top_plotter: top_plotter

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

top_plotter

Description

A function to speed up plotting GSEA results. Use this function with previously generated 'gene rankings' and 'gsea results'

Usage

top_plotter(
  gsea_results = NULL,
  ranked_genes = NULL,
  gene_set = NULL,
  top_n = 10,
  gseaParam = 1,
  plot_title = NULL,
  do.plot = T
)

Arguments

gsea_results	A previously calculated data frame containing gsea results
ranked_genes	A named numeric vector of ranked genes.
gene_set	List object containing reference gene sets for analyses. Reference pathways correspond to name of the list item.
top_n	Specify the number of top pathways to be shown
gseaParam	Numeric value to increase the bar size of the genes in enrichment plot
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.

Examples

top_plotter(gsea_results = f480_d12_gsea, ranked_genes = f480_d12_rnk, gene_set = msig_HALLMARK, top_n = #' 5, gseaParam = 0.4)

top_plotter(gsea_results = act_cd8_d12_gsea, ranked_genes = act_cd8_d12_rnk, gene_set = msig_HALLMARK, #' top_n = 5, gseaParam = 0.4)

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