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In addition to using acyclic graphs, ontologyPlot lets you to visualise ontological annotation as grids. In order to do this for a given a list of term sets (i.e. your annotation), one calls the function plot_annotation_grid, passing parameters:
ontology, i.e. an ontology_index,term_sets, the annotation list,all_terms, a character vector of term IDs indicating which terms to include in the plot. This defaults to those terms which show only the most informative common ancestors for all subsets of annotated objects (otherwise there can be an ungainly number of columns).We proceed by loading the package, and an example ontology - in our case, the Gene Ontology (GO). We then create a list containing our annotation - here we use a list of 6 genes with the actual annotation downloaded from https://geneontology.org/ - and subsequently pass it to plotannotation_grid.
library(ontologyIndex)
library(ontologyPlot)
data(go)
genes <- list(
A0A087WUJ7=c("GO:0004553", "GO:0005975"),
CTAGE8=c("GO:0016021"),
IFRD2=c("GO:0003674", "GO:0005515", "GO:0005634"),
OTOR=c("GO:0001502", "GO:0005576", "GO:0007605"),
TAMM41=c("GO:0004605", "GO:0016024", "GO:0031314", "GO:0032049"),
ZZEF1=c("GO:0005509", "GO:0008270")
)
plot_annotation_grid(go, term_sets=genes)
One can either use annotation_grid to get a logical matrix of term-inclusion, or plot directly using plot_annotation_grid. See ?annotation_grid and ?plot_annotation_grid for more details.
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They may not be fully stable and should be used with caution. We make no claims about them.
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