDR value to be annotated on the plot if annotate=TRUE
ES: numeric. manually supplied ES value to be annotated on the plot if annotate=TRUE
NES: numeric. manually supplied NES value to be annotated on the plot if annotate=TRUE
tickAlpha: alpha value of the rank tick marks
tickColor: color of the rank tick marks
lineWidth: width of the ES line
lineColor: color = the ES line. "red2" or "blue2" if lineColor=NULL, depending on the max observed ES
lineAlpha: alpha value of the ES line
hlinesColor: color of the min/max horizontal ES lines
hlinesType: linetype of the min/max horizontal ES lines
anno_x_pos: if annotate=TRUE, relative x-position of the text annotation on the plot. default (0.8)
anno_y_pos: if annotate=TRUE, relative y-position of the text annotation on the plot. default (0.8)
anno_size: if annotate=TRUE, size of the text annotation
fdr_digits: if annotate=TRUE, number of digits to round supplied FDR value by
es_digits: if annotate=TRUE, number of digits to round supplied ES value by
nes_digits: if annotate=TRUE, number of digits to round supplied NES value by

Value

ggplot2 object

Examples


pathway <- fgsea::examplePathways[["5991130_Programmed_Cell_Death"]]
stats <- fgsea::exampleRanks
plot_enrichment(pathway, stats)


# Stat annotations can be added to the plot
fgsea_res <- fgsea::fgsea(fgsea::examplePathways, fgsea::exampleRanks)
cell_death <- fgsea_res[pathway == "5991130_Programmed_Cell_Death"]

plot_enrichment(
  pathway, 
  stats, 
  annotate = TRUE,
  FDR = cell_death[, padj], 
  ES = cell_death[, ES],
  NES = cell_death[, NES],
  plotTitle = "Programmed Cell Death"
)