plotEnrichment2: plotEnrichment2
In LittleHeronCodes/Lazy2: Lazy Package

plotEnrichment2

R Documentation

plotEnrichment2

Description

Plot running score for GSEA enrichment plot. Function modified from plotEnrichment function in fgsea package.

Usage

plotEnrichment2(
  gset,
  stats,
  nes,
  qv,
  gseaParam = 1,
  mtitle = NULL,
  ytitle = "",
  ticksSize = 0.4,
  base_size = 7,
  line.col = "green",
  lwd = 2,
  ylims = NULL,
  draw = TRUE,
  statbar = FALSE
)

theme_common_gsea(base_size = 7)

Arguments

`gset`	gene set to calculate enrichment in character vector.
`stats`	gene level statistics. This should be a named vector where names match gene ids in gset.
`nes`	NES provided for annotation. Runs fgsea if not provided.
`qv`	adjusted p value provided for annotation. Runs fgsea if not provided.
`gseaParam`	gseaParam from plotEnrichment.
`mtitle`	main title
`ytitle`	y axis name
`ticksSize`	ticks lwd for geneset bars.
`base_size`	font base size. default 7
`line.col`	line colour for GSEA running score.
`lwd`	line width for GSEA running score.
`ylims`	y-axis limits.
`draw`	draw plot. default TRUE
`statbar`	show statistics tick at bottom of plot.