Quick ORA result plotting — easyGOPlot • plasmoRUtils

A convenience function to quickly plot the results of easytopGO or ORA results obtained from VEupathDB component databases.

Usage

easyGOPlot(
  res,
  title = "GO Biological processes",
  limit = 20,
  desc = "Term",
  genecounts = "Annotated",
  sortby = "ks"
)

Arguments

res: Output of easytopGO.
title: Title of the plot.
limit: No of terms to plot.
desc: Column name containing the GO description.If using VEuPathDB compnent database, this would be "Name" column.
genecounts: Column name containing number of query genes associated with GO description. Used for bubble size. For VEupathDB this would be "Result count" column.
sortby: Name of the statistics column to sort the terms by and use for plotting.

Value

A publication ready ggplot2 object.

Examples

if (FALSE) { # \dontrun{
## get enrichment results from easytopGO
gores <- easytopGO(geneID = geneList, bkggset = background.gset, stats = "ks")
baseurl <- "https://plasmodb.org/common/downloads/Current_Release/"
url <- paste0(baseurl, "Pfalciparum3D7/gaf/PlasmoDB-68_Pfalciparum3D7_GO.gaf.gz")
gores <- easytopGO(
  geneID = geneList, useGAF = TRUE, useBiomart = FALSE, gaf = url,
  bkggset = background.gset, category = "BP", stats = "ks"
)

## Then feed them to easyGOPlot
plot <- easyGOPlot(gores, title = "GO Enrichment Biological Processes")
} # }