RCX-object: Create an RCX object from aspects

In frankkramer-lab/RCX: R package implementing the Cytoscape Exchange (CX) format

Create an RCX object from aspects

Description

An RCX object consists of several aspects, but at least one node in the nodes aspect. The network can either created by creating every single aspect first and the create the network with all aspects present, or by creating the aspect only with the nodes and adding the remaining aspects one by one.

Usage

createRCX(
  nodes,
  edges,
  nodeAttributes,
  edgeAttributes,
  networkAttributes,
  cartesianLayout,
  cyGroups,
  cyVisualProperties,
  cyHiddenAttributes,
  cyNetworkRelations,
  cySubNetworks,
  cyTableColumn,
  checkReferences = TRUE
)

Arguments

nodes	Nodes aspect;
edges	Edges aspect (optional);
nodeAttributes	NodeAttributes aspect (optional);
edgeAttributes	EdgeAttributes aspect (optional);
networkAttributes	NetworkAttributes aspect (optional);
cartesianLayout	CartesianLayout aspect (optional);
cyGroups	CyGroups aspect (optional);
cyVisualProperties	CyVisualProperties aspect (optional);
cyHiddenAttributes	CyHiddenAttributes aspect (optional);
cyNetworkRelations	CyNetworkRelations aspect (optional);
cySubNetworks	CySubNetworks aspect (optional);
cyTableColumn	CyTableColumn aspect (optional);
checkReferences	logical; whether to check if references to other aspects are present in the RCX object

Details

vignette("01. RCX - an R package implementing the Cytoscape Exchange (CX) format", package = "RCX") vignette("02. Creating RCX from scratch", package = "RCX") vignette("Appendix: The RCX and CX Data Model", package = "RCX")

Value

RCX object

Examples

## minimal example
rcx = createRCX(createNodes())

## create by aspect
nodes = createNodes(name = c("a","b","c"))
edges = createEdges(source=c(0,0), target=c(1,2))

nodeAttributes = createNodeAttributes(
  propertyOf=c(1,1),
  name=c("A","B"),
  value=c("a","b")
)

edgeAttributes = createEdgeAttributes(
  propertyOf=c(0,0), 
  name=c("A", "B"), 
  value=c("a","b")
)

networkAttributes = createNetworkAttributes(
  name=c("A","B"),
  value=list("a",3.14)
)

cartesianLayout = createCartesianLayout(
  node=c(0, 1),
  x=c(5.5, 110.1), 
  y=c(200.3, 210.2)
)

cyGroups = createCyGroups(
  name = c("Group One", "Group Two"),
  nodes = list(c(0,1), 0)                   
)

vpPropertyP = createCyVisualPropertyProperties(c(NODE_BORDER_STROKE="SOLID"))
vpPropertyD = createCyVisualPropertyDependencies(c(nodeSizeLocked="false"))
vpPropertyM = createCyVisualPropertyMappings(c(NODE_FILL_COLOR="CONTINUOUS"), 
                                             "COL=directed,T=boolean,K=0=true,V=0=ARROW")
vpProperty = createCyVisualProperty(properties=vpPropertyP, 
                                    dependencies=vpPropertyD, 
                                    mappings=vpPropertyM)

cyVisualProperties = createCyVisualProperties(nodes=vpProperty)

cyHiddenAttributes = createCyHiddenAttributes(
  name=c("A","B"),
  value=list(c("a1","a2"), "b")
)

cyNetworkRelations = createCyNetworkRelations(
  child = c(0,1),
  name = c("Network A", NA)
)

cySubNetworks = createCySubNetworks(
  nodes = list("all", c(0,1,2)),
  edges = list("all", c(0,1))                    
)

cyTableColumn = createCyTableColumn(
  appliesTo=c("nodes","edges","networks"),
  name=c("weight","weight","collapsed"),
  dataType=c("double","double","boolean")
)

rcx = createRCX(nodes, edges,
                nodeAttributes, edgeAttributes,
                networkAttributes, 
                cartesianLayout,
                cyGroups, 
                cyVisualProperties, 
                cyHiddenAttributes, 
                cyNetworkRelations, 
                cySubNetworks, 
                cyTableColumn)

## create all at once
rcx = createRCX(
  createNodes(name = c("a","b","c")), 
  createEdges(source=c(0,0), target=c(1,2)),
  createNodeAttributes(
    propertyOf=c(1,1),
    name=c("A","B"),
    value=c("a","b")
  ), 
  createEdgeAttributes(
    propertyOf=c(0,0), 
    name=c("A", "B"), 
    value=c("a","b")
  ),
  networkAttributes = createNetworkAttributes(
    name=c("A","B"),
    value=list("a",3.14)
  ), 
  cartesianLayout = createCartesianLayout(
    node=c(0, 1),
    x=c(5.5, 110.1), 
    y=c(200.3, 210.2)
  ),
  createCyGroups(
    name = c("Group One", "Group Two"),
    nodes = list(c(0,1), 0)                   
  ), 
  createCyVisualProperties(
    nodes=createCyVisualProperty(
      properties=createCyVisualPropertyProperties(
        c(NODE_BORDER_STROKE="SOLID")
      ), 
      dependencies=createCyVisualPropertyDependencies(
        c(nodeSizeLocked="false")
      ), 
      mappings=createCyVisualPropertyMappings(
        c(NODE_FILL_COLOR="CONTINUOUS"), 
        "COL=directed,T=boolean,K=0=true,V=0=ARROW")
    )
  ), 
  createCyHiddenAttributes(
    name=c("A","B"),
    value=list(c("a1","a2"), "b")
  ), 
  createCyNetworkRelations(
    child = c(0,1),
    name = c("Network A", NA)
  ), 
  createCySubNetworks(
    nodes = list("all", c(0,1,2)),
    edges = list("all", c(0,1))                    
  ), 
  createCyTableColumn(
    appliesTo=c("nodes","edges","networks"),
    name=c("weight","weight","collapsed"),
    dataType=c("double","double","boolean")
  )
)

frankkramer-lab/RCX documentation built on Feb. 4, 2023, 5:12 p.m.