Networks are a popular visualization option in R often implemented as graph models by
igraph and Biocondutor’s
graph (i.e.,
graphNEL). RCy3 can create networks in Cytoscape from either igraph, graphNEL or dataframe objects (
createNetworkFrom*). Likewise, igraph and graphNEL objects can be created from networks (
create*FromNetwork), and dataframes from node and edge tables in Cytoscape (
getTableColumns).
In the case of
createNetworkFromDataFrames, two dataframes are accepted as arguments, one for nodes and one for edges. The
nodes dataframe must include a column named
"id", and the
edges dataframe must include
"source" and
"target" columns. Additional columns are imported as node and edge attributes into Cytoscape. The function can also work with just one dataframe. If a dataframe of only edges is passed to
createNetworkFromDataFrames, then a connected network will be created with all of the nodes. If a dataframe of only nodes is passed, then a network with no connections, only nodes, will be created.
RCy3 can also import network file formats supported by Cytoscape natively (e.g., SIF, xGMML and CX
7 (link)) and via user-installed apps (e.g., GPML
8 (link) and adjacency matrices). With these functions RCy3 can interoperate with any other Bioconductor packages that deal with networks in a standardized manner, providing advanced network visualization options and advanced network analytics from the Cytoscape ecosystem (see
Table 2).
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