rcxgraph_toRCX: Create RCX object from RCXgraph object
In ndexr: NDEx R client library

Description Usage Arguments Details Value See Also Examples

This function creates an RCX object from a valid RCXgraph object.

The following rules apply to convert from RCXgraph to RCX:

all graph attributes are stored as named data.frames within the RCX object
nodes receive their name value as "@id" attribute. All other node attributes are saved in the RCX object as nodeAttributes, access via rcx[["nodeAttributes"]]. Data goes from wide format (columns for each unique n with cells contianing v) to long format (column n containing attribute name and column v containing attribute value).
edges are connected via their "s"art and "t"arget fields. The "@id" and "i"nteraction attribute are stored as is and all edgeAttributes are saved as node attributes, access via rcx[["edgeAttributes"]]. Data goes from wide format (columns for each unique n with cells contianing v) to long format (column n containing attribute name and column v containing attribute value).

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rcxgraph_toRCX(rcxgraph, verbose = FALSE)

rcx_fromRCXgraph(rcxgraph, verbose = FALSE)

`rcxgraph`	`RCX` object
`verbose`	logical; whether to print out extended feedback

An RCXgraph object could look like this:

## Get some network...
> ndexcon = ndex_connect()
> rcx = ndex_get_network(ndexcon,"dd268e2f-fd4d-11e7-adc1-0ac135e8bacf")

> summary(rcxgraph)
IGRAPH f99ed1e DN-- 30 218 -- 
+ attr: metaData (g/x), numberVerification (g/x), ndexStatus (g/x), provenanceHistory (g/x), networkAttributes (g/x), cartesianLayout (g/x), cyVisualProperties
| (g/x), cyHiddenAttributes (g/x), status (g/x), name (v/c), @id (v/n), n (v/c), Basal (v/c), avg_PPR (v/c), LumA (v/c), LumB (v/c), ANOVA_FDR (v/c), ANOVA_p
| (v/c), Her2 (v/c), name (e/c), @id (e/n), i (e/c), NAME (e/c), strength (e/c), interaction (e/c)

## Attributes marked with "(g/x)" are graph attributes, "(v/x)" and "(e/x)" correspond to vertex and edge attributes respectively
## Accessing a graph attribute, e.g. "metaData"
rcxgraph$metaData
   consistencyGroup elementCount   lastUpdate               name properties version idCounter
1                 1            1 1.516391e+12         ndexStatus       NULL     1.0        NA
2                 1            1 1.516391e+12  provenanceHistory       NULL     1.0        NA
3                 1           30           NA              nodes       NULL     1.0       826
4                 1          218           NA              edges       NULL     1.0       827
5                 1           11           NA  networkAttributes       NULL     1.0        NA
6                 1          210           NA     nodeAttributes       NULL     1.0        NA
7                 1          654           NA     edgeAttributes       NULL     1.0        NA
8                 1           30           NA    cartesianLayout       NULL     1.0        NA
9                 1            3           NA cyVisualProperties       NULL     1.0        NA
10                1            1           NA cyHiddenAttributes       NULL     1.0        NA 


## The vertices:
> V(rcxgraph)[[]]
+ 30/30 vertices, named, from f99ed1e:
     name X.id      n            Basal          avg_PPR             LumA             LumB         ANOVA_FDR           ANOVA_p             Her2
1    ABL1  332   ABL1 2.10282304283E-4 0.00153239525422 2.40855043132E-4 0.00243281556888   0.0126090186692  5.20659657795E-4  0.0085750597325
2    JAK2  331   JAK2 0.00818834880039 0.00229451204468 0.00112294137386 5.02052428871E-4  2.16495388014E-4  5.05285465741E-6 0.00264438694116
3  NOTCH4  330 NOTCH4 0.00271376234049 0.00146318626692 9.53762145731E-4 0.00122487574678  2.16495388014E-4  4.79793511798E-6 0.00258535935846
4   KMT2C  329  KMT2C 0.00628341277798 0.00228045774193 0.00156001096343 0.00150488341005   0.0227077886547  9.78432545266E-4 9.99799190468E-4
5  NOTCH1  328 NOTCH1 0.00839759047274  0.0185377425722  0.0238783637494  0.0174878270867 5.65380895701E-13 4.06018596554E-15  0.0104288971099 
6 ...

## Display the igraph vertex names
> V(rcxgraph)$name
 [1] "ABL1"   "JAK2"   "NOTCH4" "KMT2C"  "NOTCH1" "INPPL1" "SPOP"   "AKT1"   "MYC"    "GATA3"  "MET"    "PTPRM"  "ACVR1B" "PTK2"   "PLCB1"
[16] "IBSP"   "ERBB2"  "PIK3CA" "EGFR"   "TLN1"   "MYCN"   "KRAS"   "CDH1"   "TP53"   "CCNE1"  "CCND1"  "CARD11" "STK11"  "MSH6"   "PER1"  

## The igraph vertex names equal to the ndex node names by default
> V(rcxgraph)$n
 [1] "ABL1"   "JAK2"   "NOTCH4" "KMT2C"  "NOTCH1" "INPPL1" "SPOP"   "AKT1"   "MYC"    "GATA3"  "MET"    "PTPRM"  "ACVR1B" "PTK2"   "PLCB1"
[16] "IBSP"   "ERBB2"  "PIK3CA" "EGFR"   "TLN1"   "MYCN"   "KRAS"   "CDH1"   "TP53"   "CCNE1"  "CCND1"  "CARD11" "STK11"  "MSH6"   "PER1"  

## If in \link{rcx_toRCXgraph} or \link{rcxgraph_fromRCX} \quote{idAsVertexName} is set, the igraph vertex names equal to the ndex node IDs ("@id")
## Note: "@id" is displayed in the vertex summary as "X.id", but can be accessed using "@id"
> V(rcxgraph)$'@id'
[1] 332 331 330 329 328 327 326 325 324 323 322 321 320 319 318 317 316 315 314 313 312 311 310 309 308 307 306 305 304 303


## The edges:
> E(rcxgraph)[[]] 
+ 218/218 edges from f99ed1e (vertex names):
      tail   head tid hid           name X.id              i                           NAME          strength    interaction
1     ABL1   EGFR   1  19 interacts with  550 interacts with     ABL1 (interacts with) EGFR   2.6501871987E-8 interacts with
2     ABL1  GATA3   1  10 interacts with  549 interacts with    ABL1 (interacts with) GATA3  0.00179423650681 interacts with
3     ABL1 INPPL1   1   6 interacts with  548 interacts with   ABL1 (interacts with) INPPL1  0.00531125201389 interacts with
4     ABL1   JAK2   1   2 interacts with  547 interacts with     ABL1 (interacts with) JAK2  0.00668830637406 interacts with
5     ABL1    MET   1  11 interacts with  546 interacts with      ABL1 (interacts with) MET  2.37014815511E-5 interacts with
6 ...

## Display the igraph edge names
> E(rcxgraph)$name
[1] "interacts with" "interacts with" "interacts with" "interacts with" "interacts with" "interacts with" "interacts with"
[8] ...

## The igraph edge names equal to the ndex edge "i"nteraction by default
> E(rcxgraph)$i
[1] "interacts with" "interacts with" "interacts with" "interacts with" "interacts with" "interacts with" "interacts with" 
[8] ...

## If in \link{rcx_toRCXgraph} or \link{rcxgraph_fromRCX} \quote{idAsEdgeName} is set, the igraph edge names equal to the ndex edge IDs ("@id")
## Note: "@id" is displayed in the edge summary as "X.id", but can be accessed using "@id"
> E(rcxgraph)$'@id'
 [1] 550 549 548 547 546 545 544 543 542 541 540 539 538 537 536 535 534 533 532 531 530 529 528 527 526 525 524 523 522 
[30] ...

returns object of class RCX if successfull, NULL otherwise

rcxgraph_fromRCX rcx_toRCXgraph rcx_fromJSON rcx_toJSON RCX igraph

## Create an RCX object
rcx = rcx_new(c('@id'=1, n='Some Name', r='HGNC:Symbol'))

## Convert to RCXgraph
rcxgraph = rcxgraph_fromRCX(rcx)
## or
rcxgraph = rcx_toRCXgraph(rcx)

## Convert RCXgraph back to RCX
rcx = rcx_fromRCXgraph(rcxgraph)
## or 
rcx = rcxgraph_toRCX(rcxgraph)