plotGseaTable2: plotGseaTable2

In atakanekiz/SCseqtools: Deal With Your Single Cell RNAseq Data With Ease

plotGseaTable2

Description

This function plots GSEA results. The function was edited from fgsea package to enable to graph naming

Usage

plotGseaTable2(
  pathways,
  stats,
  fgseaRes,
  gseaParam = 1,
  colwidths = c(5, 3, 0.8, 1.2, 1.2),
  plot_title = NULL,
  do.plot = T
)

Arguments

pathways	Pathways to plot table, as in 'fgsea' function. List object containing reference gene sets for analyses. Reference pathways correspond to name of the list item.
stats	Gene-level stats, as in 'fgsea' function. A named numeric vector of ranked genes.
fgseaRes	Table with fgsea results. A previously calculated data frame containing gsea results
gseaParam	GSEA-like parameter. Adjusts displayed statistic values, values closer to 0 flatten plots. Default = 1, value of 0.5 is a good choice too. Numeric value to increase the bar size of the genes in enrichment plot.
colwidths	Vector of five elements corresponding to column width for grid.arrange. If column width is set to zero, the column is not drawn.
plot_title	Add custom title to the summary plots. It can be useful for generating plots in a loop
do.plot	Logical. Set it to TRUE to create graphical outputs.

atakanekiz/SCseqtools documentation built on April 18, 2023, 12:55 a.m.