get_ancestors_graph() and get_descendants_graph()
returns a graph representation of all ancestors or descendants
of term identifiers of interest.
olsr_graph() constructs an olsr_graph from
R objects.
olsr_graph_edges(), olsr_graph_nodes(),
olsr_graph_ontology(), and olsr_graph_ids() extract
elements of an olsr_graph.
olsr_graph_as_visNetwork() converts an olsr_graph to
the format used by the visNetwork package for interactive
visualization.
olsr_graph_as_igraph() and igraph_as_olsr_graph()
transform olsr_graph objects to and from igraph objects.
Usage
get_ancestors_graph(ontology, ids, terms = NULL)
get_descendants_graph(ontology, ids, terms = NULL)
olsr_graph(relation, ontology, ids, edges, nodes)
olsr_graph_ontology(x)
olsr_graph_ids(x)
olsr_graph_nodes(x)
olsr_graph_edges(x)
olsr_graph_as_visNetwork(graph)
olsr_graph_as_igraph(graph)
igraph_as_olsr_graph(igraph)
# S3 method for olsr_graph
print(x, ...)Arguments
- ontology
character(1) name of ontology; must be present in the
idcolumn of `get_ontologies().- ids
character() of identifiers used to construct the graph.
- terms
a tibble from, e.g.,
terms(), containing a columnobo_idand additional columns to annotated nodes of the returned graph.- relation
character(1) type of graph, either
"ancestors"or"descendants".- edges
tibble() with columns
fromandto, containing OBO identifiers at the start and end of each node in the graph.- nodes
tibble() with column
obo_id, one for each node in the graph. Arbitrary additional columns are allowed.- x
for
print.olsr_graph(), an object of classolsr_graph.- graph
an
olsr_graphobject.- igraph
an object of class
igraph, from the igraph package.- ...
for
print.olsr_graph(), ignored.
Value
get_ancestors_graph() and get_descendants_graph()
return an olsr_graph object recording the ontology, ids,
edges, and nodes implied by the ancestor or descendant
graph. Nodes are annotated with information from terms, if
available.
olsr_graph() returns an object of class olsr_graph.
olsr_graph_as_visNetwork() returns an object created by a
call to visNetwork::visNetwork(). This object can be used for
simple interactive visualization directly, or as input to
subsequent visNetwork formatting.
olsr_graph_as_igraph() returns an igraph object;
igraph_as_olsr_graph() returns an olsr_graph object.
Details
Ancestor and descendant graphs navigate from the ids of interest via parents or children, recursively, until either the ontology root or only leaf nodes remain. For descendant graphs, this can involve hundreds or even thousands of calls to the OLS API, and can be time consuming (e.g., a minute or so) on first invocation. API calls are memoized, so fast on subsequent invocations.
olsr_graph() provides a simple representation to coordinate
information for ancestor and descendant graphs. The main purpose of
this class is as a 'way-point' for further analysis of the graph,
e.g., using the igraph package
https://CRAN.R-project.org/package=igraph for analytic work or
the visNetwork https://CRAN.R-project.org/package=visNetwork for
interactive visualization.
olsr_graph_as_visNetwork() renames the obo_id column of nodes
to id, consistent with visNetwork. The id column is copied to
title, so that it is used in mouse-over text; a label (the
short description of each term in the tibble returned by terms())
is used to label the node on the graph. Add a column color to
nodes to color individual nodes
olsr_graph_as_igraph() includes information on relation
(ancestors or descendants), ontology, and ids in the igraph
object as a graph-level attribute available with graph_attr(ig, "olsr_graph"). Workflows that use olsr_graph_as_igraph(),
perform igraph manipulations, and then use igraph_as_olsr_graph()
generally preserve this information.
Examples
cl <- get_terms("cl")
b_cell <- "CL:0000236"
anc <- get_ancestors_graph("cl", b_cell, cl) # 11 nodes
#> ⠙ 9 relatives
#> ⠹ 19 relatives
#> ⠹ 21 relatives
anc
#> class: ancestors_graph (21 nodes x 24 edges)
#> ontology: cl
#> ids (1): CL:0000236
desc <- get_descendants_graph("cl", b_cell, cl) # 64 nodes
#> ⠙ 12 relatives
#> ⠹ 25 relatives
#> ⠸ 39 relatives
#> ⠼ 51 relatives
#> ⠼ 64 relatives
desc
#> class: descendants_graph (64 nodes x 66 edges)
#> ontology: cl
#> ids (1): CL:0000236
olsr_graph_ontology(anc)
#> [1] "cl"
olsr_graph_ids(anc)
#> [1] "CL:0000236"
olsr_graph_nodes(anc)
#> # A tibble: 21 × 13
#> obo_id label description iri synonyms annotation has_children short_form
#> <chr> <chr> <chr> <chr> <list> <list> <lgl> <chr>
#> 1 CL:000… B ce… A lymphocy… http… <list> <named list> TRUE CL_0000236
#> 2 CL:000… lymp… A lymphocy… http… <NULL> <named list> TRUE CL_0000945
#> 3 CL:000… lymp… A lymphocy… http… <NULL> <named list> TRUE CL_0000542
#> 4 CL:000… mono… A leukocyt… http… <list> <named list> TRUE CL_0000842
#> 5 CL:000… leuk… An achroma… http… <list> <named list> TRUE CL_0000738
#> 6 CL:000… sing… A cell wit… http… <NULL> <NULL> TRUE CL_0000226
#> 7 CL:000… nucl… A cell con… http… <NULL> <named list> TRUE CL_0002242
#> 8 CL:000… hema… A cell of … http… <list> <named list> TRUE CL_0000988
#> 9 CL:000… moti… A cell tha… http… <NULL> <NULL> TRUE CL_0000219
#> 10 CL:000… NA NA NA <NULL> <NULL> NA NA
#> # ℹ 11 more rows
#> # ℹ 5 more variables: in_subset <list>, obo_definition_citation <list>,
#> # obo_xref <list>, obo_synonym <list>, `_links` <list>
olsr_graph_edges(anc)
#> # A tibble: 24 × 2
#> from to
#> <chr> <chr>
#> 1 CL:0000236 CL:0000945
#> 2 CL:0000945 CL:0000542
#> 3 CL:0000542 CL:0000842
#> 4 CL:0000842 CL:0000738
#> 5 CL:0000842 CL:0000226
#> 6 CL:0000738 CL:0002242
#> 7 CL:0000738 CL:0000988
#> 8 CL:0000738 CL:0000219
#> 9 CL:0000226 CL:0002242
#> 10 CL:0002242 CL:0000003
#> # ℹ 14 more rows
vis <- olsr_graph_as_visNetwork(anc)
if (interactive()) # visualize in RStudio or browser
vis
ig <- olsr_graph_as_igraph(anc)
ig
#> IGRAPH d7b5eea DN-- 21 24 --
#> + attr: olsr_graph (g/x), name (v/c), label (v/c), description (v/c),
#> | iri (v/c), synonyms (v/x), annotation (v/x), has_children (v/l),
#> | short_form (v/c), in_subset (v/x), obo_definition_citation (v/x),
#> | obo_xref (v/x), obo_synonym (v/x), _links (v/x)
#> + edges from d7b5eea (vertex names):
#> [1] CL:0000236->CL:0000945 CL:0000945->CL:0000542 CL:0000542->CL:0000842
#> [4] CL:0000842->CL:0000738 CL:0000842->CL:0000226 CL:0000738->CL:0002242
#> [7] CL:0000738->CL:0000988 CL:0000738->CL:0000219 CL:0000226->CL:0002242
#> [10] CL:0002242->CL:0000003 CL:0000988->CL:0002371 CL:0000219->CL:0000003
#> [13] CL:0000003->CL:0000000 CL:0002371->CL:0000548
#> + ... omitted several edges
igraph_as_olsr_graph(ig)
#> class: ancestors_graph (21 nodes x 24 edges)
#> ontology: cl
#> ids (1): CL:0000236