rcx_fromJSON: Create RCX object from JSON data
In ndexr: NDEx R client library
Description
Usage
Arguments
Details
Value
See Also
Examples
Description
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.
Usage
1
rcx_fromJSON(json, verbose = FALSE)
Arguments
json
JSON data
verbose
logical; whether to print out extended feedback
Details
The structure of an RCX object, as shown via str(rcx) could be a list like this:
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> 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:
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> 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
Value
returns object of class RCX if successfull, NULL otherwise
See Also
rcxgraph_fromRCX rcxgraph_toRCX rcx_toJSON
Examples
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## 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)
ndexr documentation built on March 13, 2021, 2 a.m.
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Description Usage Arguments Details Value See Also Examples
Description
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.
Usage
1 | rcx_fromJSON(json, verbose = FALSE)
|
Arguments
json |
JSON data |
verbose |
logical; whether to print out extended feedback |
Details
The structure of an RCX object, as shown via str(rcx) could be a list like this:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 | > 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:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | > 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
|
Value
returns object of class RCX if successfull, NULL otherwise
See Also
rcxgraph_fromRCX rcxgraph_toRCX rcx_toJSON
Examples
1 2 3 4 5 6 | ## 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)
|
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