enrichmentPlot: GSEA and plot

In scfurl/m3addon: This package adds to the popular "monocle3"

Description

Performs GSEA (using fgsea) and returns a GSEA-style enrichment plot. Optionally create an \ enrichment plot with multiple layers that correspong to enrichnment of a given "pathway" in a list of ranked genes \ such that each entry in a list corresponds to a different enrichment plot. Alternatively, one may supply a list of \ pathways to overlay the enrichment of multiple pathways on one ranked list. Can't do both though....

Usage

enrichmentPlot(
  pathway,
  stats,
  gseaParam = 1,
  rug = T,
  dot_enhance = "darkgrey",
  dot_enhance_size = 2,
  dot_shape = 21,
  dot_enhance_alpha = 0.7,
  dot_size = 1,
  return_data = FALSE,
  print_plot = FALSE,
  return_plot = TRUE
)

Arguments

pathway	= vector (or list) of genes. Names of list will define plot coloring.
stats	= vector (or list) of ranked gene stats (usually fold change or SNR) with names \ that contain the gene name. Names of list will define plot coloring.
rug	= whether to make a rug plot(s).
dot_enhance	character string denoting a color that enhances the dot appearance \ with another color
all_the_rest_of_them	Should be self explanatory

Value

Performs GSEA of "pathway" genes on stats'

References

fgsea package

scfurl/m3addon documentation built on Aug. 9, 2021, 5:30 p.m.