This functions add subnetworks in the form of a
CySubNetworks object to an other
CySubNetworks or an RCX object.
updateCySubNetworks( x, cySubNetworks, stopOnDuplicates = FALSE, keepOldIds = TRUE, ... ) ## S3 method for class 'CySubNetworksAspect' updateCySubNetworks( x, cySubNetworks, stopOnDuplicates = FALSE, keepOldIds = TRUE, ... ) ## S3 method for class 'RCX' updateCySubNetworks( x, cySubNetworks, stopOnDuplicates = FALSE, keepOldIds = TRUE, checkReferences = TRUE, ... )
logical; whether to stop, if duplicates in id column are found, or re-assign ids instead.
logical; if ids are re-assigned, the original ids are kept in the column oldId
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.
CySubNetworks objects can be added to an RCX or an other
The nodes and edges parameters reference the node or edge IDs that belong to a subnetwork.
When adding an
CySubNetworks object to an RCX object, those IDs must be present in the
Edges aspect respectively, otherwise an error is raised.
Unlike other aspects referring those IDs, the Cytoscape subnetwork aspect allows to refer to all nodes and edges using the keyword
When subnetworks should be added to a
CySubNetworks or a RCX object some conflicts may rise, since the
aspects might use the same IDs. If the aspects do not share any IDs, the two aspects are simply combined.
Otherwise, the IDs of the new subnetworks are re-assinged continuing with the next available ID
maxId(cySubNetworks) + 1 and
maxId(rcx$cySubNetworks) + 1, respectively).
To keep track of the changes, it is possible to keep the old IDs of the newly added nodes in the automatically added column oldId.
This can be omitted by setting keepOldIds to
Otherwise, if a re-assignment of the IDs is not desired, this can be prevented by setting stopOnDuplicates to
This forces the function to stop and raise an error, if duplicated IDs are present.
CySubNetworks or RCX object with added subnetworks
## For CySubNetworksAspects: ## prepare some aspects: cySubNetworks1 = createCySubNetworks( id = c(0,1), nodes = list("all", c(1,2,3)), edges = list("all", c(0,2)) ) cySubNetworks2 = createCySubNetworks( nodes = c(0,3), edges = c(1) ) ## subnetwork ids will be kept cySubNetworks3 = updateCySubNetworks(cySubNetworks1, cySubNetworks2) ## old subnetwork ids will be omitted cySubNetworks3 = updateCySubNetworks(cySubNetworks1, cySubNetworks2, keepOldIds=FALSE) ## Raise an error if duplicate keys are present try(updateCySubNetworks(cySubNetworks1, cySubNetworks2, stopOnDuplicates=TRUE)) ## =>ERROR: ## Elements of "id" (in updateCySubNetworks) must not contain duplicates! ## For RCX ## prepare RCX object: nodes = createNodes(name = c("a","b","c","d","e","f")) edges = createEdges(source=c(1,2,0,0,0,2), target=c(2,3,1,2,5,4)) rcx = createRCX(nodes, edges) ## add the subnetwork rcx = updateCySubNetworks(rcx, cySubNetworks1) ## add additional subnetwork rcx = updateCySubNetworks(rcx, cySubNetworks2) ## create a subnetwork with a not existing node... cySubNetworks3 = createCySubNetworks( nodes = list(9) ) ## ...and try to add them try(updateCySubNetworks(rcx, cySubNetworks3)) ## =>ERROR: ## Provided IDs of "additionalSubNetworks$nodes" (in addCySubNetworks) ## don't exist in "rcx$nodes$id" ## create a group with a not existing edge... cySubNetworks4 = createCySubNetworks( nodes = c(0,1), edges = 9 ) ## ...and try to add them try(updateCySubNetworks(rcx, cySubNetworks4)) ## =>ERROR: ## Provided IDs of "additionalSubNetworks$edges" (in addCySubNetworks) ## don't exist in "rcx$edges$id"
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