summarizeHG: Summarize hypergeometric enrichment results

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Summarize hypergeometric enrichment results

Description

Summarize hypergeometric enrichment results. Collapses HG result list into dataframe, and generates plots to visualize enrichments for each geneset.

Usage

summarizeHG(
  hg.res,
  fdr.filter = 1,
  fdr.threshold = 0.05,
  do.plot = T,
  show.n = 5,
  genesets = NULL,
  str.wrap.width = 25,
  col.pal = NULL,
  plt.title = "",
  pathway.name.size = 7
)

Arguments

hg.res	RunHG output list
fdr.filter	FDR filter threshold. Default 1 (i.e., include all)
fdr.threshold	FDR threshold line to draw on enrichment plots. Default is 0.05.
do.plot	Logical to generate enrichment plots for each geneset.
show.n	Number of top enrichments to visualize in plots. Ignored if do.plot == F.
genesets	Geneset list used for HG enrichment (i.e., RunHG input). Optional.
str.wrap.width	positive integer giving target line width in characters. A width less than or equal to 1 will put each word on its own line. Ignored if do.plot == F.
plt.title	Character specifying plot title. Ignored if do.plot == F.
pathway.name.size	Font size for pathway names in plots. Ignored if do.plot == F.

Value

list of summarized results

Author(s)

Nicholas Mikolajewicz

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.