enrichmentPlot: GSEA and plot

In scfurl/seqGlue: Makes sequencing data come together like glue

GSEA and plot

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,
  object = NULL,
  gene_names_col = "gene_short_name",
  stat_col = "stat",
  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.
object	a DESeq2 object with results calculated for the comparison desired
gene_names_col	the column in mcols to assign gene symbols to
stat_col	the column in DESeq2 results to use in GSEA
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/seqGlue documentation built on Sept. 1, 2024, 11:20 a.m.