Filter the DAG
dag_filter(
dag,
terms = NULL,
relations = NULL,
root = NULL,
leaves = NULL,
mcols_filter = NULL,
namespace = NULL
)An ontology_DAG object.
A vector of term names. The sub-DAG will only contain these terms.
A vector of relations. The sub-DAG will only contain these relations.
Valid values of "relations" should correspond to the values set in the
relations argument in the create_ontology_DAG(). If relations_DAG is
already provided, offspring relation types will all be selected. Note "is_a"
is always included.
A vector of term names which will be used as roots of the sub-DAG. Only these with their offspring terms will be kept. If there are multiple root terms, a super root will be automatically added.
A vector of leaf terms. Only these with their ancestor terms will be kept.
Filtering on columns in the meta data frame.
The prefix before ":" of the term IDs.
An ontology_DAG object.
If the DAG is reduced into several disconnected parts after the filtering, a super root is automatically added.
parents = c("a", "a", "b", "b", "c", "d")
children = c("b", "c", "c", "d", "e", "f")
dag = create_ontology_DAG(parents, children)
dag_filter(dag, terms = c("b", "d", "f"))
#> An ontology_DAG object:
#> Source: Ontology
#> 3 terms / 2 relations / a tree
#> Root: b
#> Terms: b, d, f, ...
#> Max depth: 2
#> Aspect ratio: 0.51:1
dag_filter(dag, root = "b")
#> An ontology_DAG object:
#> Source: Ontology
#> 5 terms / 4 relations / a tree
#> Root: b
#> Terms: b, c, d, e, ...
#> Max depth: 2
#> Aspect ratio: 1:1
dag_filter(dag, leaves = c("c", "b"))
#> An ontology_DAG object:
#> Source: Ontology
#> 3 terms / 3 relations
#> Root: a
#> Terms: a, b, c, ...
#> Max depth: 2
#> Avg number of parents: 1.50
#> Avg number of children: 0.50
#> Aspect ratio: 0.51:1 (based on the longest distance from root)
#> 2:1 (based on the shortest distance from root)
dag_filter(dag, root = "b", leaves = "e")
#> An ontology_DAG object:
#> Source: Ontology
#> 3 terms / 2 relations / a tree
#> Root: b
#> Terms: b, c, e, ...
#> Max depth: 2
#> Aspect ratio: 0.51:1
# \donttest{
dag = create_ontology_DAG_from_GO_db()
#> relations: is_a, part_of
dag_filter(dag, relations = "is_a")
#> An ontology_DAG object:
#> Source: GO BP / GO.db package 3.17.0
#> 27942 terms / 50938 relations
#> Root: GO:0008150
#> Terms: GO:0000001, GO:0000002, GO:0000003, GO:0000011, ...
#> Max depth: 16
#> Avg number of parents: 1.82
#> Avg number of children: 1.76
#> Aspect ratio: 385.17:1 (based on the longest distance from root)
#> 751.33:1 (based on the shortest distance from root)
#> Relations: is_a
#>
#> With the following columns in the metadata data frame:
#> id, name, definition
# }