plotEnrichmentData: Returns data required for doing an enrichment plot.

In ctlab/fgsea: Fast Gene Set Enrichment Analysis

Returns data required for doing an enrichment plot.

Description

Returns data required for doing an enrichment plot.

Usage

plotEnrichmentData(pathway, stats, gseaParam = 1)

Arguments

pathway	Gene set to plot.
stats	Gene-level statistics.
gseaParam	GSEA parameter.

Value

returns list with the following data: * 'curve' - data.table with the coordinates of the enrichment curve; * 'ticks' - data.table with statistic entries for each pathway gene,adjusted with gseaParam; * 'stats' - data.table with statistic values for all of the genes, adjusted with gseaParam; * 'posES', 'negES', 'spreadES' - values of the positive enrichment score, negative enrichment score, and difference between them; * 'maxAbsStat' - maximal absolute value of statistic entries, adjusted with gseaParam

Examples

library(ggplot2)
data(examplePathways)
data(exampleRanks)

pd <- plotEnrichmentData(
    pathway = examplePathways[["5991130_Programmed_Cell_Death"]],
    stats = exampleRanks
)

with(pd,
     ggplot(data=curve) +
         geom_line(aes(x=rank, y=ES), color="green") +
         geom_ribbon(data=stats,
                     mapping=aes(x=rank, ymin=0,
                                 ymax=stat/maxAbsStat*(spreadES/4)),
                     fill="grey") +
         geom_segment(data=ticks,
                      mapping=aes(x=rank, y=-spreadES/16,
                                  xend=rank, yend=spreadES/16),
                      size=0.2) +
         geom_hline(yintercept=posES, colour="red", linetype="dashed") +
         geom_hline(yintercept=negES, colour="red", linetype="dashed") +
         geom_hline(yintercept=0, colour="black") +
         theme(
             panel.background = element_blank(),
             panel.grid.major=element_line(color="grey92")
         ) +
         labs(x="rank", y="enrichment score"))

ctlab/fgsea documentation built on Oct. 10, 2024, 10:31 a.m.