rcx_toRCXgraph: Create RCXgraph object from RCX object
In ndexr: NDEx R client library
Description
Usage
Arguments
Details
Value
See Also
Examples
View source: R/ndex_RCXgraph.r
Description
This function creates an RCXgraph object from a supplied RCX object.
RCX objects store the CX data as a named list of data.frames containing metaData and all aspects of the network.
The RCXgraph class inherits from igraph and contains the complete (R)CX information as graph, node and edge attributes.
All igraph functionality is available, e.g. access nodes and edges of igraph g via V(g) and E(g) and their attributes via V(g)$attribute
Usage
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rcx_toRCXgraph(
rcx,
idAsVertexName = FALSE,
idAsEdgeName = FALSE,
verbose = FALSE
)
rcxgraph_fromRCX(
rcx,
idAsVertexName = FALSE,
idAsEdgeName = FALSE,
verbose = FALSE
)
Arguments
rcx
RCX object
idAsVertexName
logical; whether the ndex node id ("@id") should be used as name for the igraph node (i.e. vertex). By default the "n"ame property is used
idAsEdgeName
logical; whether the ndex edge id ("@id") should be used as name for the igraph edge. By default the "i"nteraction property is used
verbose
logical; whether to print out extended feedback
Details
The following rules apply to convert from RCX to RCXgraph:
nodes receive their name from RCX$node$n. If idAsVertexName is TRUE, the "@id" value is used as name. All other information in aspects node and nodeAttributes are saved as vertex_attr, access via V(g).
Data goes from long format (column n containing attribute name and column v containing attribute value) to wide format (columns for each unique n with cells contianing v).
edges are connected via their "s"ource and "t"arget fields. The "@id" and "i"nteraction attribute are stored as is and all edgeAttributes are saved as edge_attr, access via E(g).
Data goes from long format (column n containing attribute name and column v containing attribute value) to wide format (columns for each unique n with cells contianing v).
all other aspect data is stored as graph attributes, access via g$<aspectName>
The following rules apply to convert RCXgraph back to RCX:
Two vertex attributes "n" and "@id" have to be present in RCXgraph! Those two are mandatory RCX node properties!
The igraph vertex name is ignored for the conversion! If the name is needed, adjust manually, e.g.: V(RCXgraph)$n <- V(RCXgraph)$name
The edge attribute "@id" has to be present in RCXgraph! This is a mandatory RCX edge property!
An RCXgraph object could look like this:
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## 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)$'@id'
[1] 550 549 548 547 546 545 544 543 542 541 540 539 538 537 536 535 534 533 532 531 530 529 528 527 526 525 524 523 522
[30] ...
Value
returns object of class RCXgraph if successfull, NULL otherwise
See Also
rcxgraph_toRCX rcx_fromRCXgraph rcx_fromJSON rcx_toJSON RCX igraph
Examples
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## Create an RCX object
rcx = rcx_new(c('@id'=1, n='Some Name', r='HGNC:Symbol'))
## Convert to RCXgraph
rcxgraph = rcxgraph_fromRCX(rcx)
## or
rcxgraph = rcx_toRCXgraph(rcx)
## Convert RCXgraph back to RCX
rcx = rcx_fromRCXgraph(rcxgraph)
## or
rcx = rcxgraph_toRCX(rcxgraph)
ndexr documentation built on March 13, 2021, 2 a.m.
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Description Usage Arguments Details Value See Also Examples
View source: R/ndex_RCXgraph.r
Description
This function creates an RCXgraph object from a supplied RCX object.
RCX objects store the CX data as a named list of data.frames containing metaData and all aspects of the network.
The RCXgraph class inherits from igraph and contains the complete (R)CX information as graph, node and edge attributes.
All igraph functionality is available, e.g. access nodes and edges of igraph g via V(g) and E(g) and their attributes via V(g)$attribute
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 | rcx_toRCXgraph(
rcx,
idAsVertexName = FALSE,
idAsEdgeName = FALSE,
verbose = FALSE
)
rcxgraph_fromRCX(
rcx,
idAsVertexName = FALSE,
idAsEdgeName = FALSE,
verbose = FALSE
)
|
Arguments
rcx |
|
idAsVertexName |
logical; whether the ndex node id ("@id") should be used as name for the igraph node (i.e. vertex). By default the "n"ame property is used |
idAsEdgeName |
logical; whether the ndex edge id ("@id") should be used as name for the igraph edge. By default the "i"nteraction property is used |
verbose |
logical; whether to print out extended feedback |
Details
The following rules apply to convert from RCX to RCXgraph:
nodes receive their name from RCX$node$n. If idAsVertexName is TRUE, the "@id" value is used as name. All other information in aspects node and nodeAttributes are saved as
vertex_attr, access via V(g). Data goes from long format (column n containing attribute name and column v containing attribute value) to wide format (columns for each unique n with cells contianing v).edges are connected via their "s"ource and "t"arget fields. The "@id" and "i"nteraction attribute are stored as is and all edgeAttributes are saved as
edge_attr, access via E(g). Data goes from long format (column n containing attribute name and column v containing attribute value) to wide format (columns for each unique n with cells contianing v).all other aspect data is stored as graph attributes, access via g$<aspectName>
The following rules apply to convert RCXgraph back to RCX:
Two vertex attributes "n" and "@id" have to be present in RCXgraph! Those two are mandatory
RCXnode properties!The igraph vertex name is ignored for the conversion! If the name is needed, adjust manually, e.g.: V(RCXgraph)$n <- V(RCXgraph)$name
The edge attribute "@id" has to be present in RCXgraph! This is a mandatory
RCXedge property!
An RCXgraph object could look like this:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 | ## Get some network...
> ndexcon = ndex_connect()
> rcx = ndex_get_network(ndexcon,"dd268e2f-fd4d-11e7-adc1-0ac135e8bacf")
> summary(rcxgraph)
IGRAPH f99ed1e DN-- 30 218 --
+ attr: metaData (g/x), numberVerification (g/x), ndexStatus (g/x), provenanceHistory (g/x), networkAttributes (g/x), cartesianLayout (g/x), cyVisualProperties
| (g/x), cyHiddenAttributes (g/x), status (g/x), name (v/c), @id (v/n), n (v/c), Basal (v/c), avg_PPR (v/c), LumA (v/c), LumB (v/c), ANOVA_FDR (v/c), ANOVA_p
| (v/c), Her2 (v/c), name (e/c), @id (e/n), i (e/c), NAME (e/c), strength (e/c), interaction (e/c)
## Attributes marked with "(g/x)" are graph attributes, "(v/x)" and "(e/x)" correspond to vertex and edge attributes respectively
## Accessing a graph attribute, e.g. "metaData"
rcxgraph$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] ...
|
Value
returns object of class RCXgraph if successfull, NULL otherwise
See Also
rcxgraph_toRCX rcx_fromRCXgraph rcx_fromJSON rcx_toJSON RCX igraph
Examples
1 2 3 4 5 6 7 8 9 10 11 12 | ## 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)
|
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