plotGSEA: Plot for gene enrichment analysis of GSEA method

In genekitr: Gene Analysis Toolkit

Plot for gene enrichment analysis of GSEA method

Description

Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).

Usage

plotGSEA(
  gsea_list,
  plot_type = c("volcano", "classic", "fgsea", "ridge", "bar"),
  stats_metric = c("p.adjust", "pvalue", "qvalue"),
  show_pathway = NULL,
  show_gene = NULL,
  colour = NULL,
  wrap_length = NULL,
  label_by = c("id", "description"),
  ...
)

Arguments

gsea_list	GSEA result from 'genGSEA' function
plot_type	GSEA plot type, one of 'volcano', 'classic', 'fgsea', 'ridge' or 'bar'.
stats_metric	Statistic metric from one of "pvalue", "p.adjust", "qvalue".
show_pathway	Select plotting pathways by number (will choose top N pathways) or pathway name (choose from ID column).
show_gene	Select genes to show. Default is "all". Used in "classic" plot.
colour	Colour vector. Deafault is NULL. Used in volcano, ridge and bar plot.
wrap_length	Numeric, wrap text if longer than this length. Default is NULL.
label_by	Select which column as the label. If user wants to modify labels in plot, please modify the "Description" column and set the argument as "description". Default is by 'id'.
...	other arguments transfer to 'plot_theme' function

Value

A ggplot object

Examples

k1 = requireNamespace("cowplot",quietly = TRUE)
k2 = requireNamespace("fgsea",quietly = TRUE)
k3 = requireNamespace("ggplotify",quietly = TRUE)
k4 = requireNamespace("ggridges",quietly = TRUE)
if(k1&k2&k3&k4){
library(ggplot2)
## get GSEA result
data(geneList, package = "genekitr")
gs <- geneset::getMsigdb(org = "human",category = "H")
gse <- genGSEA(genelist = geneList, geneset = gs)

## volcano plot
# get top3 of up and down pathways
plotGSEA(gse, plot_type = "volcano", show_pathway = 3)
# choose pathway by character
pathways <- c('HALLMARK_KRAS_SIGNALING_UP','HALLMARK_P53_PATHWAY','HALLMARK_GLYCOLYSIS')
plotGSEA(gse, plot_type = "volcano", show_pathway = pathways)

## classic pathway plot
genes <- c('ENG','TP53','MET')
plotGSEA(gse, plot_type = "classic", show_pathway = pathways, show_gene = genes)

## fgsea table plot
plotGSEA(gse, plot_type = "fgsea", show_pathway = 3)

## ridgeplot
plotGSEA(gse,
  plot_type = "ridge",
  show_pathway = 10, stats_metric = "p.adjust"
)

## two-side barplot
plotGSEA(gse,
  plot_type = "bar", main_text_size = 8,
  colour = c("navyblue", "orange")
)
}

genekitr documentation built on Sept. 11, 2024, 9:10 p.m.