plot_gsea: Plot GSEA normalized enrichment

In BIGslu/BIGpicture: Standard Plots for BIGslu

Plot GSEA normalized enrichment

Description

Plot GSEA normalized enrichment

Usage

plot_gsea(
  gsea,
  fdr_cutoff = 0.2,
  fdr_colors = c(0.01, 0.05, 0.1, 0.2),
  show_overlap = TRUE,
  fdr.cutoff = NULL,
  fdr.colors = NULL,
  show.overlap = NULL
)

Arguments

gsea	Data frame output by SEARchways::BIGsea including pathway, FDR, and NES
fdr_cutoff	Numeric. Maximum FDR to plot. Default is 0.2
fdr_colors	Numeric vector. Cutoffs for color groups. Default is c(0.01, 0.05, 0.1, 0.2)
show_overlap	Logical if should show overlap across all facets even if some missing (TRUE) or give each facet it's own axis labels (FALSE). Default is TRUE
fdr.cutoff	Deprecated form of fdr_cutoff
fdr.colors	Deprecated form of fdr_colors
show.overlap	Deprecated form of show_overlap

Value

ggplot2 object

Examples

library(SEARchways)
library(dplyr)
#Get fold change information from example model
genes.FC <- example.model$lmerel %>%
            filter(variable %in% c("virus", "asthma")) %>%
            select(variable, gene, estimate)
#Run GSEA
example_gsea <- SEARchways::BIGsea(gene_df = genes.FC, category = "H", ID = "ENSEMBL")

#Plot
plot_gsea(example_gsea, fdr_cutoff = 0.5,
         fdr_colors = c(0.1, 0.5))

BIGslu/BIGpicture documentation built on Oct. 14, 2024, 9:30 p.m.