rcx_fromJSON {ndexr} | R Documentation |
This function creates an RCX object from a supplied JSON-encoded CX object. RCX objects store the CX data as a named list of data.frames containing metaData and all aspects of the network.
rcx_fromJSON(json, verbose = FALSE)
json |
JSON data |
verbose |
logical; whether to print out extended feedback |
The structure of an RCX object, as shown via str(rcx) could be a list like this:
> str(rcx) List of 12 $ metaData :'data.frame': 11 obs. of 7 variables: ..$ name : chr [1:11] "citations" "@context" "edgeAttributes" "edgeCitations" ... ..$ consistencyGroup: int [1:11] 1 1 1 1 1 1 1 1 1 1 ... ..$ elementCount : int [1:11] 4 23 NA NA 11 1 NA NA NA 5 ... ..$ lastUpdate : num [1:11] 1.44e+12 1.44e+12 1.44e+12 1.44e+12 1.44e+12 ... ..$ version : chr [1:11] "1.0" "1.0" "1.0" "1.0" ... ..$ idCounter : int [1:11] 60714397 NA NA NA 60714399 NA NA NA NA 60714395 ... ..$ properties :List of 11 $ numberVerification:'data.frame': 1 obs. of 1 variable: ..$ longNumber: num 2.81e+14 $ ndexStatus :'data.frame': 1 obs. of 10 variables: ..$ externalId : chr "eac8a4b8-6194-11e5-8ac5-06603eb7f303" ..$ creationTime : num 1.44e+12 ..$ modificationTime: num 1.44e+12 ..$ visibility : chr "PUBLIC" ..$ published : logi FALSE ..$ nodeCount : int 5 ..$ edgeCount : int 11 ..$ owner : chr "nci-pid" ..$ ndexServerURI : chr "http://public.ndexbio.org" ..$ readOnly : logi FALSE $ @context :'data.frame': 1 obs. of 23 variables: ..$ GENPEPT : chr "http://www.ncbi.nlm.nih.gov/protein/" ..$ NCBI GENE : chr "http://identifiers.org/ncbigene/" ..$ ENSEMBL : chr "http://identifiers.org/ensembl/" [...] $ networkAttributes :'data.frame': 4 obs. of 2 variables: ..$ n: chr [1:4] "name" "description" "version" "ndex:sourceFormat" ..$ v: chr [1:4] "PLK3 signaling events" "This network ..." [...] $ citations :'data.frame': 4 obs. of 7 variables: ..$ @id : int [1:4] 60714380 60714383 60714386 60714397 ..$ dc:identifier : chr [1:4] "pmid:17264206" "pmid:14968113" "pmid:12242661" "pmid:11551930" ..$ dc:type : chr [1:4] "URI" "URI" "URI" "URI" ..$ attributes :List of 4 [...] $ nodes :'data.frame': 5 obs. of 2 variables: ..$ @id: int [1:5] 60714376 60714377 60714381 60714384 60714395 ..$ n : chr [1:5] "CCNE1" "PLK3" "MPIP3" "CHK2" ... $ nodeAttributes :'data.frame': 10 obs. of 4 variables: ..$ po: int [1:10] 60714376 60714376 60714377 60714377 60714381 60714381 60714384 60714384 60714395 60714395 ..$ n : chr [1:10] "alias" "relatedTo" "alias" "relatedTo" ... ..$ v :List of 10 .. ..$ : chr [1:6] "UniProt Knowledgebase:Q92501" "UniProt Knowledgebase:Q9UD21" ... .. ..$ : chr [1:98] "GENE ONTOLOGY:GO:0003713" "GENE ONTOLOGY:GO:0005515" ... [...] ..$ d : chr [1:10] "list_of_string" ... $ edges :'data.frame': 11 obs. of 4 variables: ..$ @id: int [1:11] 60714379 60714382 ... ..$ s : int [1:11] 60714376 60714381 ... ..$ t : int [1:11] 60714377 60714377 ... ..$ i : chr [1:11] "neighbor-of" "neighbor-of" ... $ edgeCitations :'data.frame': 11 obs. of 2 variables: ..$ po :List of 11 .. ..$ : int 60714379 .. ..$ : int 60714382 [...] ..$ citations:List of 11 .. ..$ : int 60714380 .. ..$ : int 60714383 [...] $ status :'data.frame': 1 obs. of 2 variables: ..$ error : chr "" ..$ success: logi TRUE - attr(*, "class")= chr [1:2] "RCX" "list"
The data.frames representing nodes and edges could look like this:
> rcx[["nodes"]] @id n 1 60714376 CCNE1 2 60714377 PLK3 3 60714381 MPIP3 4 60714384 CHK2 5 60714395 P53 > rcx[["edges"]] @id s t i 1 60714379 60714376 60714377 neighbor-of 2 60714382 60714381 60714377 neighbor-of 3 60714385 60714384 60714377 neighbor-of 4 60714388 60714377 60714376 controls-expression-of 5 60714390 60714377 60714381 controls-phosphorylation-of 6 60714392 60714377 60714381 controls-state-change-of 7 60714393 60714377 60714384 controls-phosphorylation-of 8 60714394 60714377 60714384 controls-state-change-of 9 60714396 60714377 60714395 controls-phosphorylation-of 10 60714398 60714377 60714395 controls-state-change-of 11 60714399 60714377 60714395 neighbor-of
returns object of class RCX if successfull, NULL otherwise
rcxgraph_fromRCX
rcxgraph_toRCX
rcx_toJSON
## Create an RCX object rcx = rcx_new(c('@id'=1, n='Some Name', r='HGNC:Symbol')) ## Convert to JSON json = rcx_toJSON(rcx) ## Convert it back from JSON rcx = rcx_fromJSON(json)