createNetworkFromDataFrames: Create a network from data frames

In cytoscape/RCy3: Functions to Access and Control Cytoscape

Create a network from data frames

Description

Takes data frames for nodes and edges, as well as naming parameters to generate the JSON data format required by the "networks" POST operation via CyREST. Returns the network.suid and applies the perferred layout set in Cytoscape preferences.

Usage

createNetworkFromDataFrames(
  nodes = NULL,
  edges = NULL,
  title = "From dataframe",
  collection = "My Dataframe Network Collection",
  base.url = .defaultBaseUrl,
  ...
)

Arguments

nodes	(data.frame) see details and examples below; default NULL to derive nodes from edge sources and targets
edges	(data.frame) see details and examples below; default NULL for disconnected set of nodes
title	(char) network name
collection	(char) network collection name
base.url	(optional) Ignore unless you need to specify a custom domain, port or version to connect to the CyREST API. Default is http://localhost:1234 and the latest version of the CyREST API supported by this version of RCy3.
...	params for nodeSet2JSON() and edgeSet2JSON()

Details

NODES should contain a column of character strings named: id. This name can be overridden by the arg: node.id.list. Additional columns are loaded as node attributes. EDGES should contain columns of character strings named: source, target and interaction. These names can be overridden by args: source.id.list, target.id.list, interaction.type.list. Additional columns are loaded as edge attributes. The 'interaction' list can contain a single value to apply to all rows; and if excluded altogether, the interaction type wiil be set to "interacts with". NOTE: attribute values of types (num) will be imported as (Double); (int) as (Integer); (chr) as (String); and (logical) as (Boolean). (Lists) will be imported as (Lists) in CyREST v3.9+.

Value

(int) network SUID

Examples

nodes <- data.frame(id=c("node 0","node 1","node 2","node 3"),
           group=c("A","A","B","B"), # categorical strings
           score=as.integer(c(20,10,15,5))) # integers
edges <- data.frame(source=c("node 0","node 0","node 0","node 2"),
           target=c("node 1","node 2","node 3","node 3"),
           interaction=c("inhibits","interacts",
                         "activates","interacts"),  # optional
           weight=c(5.1,3.0,5.2,9.9)) # numeric

createNetworkFromDataFrames(nodes,edges)

cytoscape/RCy3 documentation built on Nov. 1, 2024, 2:49 a.m.