plotEnrichment: Plot enrichment results.

In nlhuong/TimeSeriesExperiment: Analysis for short time-series data

Description

Plotting top most enriched terms found with DE methods and tested for overrepresentation in GO/KEGG db using goana/kegga from limma package.

Usage

plotEnrichment(enrich, n_max = 15)

Arguments

enrich	a data matrix or data.frame with enrichment result - outputs from pathwayEnrichment function or goana, limma::kegga(). Must contain columns Term, DE, and P.DE.
n_max	max number of terms to show

Value

a ggplot object

Examples

data("endoderm_small")
selected_genes <- c('114299', '2825', '3855', '221400', '7941',
                    '6164', '1292', '6161', '6144', '23521')
enrich_res <- pathwayEnrichment(
  object = endoderm_small, clustered = FALSE,
  features = selected_genes,
  species = "Hs", ontology = "BP", fltr_DE = 0,
  fltr_N = Inf, fltr_P.DE = 0.05)
plotEnrichment(enrich = enrich_res, n_max = 15)

nlhuong/TimeSeriesExperiment documentation built on Sept. 8, 2021, 12:30 a.m.