Get Cnet node set by connected Sets
get_cnet_nodeset(g, set_nodes = NULL, sep = ",", filter_set_only = TRUE, ...)igraph object specifically containing Cnet plot data,
with node attribute "nodeType" that has values c("Gene", "Set").
character vector of one or more set names, which are
defined here as the names of the nodes with nodeType="Set"
to which each node with nodeType="Gene" is connected.
For example set_nodes=c("A", "B") will return all Gene nodes
that are connected only to Set nodes "A" and "B". If
set_nodes=NULL then this function returns a list with
all set_nodes observed.
character string used as a delimited when combining
set_nodes into a name.
additional arguments are ignored.
character vector when argument set_nodes is supplied
as a character vector; when set_nodes is NULL,
this function returns a list of character vectors whose
names represent the Set node names connected to each
Gene node, where multiple Set node names are
delimited by sep.
This function operates on a Cnet igraph object,
distinguished by node attribute "nodeType" with
value "Gene" for Gene nodes, and "Set" for Set nodes.
This function returns Gene nodes that are connected
to the Sets given by argument set_nodes. It is
useful to identify which genes are connected to
Set "A" and "B" for example, in other words the
Gene nodes in a specific subcluster of the Cnet
igraph.
When set_nodes is NULL, this function returns a list
containing character vectors, where each vector represents
Gene nodes that are connected to each combination of
Set nodes. This option is useful for obtaining all
possible Gene subclusters.
This function is also called by adjust_cnet_nodeset() in
order to manipulate all nodes in a subcluster as a group,
for example calling nudge_igraph_node() on the whole set
of nodes.
Other jam cnet igraph functions:
adjust_cnet_nodeset(),
adjust_cnet_set_relayout_gene(),
apply_cnet_direction(),
apply_nodeset_spacing(),
make_cnet_test(),
nudge_igraph_node(),
rotate_igraph_layout()