View source: R/RCX-Cytoscape-HiddenAttributes.R
updateCyHiddenAttributes | R Documentation |
This functions add hidden attributes in the form of a CyHiddenAttributes
object to an other CyHiddenAttributes
or an
RCX object.
updateCyHiddenAttributes( x, hiddenAttributes, replace = TRUE, stopOnDuplicates = FALSE, ... ) ## S3 method for class 'CyHiddenAttributesAspect' updateCyHiddenAttributes( x, hiddenAttributes, replace = TRUE, stopOnDuplicates = FALSE, ... ) ## S3 method for class 'RCX' updateCyHiddenAttributes( x, hiddenAttributes, replace = TRUE, stopOnDuplicates = FALSE, checkReferences = TRUE, ... )
x |
RCX or |
hiddenAttributes |
|
replace |
logical; if existing values are updated (or ignored) |
stopOnDuplicates |
logical; whether to stop, if duplicates in |
... |
additional parameters |
checkReferences |
logical; whether to check if references to other aspects are present in the RCX object |
Cytoscape subnetworks allow to group a set of nodes and corresponding edges together, and network relations define the relations between those
networks.
CyHiddenAttributes
objects can be added to an RCX or an other CyHiddenAttributes
object.
In the case, that a CyHiddenAttributes
object is added to an other, or the RCX object already contains a
CyHiddenAttributes
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.
CyHiddenAttributes
or RCX object with added hidden attributes
## For CyHiddenAttributesAspects: ## prepare some aspects: hiddenAttributes1 = createCyHiddenAttributes( 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 hiddenAttributes2 = createCyHiddenAttributes( 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 hiddenAttributes3 = updateCyHiddenAttributes(hiddenAttributes1, hiddenAttributes2) ## Ignore already present keys hiddenAttributes3 = updateCyHiddenAttributes(hiddenAttributes1, hiddenAttributes2, replace=FALSE) ## Raise an error if duplicate keys are present try(updateCyHiddenAttributes(hiddenAttributes1, hiddenAttributes2, stopOnDuplicates=TRUE)) ## =>ERROR: ## Elements of "name" and "subnetworkId" (in updateCyHiddenAttributes) ## must not contain 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 a network relation rcx = updateCyHiddenAttributes(rcx, hiddenAttributes1) ## add an additional relation (update with new values) rcx = updateCyHiddenAttributes(rcx, hiddenAttributes2) ## create a relation with a not existing subnetwork... hiddenAttributes3 = createCyHiddenAttributes( name="X", value="new x", subnetworkId=9 ) ## ...and try to add them try(updateCyHiddenAttributes(rcx, hiddenAttributes3)) ## =>ERROR: ## Provided IDs of "additionalAttributes$subnetworkId" (in updateCyHiddenAttributes) ## don't exist in "rcx$cySubNetworks$id"
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