updateNetworkAttributes: Update network attributes

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

Update network attributes

Description

This functions add network attributes in the form of a NetworkAttributes object to an RCX or an other NetworkAttributes object.

Usage

updateNetworkAttributes(
  x,
  networkAttributes,
  replace = TRUE,
  stopOnDuplicates = FALSE,
  ...
)

## S3 method for class 'NetworkAttributesAspect'
updateNetworkAttributes(
  x,
  networkAttributes,
  replace = TRUE,
  stopOnDuplicates = FALSE,
  ...
)

## S3 method for class 'RCX'
updateNetworkAttributes(
  x,
  networkAttributes,
  replace = TRUE,
  stopOnDuplicates = FALSE,
  checkReferences = TRUE,
  ...
)

Arguments

x	RCX object; (to which the new network attributes will be added)
networkAttributes	NetworkAttributes object; (the new aspect, that will be added)
replace	logical; if existing values are updated (or ignored)
stopOnDuplicates	logical; whether to stop, if duplicates in name (and subnetworkId if present) column are found
...	additional parameters
checkReferences	logical; whether to check if references to other aspects are present in the RCX object

Details

Networks may have attributes, that are represented as NetworkAttributes objects. NetworkAttributes objects can be added to an RCX or an other NetworkAttributes object.

In the case, that a NetworkAttributes object is added to an other, or the RCX object already contains a NetworkAttributes object, some attributes might be present in both. By default, the attributes are updated with the values of the latest one. This can prevented by setting the replace parameter to FALSE, in that case only new attributes are added and the existing attributes remain untouched.

Furthermore, if duplicated attributes are considered as a preventable mistake, an error can be raised by setting stopOnDuplicates to TRUE. This forces the function to stop and raise an error, if duplicated attributes are present.

Value

NetworkAttributes or RCX object with added network attributes

See Also

NetworkAttributes; NodeAttributes, EdgeAttributes

Examples

## For NetworkAttributesAspects: 
## prepare some aspects:
networkAttributes1 = createNetworkAttributes(
  name=c("A","A","B","B"),
  value=list(c("a1","a2"),
             "a with subnetwork",
             "b",
             "b with subnetwork"),
  isList=c(TRUE,FALSE,TRUE,FALSE),
  subnetworkId=c(NA,1,NA,1)
)

## A is updated, C is new 
networkAttributes2 = createNetworkAttributes(
  name=c("A","A","C"),
  value=list("new a",
             "new a with subnetwork",
             c(1,2)),
  subnetworkId=c(NA,1,NA)
)

## Simply update with new values
networkAttributes3 = updateNetworkAttributes(networkAttributes1, networkAttributes2)

## Ignore already present keys
networkAttributes3 = updateNetworkAttributes(networkAttributes1, networkAttributes2, 
                                             replace=FALSE)

## Raise an error if duplicate keys are present
try(updateNetworkAttributes(networkAttributes1, networkAttributes2, 
                            stopOnDuplicates=TRUE))
## =>ERROR: 
## Provided IDs (name, subnetworkId) countain duplicates!

## For RCX
## prepare RCX object:
nodes = createNodes(name = c("a","b","c","d","e","f"))
edges = createEdges(source=c(1,2,0,0,0,2), 
                    target=c(2,3,1,2,5,4))
rcx = createRCX(nodes, edges)
cySubNetworks = createCySubNetworks(
  id = c(1,2),
  nodes = list("all", c(1,2,3)),
  edges = list("all", c(0,2))                    
)
rcx = updateCySubNetworks(rcx, cySubNetworks)

## add the network attributes
rcx = updateNetworkAttributes(rcx, networkAttributes1)

## add additional network attributes and update existing
rcx = updateNetworkAttributes(rcx, networkAttributes2)

## create a relation with a not existing subnetwork...
networkAttributes3 = createNetworkAttributes(
  name="X",
  value="new x",
  subnetworkId=9
)

## ...and try to add them
try(updateNetworkAttributes(rcx, networkAttributes3))
## =>ERROR: 
## NetworkAttributesAspect$subnetworkId IDs don't exist in CySubNetworksAspect

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