Plotting Term Grids

Daniel Greene


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:

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 - and subsequently pass it to plotannotation_grid.


genes <- list(
    A0A087WUJ7=c("GO:0004553", "GO:0005975"),
    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.