The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

Plotting Term Grids

Daniel Greene

2024-02-20

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 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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.