Plots the most significant GO terms from easytopGO() or a VEuPathDB
enrichment table. Input p-values are sorted before selecting the top terms.
Redundant rows are identified using GO.ID when available, otherwise the term
description; this is a display-only reduction, not a change to enrichment.
Usage
easyGOPlot(
res,
title = "GO Biological processes",
limit = 20L,
desc = "Term",
genecounts = "Significant",
sortby = NULL,
min_genes = NULL
)Arguments
- res
A data.frame of GO enrichment results.
- title
Plot title.
- limit
Maximum number of terms to display (positive integer).
- desc
Name of the term-description column (e.g. "Term" or "Name").
- genecounts
Name of the gene-count column (e.g. "Significant" or "Result count"). For KS, Significant may refer to a nominal gene cutoff.
- sortby
Name of a numeric GO p-value column. When NULL (default), uses the first available among padj, fisher, ks, P-value and p-value.
- min_genes
Optional minimum count for plotting (NULL means no filter). Applied only to the displayed terms, not before GO enrichment/FDR testing.
Examples
if (FALSE) { # \dontrun{
gores <- easytopGO(
geneID = down_padj, bkggset = background,
gaf = "annotation.gaf.gz", useBiomart = FALSE,
useGAF = TRUE, stats = "fisher"
)
easyGOPlot(gores, sortby = "fisher", min_genes = 3)
# For KS output:
# easyGOPlot(ks_result, sortby = "ks")
# For a VEuPathDB result with numeric p-values:
# easyGOPlot(veupath, desc = "Name", genecounts = "Result count",
# sortby = "P-value")
} # }