Package 'RCX'

Description

To get the aspect classes it is advised to always use the getAspectClasses() function to ensure the correct functionality. aspectClasses and subAspectClasses contain the default RCX accession name and the classes of the corresponding (sub)aspect. The getAspectClasses() function standardizes access to the accession names and classes, and also allows to include installed extensions of the RCX data model. Only installed and loaded extensions are included in the result: New extensions should register on load using the setExtension function to be added to options()$RCX.options$extensions, and therefore to getAspectClasses().

Usage

aspectClasses

getAspectClasses(extensions = TRUE)

subAspectClasses

updateAspectClasses(aspectClasses = aspectClasses)

Arguments

Format

An object of class character of length 14.

An object of class character of length 4.

Details

updateAspectClasses sets the default aspect classes in options()$RCX.options, either from aspectClasses or manually provided options.

Value

named character; accession names and aspect classes

See Also

setExtension

Examples

## default aspect classes
aspectClasses

## get set aspect classes from options()
aspectClasses = getAspectClasses()

## get aspect classes without extensions
aspectClasses = getAspectClasses(extensions=FALSE)

## set default updateClasses
updateAspectClasses(
  aspectClasses = aspectClasses
)

## default sub aspect classes
subAspectClasses

Description

This function creates a cartesian layout aspect, that stores coordinates of nodes.

Usage

createCartesianLayout(node, x, y, z = NULL, view = NULL)

Arguments

Details

The layout of networks can be influenced by setting the node position manually. While x an y coordinates are mandatory, the z coordinates are optional and can, for example, be used to define the vertical stacking order of overlapping nodes.

Similar to Cytoscape https://cytoscape.org/, it is possible to define different views of the same network. The views itself are definded in CySubNetworks and CyNetworkRelations, and only referenced by a unique subnetwork id.

Value

CartesianLayoutAspect object

See Also

updateCartesianLayout;

Examples

## a minimal example
cartesianLayout = createCartesianLayout(
  node=0,
  x=5.5, 
  y=200.3
)

## defining several coordinates at once
cartesianLayout = createCartesianLayout(
  node=c(0, 1),
  x=c(5.5, 110.1), 
  y=c(200.3, 210.2)
)

## with all parameters
cartesianLayout = createCartesianLayout(
  node=c(0, 1, 0),
  x=c(5.5, 110.1, 7.2), 
  y=c(200.3, 210.2, 13.9),
  z=c(-1, 3.1, NA),
  view=c(NA, NA, 1476)
)

Description

The aspects in an RCX object are accessed by a name and return the aspect as an object of cls. To simplify the conversion between those, these functions return the corresponding name.

Usage

aspectName2Class(name)

aspectClass2Name(cls)

Arguments

Details

The following accessions/classes are available within the standard RCX implementation:

accession name <=> class name

metaData  <=>  MetaDataAspect
nodes  <=>  NodesAspect
edges  <=>  EdgesAspect
nodeAttributes  <=>  NodeAttributesAspect
edgeAttributes  <=>  EdgeAttributesAspect
networkAttributes  <=>  NetworkAttributesAspect
cartesianLayout  <=>  CartesianLayoutAspect
cyGroups  <=>  CyGroupsAspect
cyVisualProperties  <=>  CyVisualPropertiesAspect
cyHiddenAttributes  <=>  CyHiddenAttributesAspect
cyNetworkRelations  <=>  CyNetworkRelationsAspect
cySubNetworks  <=>  CySubNetworksAspect
cyTableColumn  <=>  CyTableColumnAspect```

Value

accession or class name

Examples

aspectName2Class("nodes")
##[1] "NodesAspect"

aspectClass2Name("NodesAspect")
##[1] "nodes"

aspectClasses

subAspectClasses

Description

This function returns the number of elements in an aspect.

Usage

countElements(x)

## Default S3 method:
countElements(x)

## S3 method for class 'RCX'
countElements(x)

## S3 method for class 'CyVisualPropertiesAspect'
countElements(x)

## S3 method for class 'MetaDataAspect'
countElements(x)

Arguments

Details

Uses method dispatch, so the default methods already returns the correct number for the most aspect classes. This way it is easier to extend the data model.

There are only two exceptions in the core and Cytoscape aspects: Meta-data and CyVisualProperties.

Meta-data is a meta-aspect and therefore not included in Meta-data, and so its return is NA.

CyVisualProperties is the only aspect with a complex data structure beneath. Therefore its number of elements is just the number of how many of the following properties are set: network, nodes, edges, defaultNodes or defaultEdges.

Value

integer; number of elements. For RCX objects all counts are returned in the vector named by the aspect class.

See Also

hasIds(), idProperty(), refersTo(), referredBy(), maxId()

Examples

nodes = createNodes(name = c("ĆDK1","CDK2","CDK3"))
edges = createEdges(source = c(0,0), target = c(1,2))
rcx = createRCX(nodes = nodes, edges = edges)

countElements(nodes)

countElements(rcx)

Description

These functions attempt to print RCX and aspect objects in a more readable form.

Usage

## S3 method for class 'MetaDataAspect'
print(x, ...)

## S3 method for class 'NodesAspect'
print(x, ...)

## S3 method for class 'EdgesAspect'
print(x, ...)

## S3 method for class 'NodeAttributesAspect'
print(x, ...)

## S3 method for class 'EdgeAttributesAspect'
print(x, ...)

## S3 method for class 'NetworkAttributesAspect'
print(x, ...)

## S3 method for class 'CartesianLayoutAspect'
print(x, ...)

## S3 method for class 'CyGroupsAspect'
print(x, ...)

## S3 method for class 'CyVisualPropertyProperties'
print(x, ...)

## S3 method for class 'CyVisualPropertyDependencies'
print(x, ...)

## S3 method for class 'CyVisualPropertyMappings'
print(x, ...)

## S3 method for class 'CyVisualProperty'
print(x, fields = c("all"), ...)

## S3 method for class 'CyVisualPropertiesAspect'
print(x, propertyOf = "all", fields = "all", ...)

## S3 method for class 'CyHiddenAttributesAspect'
print(x, ...)

## S3 method for class 'CyNetworkRelationsAspect'
print(x, ...)

## S3 method for class 'CySubNetworksAspect'
print(x, ...)

## S3 method for class 'CyTableColumnAspect'
print(x, ...)

## S3 method for class 'RCX'
print(x, inofficial = TRUE, ...)

Arguments

Value

prints the object and returns it invisibly (invisible)

See Also

summary

Examples

rcx = createRCX(createNodes())
print(rcx)

Description

This function is used to create Cytoscape "groups" aspects.

Usage

createCyGroups(
  id = NULL,
  name,
  nodes = NULL,
  externalEdges = NULL,
  internalEdges = NULL,
  collapsed = NULL
)

Arguments

Details

Cytoscape contributes aspects that organize subnetworks, attribute tables, and visual attributes for use by its own layout and analysis tools. Furthermore are the aspects used in web-based visualizations like within the NDEx platform.

Cytoscape groups allow to group a set of Nodes and corresponding internal and external Edges together, and represent a group as a single node in the visualization. A group is defined by its unique id, which must be an (positive) integer, which serves as reference to other aspects. If no ids are provided, they are created automatically.

Value

CyGroupsAspect object

See Also

updateCyGroups;

Examples

## a minimal example
cyGroups = createCyGroups(
  name = "Group One",
  nodes = list(c(1,2,3)),
  internalEdges = list(c(0,1))
)

## defining several groups at once
cyGroups = createCyGroups(
  name = c("Group One", "Group Two"),
  nodes = list(c(1,2,3), 0),
  internalEdges = list(c(0,1),NA)
)

## with all parameters
cyGroups = createCyGroups(
  id = c(0,1),
  name = c("Group One", "Group Two"),
  nodes = list(c(1,2,3), 0),
  internalEdges = list(c(0,1),NA),
  externalEdges = list(NA,c(1,3)),
  collapsed = c(TRUE,NA)                     
)

Description

This function is used to create Cytoscape hidden attributes aspects.

Usage

createCyHiddenAttributes(
  name,
  value,
  dataType = NULL,
  isList = NULL,
  subnetworkId = NULL
)

Arguments

Details

Cytoscape contributes aspects that organize subnetworks, attribute tables, and visual attributes for use by its own layout and analysis tools. Furthermore are the aspects used in web-based visualizations like within the NDEx platform.

Besides network attributes, networks may have additional describing attributes originated from and used by Cytoscape. They are also defined in a key-value like manner, with the name of the attribute as key. The same attribute can also be defined for different subnetworks with different values. The values itself may differ in their data types, therefore it is necessary to provide the values as a list of the single values instead of a vector.

With isList it can be set, if a value should be considered as a list. This is of minor significance while working solely with RCX objects, unless it will be transformed to JSON. For some attributes it might be necessary that the values are encoded as lists, even if they contain only one element (or even zero elements). To force an element to be encoded correctly, this parameter can be used, for example: ⁠name="A", value=a, isList=T⁠ will be encoded in JSON as ⁠A=["a"]⁠.

Value

CyHiddenAttributesAspect object

See Also

updateCyHiddenAttributes;

Examples

## a minimal example
hiddenAttributes = createCyHiddenAttributes(
  name="A", 
  value="a"
)

## defining several properties at once
hiddenAttributes = createCyHiddenAttributes(
  name=c("A", "B"), 
  value=c("a","b")
)

## with characters and numbers mixed
hiddenAttributes = createCyHiddenAttributes(
  name=c("A","B"),
  value=list("a",3.14)
)

## force the number to be characters
hiddenAttributes = createCyHiddenAttributes(
  name=c("A","B"),
  value=list("a",3.14),
  dataType=c("character","character")
)

## with a list as input for one value
hiddenAttributes = createCyHiddenAttributes(
  name=c("A","B"),
  value=list(c("a1","a2"),
             "b")
)

## force "B" to be a list as well
hiddenAttributes = createCyHiddenAttributes(
  name=c("A","B"),
  value=list(c("a1","a2"),
             "b"),
  isList=c(TRUE,TRUE)
)

## with a subnetwork
hiddenAttributes = createCyHiddenAttributes(
  name=c("A","A"),
  value=c("a","a with subnetwork"),
  subnetworkId=c(NA,1)
)

## with all parameters
hiddenAttributes = createCyHiddenAttributes(
  name=c("A","A","B","B"),
  value=list(c("a1","a2"),
             "a with subnetwork",
             "b",
             "b with subnetwork"),
  isList=c(TRUE,FALSE,TRUE,FALSE),
  subnetworkId=c(NA,1,NA,1)
)

Description

This function is used to create Cytoscape network relations aspects.

Usage

createCyNetworkRelations(child, parent = NULL, name = NULL, isView = FALSE)

Arguments

Details

Cytoscape contributes aspects that organize subnetworks, attribute tables, and visual attributes for use by its own layout and analysis tools. Furthermore are the aspects used in web-based visualizations like within the NDEx platform.

Cytoscape network relations define the relationship between the main network, subnetworks and views and also a name can be assigned to the relationship. Both, subnetworks and views are defined as subnetworks aspect, but their type is defined here by the isView property. The parent of a subnetwork or view can be an other subnetwork or the root network.

Value

CyNetworkRelationsAspect object

See Also

updateCyNetworkRelations;

Examples

## a minimal example
cyNetworkRelations = createCyNetworkRelations(
  child = 1
)

## with all parameters
cyNetworkRelations = createCyNetworkRelations(
  child = c(1,2),
  parent = c(NA,1),
  name = c("Network A",
           "View A"),
  isView = c(FALSE, TRUE)
)

Description

This function is used to create Cytoscape subnetwork aspects.

Usage

createCySubNetworks(id, nodes = NULL, edges = NULL)

Arguments

Details

Cytoscape contributes aspects that organize subnetworks, attribute tables, and visual attributes for use by its own layout and analysis tools. Furthermore are the aspects used in web-based visualizations like within the NDEx platform.

A group is defined by its unique id, which must be an (positive) integer, which serves as reference to other aspects. If no IDs are provided, they are created automatically.

Nodes and edges are referred by the IDs of the corresponding aspect. Unlike other aspects referring those IDs, the Cytoscape subnetwork aspect allows to refer to all nodes and edges using the keyword all.

The relationship between (sub-)networks and views, and also the type (subnetwork or view) is defined in CyNetworkRelations.

Value

CySubNetworksAspect object

See Also

updateCySubNetworks;

Examples

## a minimal example
cySubNetworks = createCySubNetworks(
  nodes = "all",
  edges = "all"
)

## defining several subnetworks at once
cySubNetworks = createCySubNetworks(
  nodes = list("all",
               c(1,2,3)),
  edges = list("all",
               c(0,2))
)

## with all parameters
cySubNetworks = createCySubNetworks(
  id = c(0,1),
  nodes = list("all",
               c(1,2,3)),
  edges = list("all",
               c(0,2))                    
)

Description

This function is used to create Cytoscape table column aspects.

Usage

createCyTableColumn(
  appliesTo,
  name,
  dataType = NULL,
  isList = NULL,
  subnetworkId = NULL
)

Arguments

Details

Cytoscape contributes aspects that organize subnetworks, attribute tables, and visual attributes for use by its own layout and analysis tools. Furthermore are the aspects used in web-based visualizations like within the NDEx platform.

These elements are used to represent Cytoscape table column labels and types. Its main use is to disambiguate empty table columns. The same attribute can also be defined for different subnetworks with different values. Cytoscape does not currently support table columns for the root network, but this is option is included here for consistency.

With isList it can be set, if a value should be considered as a list. This is of minor significance while working solely with RCX objects, unless it will be transformed to JSON.

Value

CyTableColumnAspect object

See Also

updateCyTableColumn; CyNetworkRelations

Examples

## a minimal example
tableColumn = createCyTableColumn(
  appliesTo="nodes",
  name="weight"
)

## defining several properties at once
tableColumn = createCyTableColumn(
  appliesTo=c("nodes","edges"),
  name=c("weight","weight")
)

## with all parameters
tableColumn = createCyTableColumn(
  appliesTo=c("nodes","edges","networks"),
  name=c("weight","weight","collapsed"),
  dataType=c("numeric","numeric","logical"),
  isList=c(FALSE,FALSE,TRUE),
  subnetworkId=c(NA,NA,1)
)

Description

This function is used to create Cytoscape visual properties aspects, that consists of CyVisualProperty objects for networks, nodes, edges, and default nodes and edges.

Usage

createCyVisualProperties(
  network = NULL,
  nodes = NULL,
  edges = NULL,
  defaultNodes = NULL,
  defaultEdges = NULL
)

Arguments

Details

Cytoscape contributes aspects that organize subnetworks, attribute tables, and visual attributes for use by its own layout and analysis tools. Furthermore are the aspects used in web-based visualizations like within the NDEx platform.

The visual properties aspect is the only aspect (CyVisualProperties) with a complex structure. It is composed of several sub-property classes and consists of CyVisualProperty objects, that belong to, or more precisely describe one of the following network elements: network, nodes, edges, defaultNodes or defaultEdges.

A single visual property (i.e. CyVisualProperty object) organizes the information as properties, dependencies and mappings, as well as the single values appliesTo and view, that define the subnetwork or view to which the IDs apply.

Properties are CyVisualPropertyProperties objects, that hold information like "NODE_FILL_COLOR" : "#26CCC9" or "NODE_LABEL_TRANSPARENCY" : "255" in a key-value like manner.

Dependencies are CyVisualPropertyDependencies objects, that hold information about dependencies between visual properties. Currently there are only three dependencies supported:

• Lock Node with and height: nodeSizeLocked = "false"

• Fit Custom Graphics to node: nodeCustomGraphicsSizeSync = "true"

• Edge color to arrows: arrowColorMatchesEdge = "false"

Mappings are CyVisualPropertyMappings objects, that hold information as a triplet consisting of name, type and definition, like "NODE_FILL_COLOR" : "DISCRETE" : "COL=molecule_type,T=string,K=0=miRNA,V=0=#FCEC00", ⁠"NODE_FILL_COLOR" : "CONTINUOUS" : "COL=gal1RGexp,T=double...⁠ or "NODE_LABEL" : "PASSTHROUGH" : "COL=COMMON,T=string".

For further information about Cytoscape visual properties see the Styles topic of the official Cytoscape documentation: http://manual.cytoscape.org/en/stable/Styles.html

Structure of Cytoscape Visual Properties

CyVisualProperties
|---network = CyVisualProperty
|---nodes = CyVisualProperty
|---edges = CyVisualProperty
|---defaultNodes = CyVisualProperty
|---defaultEdges = CyVisualProperty

CyVisualProperty
|---properties = CyVisualPropertyProperties
|   |--name
|   |--value 
|---dependencies = CyVisualPropertyDependencies
|   |--name
|   |--value 
|---mappings = CyVisualPropertyMappings
|   |--name
|   |--type
|   |--definition 
|---appliesTo = <reference to subnetwork id>
|---view = <reference to subnetwork id>

Value

CyVisualPropertiesAspect object

See Also

updateCyVisualProperties, updateCyVisualProperty, getCyVisualProperty

Examples

## Prepare used properties
## Visual property: Properties
vpPropertyP1 = createCyVisualPropertyProperties(c(NODE_BORDER_STROKE="SOLID"))

## Visual property: Dependencies
vpPropertyD1 = createCyVisualPropertyDependencies(c(nodeSizeLocked="false"))

## Visual property: Mappings
vpPropertyM1 = createCyVisualPropertyMappings(c(NODE_FILL_COLOR="CONTINUOUS"), 
                                              "COL=directed,T=boolean,K=0=true,V=0=ARROW")

## Create visual property object 
vpProperty1 = createCyVisualProperty(properties=vpPropertyP1, 
                                     dependencies=vpPropertyD1, 
                                     mappings=vpPropertyM1)

## Create a visual properties aspect
## (using the same visual property object for simplicity)
createCyVisualProperties(network=vpProperty1, 
                         nodes=vpProperty1, 
                         edges=vpProperty1, 
                         defaultNodes=vpProperty1, 
                         defaultEdges=vpProperty1)

Description

This function is used to create Cytoscape visual property objects, that define networks, nodes, edges, and default nodes and edges in a CyVisualProperties aspect.

Usage

createCyVisualProperty(
  properties = NULL,
  dependencies = NULL,
  mappings = NULL,
  appliesTo = NULL,
  view = NULL
)

Arguments

Details

Cytoscape contributes aspects that organize subnetworks, attribute tables, and visual attributes for use by its own layout and analysis tools. Furthermore are the aspects used in web-based visualizations like within the NDEx platform.

The visual properties aspect is the only aspect (CyVisualProperties) with a complex structure. It is composed of several sub-property classes and consists of CyVisualProperty objects, that belong to, or more precisely describe one of the following network elements: network, nodes, edges, defaultNodes or defaultEdges.

A single visual property (i.e. CyVisualProperty object) organizes the information as properties, dependencies and mappings, as well as the single values appliesTo and view, that define the subnetwork or view to which the IDs apply.

Properties are CyVisualPropertyProperties objects, that hold information like "NODE_FILL_COLOR" : "#26CCC9" or "NODE_LABEL_TRANSPARENCY" : "255" in a key-value like manner.

Dependencies are CyVisualPropertyDependencies objects, that hold information about dependencies between visual properties. Currently there are only three dependencies supported:

• Lock Node with and height: nodeSizeLocked = "false"

• Fit Custom Graphics to node: nodeCustomGraphicsSizeSync = "true"

• Edge color to arrows: arrowColorMatchesEdge = "false"

Mappings are CyVisualPropertyMappings objects, that hold information as a triplet consisting of name, type and definition, like "NODE_FILL_COLOR" : "DISCRETE" : "COL=molecule_type,T=string,K=0=miRNA,V=0=#FCEC00", ⁠"NODE_FILL_COLOR" : "CONTINUOUS" : "COL=gal1RGexp,T=double...⁠ or "NODE_LABEL" : "PASSTHROUGH" : "COL=COMMON,T=string".

For further information about Cytoscape visual properties see the Styles topic of the official Cytoscape documentation: http://manual.cytoscape.org/en/stable/Styles.html

Structure of Cytoscape Visual Properties

CyVisualProperties
|---network = CyVisualProperty
|---nodes = CyVisualProperty
|---edges = CyVisualProperty
|---defaultNodes = CyVisualProperty
|---defaultEdges = CyVisualProperty

CyVisualProperty
|---properties = CyVisualPropertyProperties
|   |--name
|   |--value 
|---dependencies = CyVisualPropertyDependencies
|   |--name
|   |--value 
|---mappings = CyVisualPropertyMappings
|   |--name
|   |--type
|   |--definition 
|---appliesTo = <reference to subnetwork id>
|---view = <reference to subnetwork id>

Value

CyVisualProperty object

See Also

updateCyVisualProperty, updateCyVisualProperties

Examples

## Prepare used properties
## Visual property: Properties
vpPropertyNamedValue = c(NODE_BORDER_STROKE="SOLID", 
                         NODE_BORDER_WIDTH="1.5")
vpPropertyP = createCyVisualPropertyProperties(vpPropertyNamedValue)

## Visual property: Dependencies
vpDependencyNamedValue = c(nodeSizeLocked="false", 
                           arrowColorMatchesEdge="true")
vpPropertyD = createCyVisualPropertyDependencies(vpDependencyNamedValue)

## Visual property: Mappings
vpMappingNamedType = c(NODE_FILL_COLOR="CONTINUOUS",
                       EDGE_TARGET_ARROW_SHAPE="DISCRETE")
vpMappingDefinition = c("COL=gal1RGexp,T=double,...",
                        "COL=directed,T=boolean,K=0=true,V=0=ARROW")
vpPropertyM = createCyVisualPropertyMappings(vpMappingNamedType, 
                                             vpMappingDefinition)

## Create visual property object 
createCyVisualProperty(properties=vpPropertyP, 
                       dependencies=vpPropertyD, 
                       mappings=vpPropertyM)

## Create visual property object with different subnetworks
createCyVisualProperty(properties=list(vpPropertyP, 
                                       vpPropertyP), 
                       dependencies=list(vpPropertyD,
                                         NA),
                       mappings=list(NA,
                                     vpPropertyM),
                       appliesTo = c(NA,
                                     1),
                       view = c(1,
                                NA))

Description

This function is used to create aspects for mappings in Cytoscape visual properties. Networks, nodes, edges, and default nodes and edges mappings are realized as CyVisualProperty objects, that each consist of properties (CyVisualPropertyProperties objects), dependencies (this here) and mappings (CyVisualPropertyMappings objects).

Usage

createCyVisualPropertyDependencies(value, name = NULL)

Arguments

Details

Cytoscape contributes aspects that organize subnetworks, attribute tables, and visual attributes for use by its own layout and analysis tools. Furthermore are the aspects used in web-based visualizations like within the NDEx platform.

The visual properties aspect is the only aspect (CyVisualProperties) with a complex structure. It is composed of several sub-property classes and consists of CyVisualProperty objects, that belong to, or more precisely describe one of the following network elements: network, nodes, edges, defaultNodes or defaultEdges.

A single visual property (i.e. CyVisualProperty object) organizes the information as properties, dependencies and mappings, as well as the single values appliesTo and view, that define the subnetwork or view to which the IDs apply.

Properties are CyVisualPropertyProperties objects, that hold information like "NODE_FILL_COLOR" : "#26CCC9" or "NODE_LABEL_TRANSPARENCY" : "255" in a key-value like manner.

Dependencies are CyVisualPropertyDependencies objects, that hold information about dependencies between visual properties. Currently there are only three dependencies supported:

• Lock Node with and height: nodeSizeLocked = "false"

• Fit Custom Graphics to node: nodeCustomGraphicsSizeSync = "true"

• Edge color to arrows: arrowColorMatchesEdge = "false"

Mappings are CyVisualPropertyMappings objects, that hold information as a triplet consisting of name, type and definition, like "NODE_FILL_COLOR" : "DISCRETE" : "COL=molecule_type,T=string,K=0=miRNA,V=0=#FCEC00", ⁠"NODE_FILL_COLOR" : "CONTINUOUS" : "COL=gal1RGexp,T=double...⁠ or "NODE_LABEL" : "PASSTHROUGH" : "COL=COMMON,T=string".

For further information about Cytoscape visual properties see the Styles topic of the official Cytoscape documentation: http://manual.cytoscape.org/en/stable/Styles.html

Value

CyVisualPropertyDependencies object

Note

If name is not provided, the names(value) is used instead to infer the names.

See Also

updateCyVisualProperty, updateCyVisualProperties

Examples

## Using a named vector
vpDependencyNamedValue = c(nodeSizeLocked="false", 
                           arrowColorMatchesEdge="true")
createCyVisualPropertyDependencies(vpDependencyNamedValue)

## Using two separate vectors
vpDependencyName = c("nodeSizeLocked", 
                     "arrowColorMatchesEdge")
vpDependencyValue = c("false", 
                      "true")
createCyVisualPropertyDependencies(vpDependencyValue, 
                                   vpDependencyName)

# Result for either:
#                    name value
# 1        nodeSizeLocked false
# 2 arrowColorMatchesEdge  true

Description

This function is used to create objects for mappings in Cytoscape visual properties. Networks, nodes, edges, and default nodes and edges mappings are realized as CyVisualProperty objects, that each consist of properties (CyVisualPropertyProperties objects), dependencies (CyVisualPropertyDependencies objects) and mappings (this here).

Usage

createCyVisualPropertyMappings(type, definition, name = NULL)

Arguments

Details

Cytoscape contributes aspects that organize subnetworks, attribute tables, and visual attributes for use by its own layout and analysis tools. Furthermore are the aspects used in web-based visualizations like within the NDEx platform.

The visual properties aspect is the only aspect (CyVisualProperties) with a complex structure. It is composed of several sub-property classes and consists of CyVisualProperty objects, that belong to, or more precisely describe one of the following network elements: network, nodes, edges, defaultNodes or defaultEdges.

A single visual property (i.e. CyVisualProperty object) organizes the information as properties, dependencies and mappings, as well as the single values appliesTo and view, that define the subnetwork or view to which the IDs apply.

Properties are CyVisualPropertyProperties objects, that hold information like "NODE_FILL_COLOR" : "#26CCC9" or "NODE_LABEL_TRANSPARENCY" : "255" in a key-value like manner.

Dependencies are CyVisualPropertyDependencies objects, that hold information about dependencies between visual properties. Currently there are only three dependencies supported:

• Lock Node with and height: nodeSizeLocked = "false"

• Fit Custom Graphics to node: nodeCustomGraphicsSizeSync = "true"

• Edge color to arrows: arrowColorMatchesEdge = "false"

Mappings are CyVisualPropertyMappings objects, that hold information as a triplet consisting of name, type and definition, like "NODE_FILL_COLOR" : "DISCRETE" : "COL=molecule_type,T=string,K=0=miRNA,V=0=#FCEC00", ⁠"NODE_FILL_COLOR" : "CONTINUOUS" : "COL=gal1RGexp,T=double...⁠ or "NODE_LABEL" : "PASSTHROUGH" : "COL=COMMON,T=string".

For further information about Cytoscape visual properties see the Styles topic of the official Cytoscape documentation: http://manual.cytoscape.org/en/stable/Styles.html

Structure of Cytoscape Visual Properties

CyVisualProperties
|---network = CyVisualProperty
|---nodes = CyVisualProperty
|---edges = CyVisualProperty
|---defaultNodes = CyVisualProperty
|---defaultEdges = CyVisualProperty

CyVisualProperty
|---properties = CyVisualPropertyProperties
|   |--name
|   |--value 
|---dependencies = CyVisualPropertyDependencies
|   |--name
|   |--value 
|---mappings = CyVisualPropertyMappings
|   |--name
|   |--type
|   |--definition 
|---appliesTo = <reference to subnetwork id>
|---view = <reference to subnetwork id>

Value

CyVisualPropertyMappings object

Note

If name is not provided, the names(type) is used instead to infer the names.

See Also

updateCyVisualProperty, updateCyVisualProperties

Examples

## Using a named vector
vpMappingNamedType = c(NODE_FILL_COLOR="CONTINUOUS",
                       EDGE_TARGET_ARROW_SHAPE="DISCRETE")
vpMappingDefinition = c("COL=gal1RGexp,T=double,...",
                        "COL=directed,T=boolean,K=0=true,V=0=ARROW")
createCyVisualPropertyMappings(vpMappingNamedType, 
                               vpMappingDefinition)

## Using three separate vectors
vpMappingName = c("NODE_FILL_COLOR", 
                  "EDGE_TARGET_ARROW_SHAPE")
vpMappingType = c("CONTINUOUS", 
                  "DISCRETE")
createCyVisualPropertyMappings(vpMappingType, 
                               vpMappingDefinition, 
                               vpMappingName)

# Result for either:
#                      name       type                                definition
# 1         NODE_FILL_COLOR CONTINUOUS                COL=gal1RGexp,T=double,...
# 2 EDGE_TARGET_ARROW_SHAPE   DISCRETE COL=directed,T=boolean,K=0=true,V=0=ARROW

Description

This function is used to create aspects for mappings in Cytoscape visual properties. Networks, nodes, edges, and default nodes and edges mappings are realized as CyVisualProperty objects, that each consist of properties (this here), dependencies (CyVisualPropertyDependencies objects) and mappings (CyVisualPropertyMappings objects).

Usage

createCyVisualPropertyProperties(value, name = NULL)

Arguments

Details

Cytoscape contributes aspects that organize subnetworks, attribute tables, and visual attributes for use by its own layout and analysis tools. Furthermore are the aspects used in web-based visualizations like within the NDEx platform.

The visual properties aspect is the only aspect (CyVisualProperties) with a complex structure. It is composed of several sub-property classes and consists of CyVisualProperty objects, that belong to, or more precisely describe one of the following network elements: network, nodes, edges, defaultNodes or defaultEdges.

A single visual property (i.e. CyVisualProperty object) organizes the information as properties, dependencies and mappings, as well as the single values appliesTo and view, that define the subnetwork or view to which the IDs apply.

Properties are CyVisualPropertyProperties objects, that hold information like "NODE_FILL_COLOR" : "#26CCC9" or "NODE_LABEL_TRANSPARENCY" : "255" in a key-value like manner.

Dependencies are CyVisualPropertyDependencies objects, that hold information about dependencies between visual properties. Currently there are only three dependencies supported:

• Lock Node with and height: nodeSizeLocked = "false"

• Fit Custom Graphics to node: nodeCustomGraphicsSizeSync = "true"

• Edge color to arrows: arrowColorMatchesEdge = "false"

Mappings are CyVisualPropertyMappings objects, that hold information as a triplet consisting of name, type and definition, like "NODE_FILL_COLOR" : "DISCRETE" : "COL=molecule_type,T=string,K=0=miRNA,V=0=#FCEC00", ⁠"NODE_FILL_COLOR" : "CONTINUOUS" : "COL=gal1RGexp,T=double...⁠ or "NODE_LABEL" : "PASSTHROUGH" : "COL=COMMON,T=string".

For further information about Cytoscape visual properties see the Styles topic of the official Cytoscape documentation: http://manual.cytoscape.org/en/stable/Styles.html

Structure of Cytoscape Visual Properties

CyVisualProperties
|---network = CyVisualProperty
|---nodes = CyVisualProperty
|---edges = CyVisualProperty
|---defaultNodes = CyVisualProperty
|---defaultEdges = CyVisualProperty

CyVisualProperty
|---properties = CyVisualPropertyProperties
|   |--name
|   |--value 
|---dependencies = CyVisualPropertyDependencies
|   |--name
|   |--value 
|---mappings = CyVisualPropertyMappings
|   |--name
|   |--type
|   |--definition 
|---appliesTo = <reference to subnetwork id>
|---view = <reference to subnetwork id>

Value

CyVisualPropertyProperties object

Note

If name is not provided, the names(value) is used instead to infer the names.

See Also

updateCyVisualProperty, updateCyVisualProperties

Examples

## Using a named vector
vpPropertyNamedValue = c(NODE_BORDER_STROKE="SOLID", 
                         NODE_BORDER_WIDTH="1.5")
createCyVisualPropertyProperties(vpPropertyNamedValue)

## Using two separate vectors
vpPropertyName = c("NODE_BORDER_STROKE", 
                   "NODE_BORDER_WIDTH")
vpPropertyValue = c("SOLID", 
                    "1.5")
createCyVisualPropertyProperties(vpPropertyValue, 
                                 vpPropertyName)

# Result for either:
#                 name value
# 1 NODE_BORDER_STROKE SOLID
# 2  NODE_BORDER_WIDTH   1.5

Description

This function creates an aspect for additional attributes of edges.

Usage

createEdgeAttributes(
  propertyOf,
  name,
  value,
  dataType = NULL,
  isList = NULL,
  subnetworkId = NULL
)

Arguments

Details

Edges may have additional attributes besides a name and a representation. Those additional attributes reference a edge by its id and are defined in a key-value like manner, with the name of the attribute as key. The same attribute can also be defined for different subnetworks with different values. The values itself may also differ in their data types, therefore it is necessary to provide the values as a list of the single values instead of a vector.

With isList it can be set, if a value should be considered as a list. This is of minor significance while working solely with RCX objects, unless it will be transformed to JSON. For some attributes it might be necessary that the values are encoded as lists, even if they contain only one element (or even zero elements). To force an element to be encoded correctly, this parameter can be used, for example: ⁠name="A", value=a, isList=T⁠ will be encoded in JSON as ⁠A=["a"]⁠.

Value

EdgeAttributesAspect object

Note

The propertyOf parameter references the edge ids to which the attributes belong to. When adding an EdgeAttributesAspect object to an RCX object, those ids must be present in the Edges aspect, otherwise an error is raised.

See Also

updateEdgeAttributes

Examples

## a minimal example
edgeAttributes = createEdgeAttributes(
  propertyOf=1, 
  name="A", 
  value="a"
)

## defining several properties at once
edgeAttributes = createEdgeAttributes(
  propertyOf=c(1,1), 
  name=c("A", "B"), 
  value=c("a","b")
)

## with characters and numbers mixed
edgeAttributes = createEdgeAttributes(
  propertyOf=c(1,1),
  name=c("A","B"),
  value=list("a",3.14)
)

## force the number to be characters
edgeAttributes = createEdgeAttributes(
  propertyOf=c(1,1),
  name=c("A","B"),
  value=list("a",3.14),
  dataType=c("character","character")
)

## with a list as input for one value
edgeAttributes = createEdgeAttributes(
  propertyOf=c(1,1),
  name=c("A","B"),
  value=list(c("a1","a2"),
             "b")
)

## force "B" to be a list as well
edgeAttributes = createEdgeAttributes(
  propertyOf=c(1,1),
  name=c("A","B"),
  value=list(c("a1","a2"),
             "b"),
  isList=c(TRUE,TRUE)
)

## with a subnetwork
edgeAttributes = createEdgeAttributes(
  propertyOf=c(1,1),
  name=c("A","A"),
  value=c("a","a with subnetwork"),
  subnetworkId=c(NA,1)
)

## with all parameters
edgeAttributes = createEdgeAttributes(
  propertyOf=c(1,1,1,1),
  name=c("A","A","B","B"),
  value=list(c("a1","a2"),
             "a with subnetwork",
             "b",
             "b with subnetwork"),
  isList=c(TRUE,FALSE,TRUE,FALSE),
  subnetworkId=c(NA,1,NA,1)
)

Description

This function creates edges between nodes in networks.

Usage

createEdges(id = NULL, source, target, interaction = NULL)

Arguments

Details

Edges are represented by EdgesAspect objects. Edges connect two nodes, which means that source and target must reference the IDs of nodes in a Nodes object. On creation, the IDs don't matter yet, but at least while adding the EdgesAspect object to an RCX-object, the IDs must be present in the nodes aspect of the RCX-object.

Similar to nodes, an edge also has a unique id, which must be an (positive) integer, which serves as reference to other aspects. If no IDs are provided, those are assigned automatically. Optionally, edges can have an interaction attribute to define the type of interaction between the nodes.

Value

EdgesAspect object

See Also

updateEdges for adding a EdgesAspect object to an EdgesAspect or RCX object

Examples

## create some simple edges
edges1 = createEdges(source=1, target=2)

## create edges with more information
edges2 = createEdges(id=c(3,2,4),
                    source=c(0,0,1), 
                    target=c(1,2,2),
                    interaction=c("activates","inhibits", NA))

Description

This function helps filtering CyVisualProperty objects by appliesTo and view attributes (i.e. a unique combination of both). If nothing matches the searched pattern NULL is returned.

Usage

getCyVisualProperty(cyVisualProperty, appliesTo = NA, view = NA)

Arguments

Details

Cytoscape contributes aspects that organize subnetworks, attribute tables, and visual attributes for use by its own layout and analysis tools. Furthermore are the aspects used in web-based visualizations like within the NDEx platform.

The visual properties aspect is the only aspect (CyVisualProperties) with a complex structure. It is composed of several sub-property classes and consists of CyVisualProperty objects, that belong to, or more precisely describe one of the following network elements: network, nodes, edges, defaultNodes or defaultEdges.

A single visual property (i.e. CyVisualProperty object) organizes the information as properties, dependencies and mappings, as well as the single values appliesTo and view, that define the subnetwork or view to which the IDs apply.

Properties are CyVisualPropertyProperties objects, that hold information like "NODE_FILL_COLOR" : "#26CCC9" or "NODE_LABEL_TRANSPARENCY" : "255" in a key-value like manner.

Dependencies are CyVisualPropertyDependencies objects, that hold information about dependencies between visual properties. Currently there are only three dependencies supported:

• Lock Node with and height: nodeSizeLocked = "false"

• Fit Custom Graphics to node: nodeCustomGraphicsSizeSync = "true"

• Edge color to arrows: arrowColorMatchesEdge = "false"

Mappings are CyVisualPropertyMappings objects, that hold information as a triplet consisting of name, type and definition, like "NODE_FILL_COLOR" : "DISCRETE" : "COL=molecule_type,T=string,K=0=miRNA,V=0=#FCEC00", ⁠"NODE_FILL_COLOR" : "CONTINUOUS" : "COL=gal1RGexp,T=double...⁠ or "NODE_LABEL" : "PASSTHROUGH" : "COL=COMMON,T=string".

For further information about Cytoscape visual properties see the Styles topic of the official Cytoscape documentation: http://manual.cytoscape.org/en/stable/Styles.html

Structure of Cytoscape Visual Properties

CyVisualProperties
|---network = CyVisualProperty
|---nodes = CyVisualProperty
|---edges = CyVisualProperty
|---defaultNodes = CyVisualProperty
|---defaultEdges = CyVisualProperty

CyVisualProperty
|---properties = CyVisualPropertyProperties
|   |--name
|   |--value 
|---dependencies = CyVisualPropertyDependencies
|   |--name
|   |--value 
|---mappings = CyVisualPropertyMappings
|   |--name
|   |--type
|   |--definition 
|---appliesTo = <reference to subnetwork id>
|---view = <reference to subnetwork id>

Value

CyVisualProperty object containing only one element, or NULL

See Also

updateCyVisualProperty, updateCyVisualProperties

Examples

## Visual property: Properties
vpPropertyP1 = createCyVisualPropertyProperties(c(NODE_BORDER_STROKE="SOLID"))

## Visual property: Dependencies
vpPropertyD1 = createCyVisualPropertyDependencies(c(nodeSizeLocked="false"))

## Visual property: Mappings
vpPropertyM1 = createCyVisualPropertyMappings(c(NODE_FILL_COLOR="CONTINUOUS"), 
                                              "COL=directed,T=boolean,K=0=true,V=0=ARROW")

## Create visual property object 
vpProperty = createCyVisualProperty(properties=list(vpPropertyP1,
                                                    vpPropertyP1,
                                                    vpPropertyP1), 
                                    dependencies=list(vpPropertyD1,
                                                      vpPropertyD1,
                                                      NA), 
                                    mappings=list(vpPropertyM1,
                                                  NA,
                                                  vpPropertyM1),
                                    appliesTo = c(NA,
                                                  NA,
                                                  1),
                                    view = c(NA,
                                             1,
                                             1))

## Get VP for no subnetwork an no view
getCyVisualProperty(vpProperty)

getCyVisualProperty(vpProperty, 
                    appliesTo = 1,
                    view = 1)

Description

Convert an RCX object to an graphNEL object

Usage

toGraphNEL(rcx, directed = FALSE)

fromGraphNEL(
  graphNEL,
  nodeId = "id",
  nodeName = "nodeName",
  nodeIgnore = c("name"),
  edgeId = "id",
  edgeInteraction = "edgeInteraction",
  edgeIgnore = c(),
  suppressWarning = FALSE
)

Arguments

Details

In the graphNEL object the attributes are not separated from the graph like in RCX. Therefore, for converting an RCX object to an graphNEL object, and back, some adjustments in the naming of the attributes have to be made.

For nodes the name can be present in the nodes aspect, as name in the nodeAttributes aspect. Also name is used in graphNEL for naming the vertices. To avoid collisions in the conversion, the nodes name is saved in graphNEL as nodeName, while the nodeAttributes property name is saved as "attribute...name". These names are also used for the conversion back to RCX, but here the name used in the nodes aspect can be changed by the nodeName parameter.

Similar to the node name, if "represents" is present as property in nodeAttributes its name is changed to "attribute...represents".

The conversion of edges works analogously: If "interaction" is present as property in edgeAttributes its name is changed to "attribute...interaction".

Nodes and edges must have IDs in the RCX, but not in the graphNEL object. To define an vertex or edge attribute to be used as ID, the parameters nodeId and edgeId can be used to define ether an attribute name (default:"id") or set it to NULL to generate ID automatically.

The attributes also may have a special data type assigned. The data type then is saved by adding "...dataType" to the attribute name.

The cartesian layout is also stored in the graphNEL object. To make those graph vertex attributes distinguishable from nodeAttributes they are named "cartesianLayout...x", "cartesianLayout...y" and "cartesianLayout...z".

In the RCX attributes it is also possible to define a subnetwork, to which an attribute applies. Those attributes are added with "...123" added to its name, where "123" is the subnetwork id. The subnetwork id itself are added as graph graph attributes, and are named ⁠subnetwork...123...nodes"⁠ and "subnetwork...123...edges", where "123" is the subnetwork id.

Altogether, the conventions look as follows: "[attribute...]<name>[...<subnetwork>][...dataType]"

Value

graphNEL or RCX object

See Also

Igraph, igraph::as_graphnel()

Examples

## Read from a CX file
## reading the provided example network of the package
cxFile <- system.file(
 "extdata", 
 "Imatinib-Inhibition-of-BCR-ABL-66a902f5-2022-11e9-bb6a-0ac135e8bacf.cx", 
 package = "RCX"
)

rcx = readCX(cxFile)

## graphNEL can handle multi-edges, but only if the graph is directed and the 
## source and target start and end not between the same nodes.
## Unfortunaltelly this is the case in our sample network.
## A quick fix is simply switching the direction of source and target 
## for the multi-edges:
dubEdges = duplicated(rcx$edges[c("source","target")])

s = rcx$edges$source
rcx$edges$source[dubEdges] = rcx$edges$target[dubEdges]
rcx$edges$target[dubEdges] = s[dubEdges]

## convert the network to graphNEL
gNel = toGraphNEL(rcx, directed = TRUE)

## convert it back
rcxFromGraphNel = fromGraphNEL(gNel)

Description

This function checks, if an aspect has IDs that may be referenced by other aspects.

By default aspects don't have IDs, so only the implemented classes have IDs. Aspects with IDs will be considered in the meta-data aspect to determine properties like: idCounter and elementCount.

Usage

hasIds(aspect)

## Default S3 method:
hasIds(aspect)

## S3 method for class 'NodesAspect'
hasIds(aspect)

## S3 method for class 'EdgesAspect'
hasIds(aspect)

## S3 method for class 'CyGroupsAspect'
hasIds(aspect)

## S3 method for class 'CySubNetworksAspect'
hasIds(aspect)

Arguments

Details

Uses method dispatch, so the default return is FALSE and only aspect classes with IDs are implemented. This way it is easier to extend the data model.

Value

logical

See Also

idProperty(), refersTo(), referredBy(), maxId()

Examples

edges = createEdges(source = c(0,0), target = c(1,2))
hasIds(edges)

Description

This function returns the name of the property, if an aspect uses IDs for its elements. As example, the aspect NodesAspect has the property id that represents the IDs of the aspect.

Usage

idProperty(aspect)

## Default S3 method:
idProperty(aspect)

## S3 method for class 'NodesAspect'
idProperty(aspect)

## S3 method for class 'EdgesAspect'
idProperty(aspect)

## S3 method for class 'CyGroupsAspect'
idProperty(aspect)

## S3 method for class 'CySubNetworksAspect'
idProperty(aspect)

Arguments

Details

By default aspects don't have IDs, so only the implemented classes have IDs. Aspects with IDs will be considered in the meta-data aspect to determine properties like: idCounter and elementCount.

Uses method dispatch, so the default return is NULL and only aspect classes with IDs are implemented. This way it is easier to extend the data model.

Value

character; Name of the ID property or NULL

See Also

hasIds(), refersTo(), referredBy(), maxId()

Examples

edges = createEdges(source = c(0,0), target = c(1,2))
idProperty(edges)

Description

Convert an RCX object to an igraph object

Usage

toIgraph(rcx, directed = FALSE)

fromIgraph(
  ig,
  nodeId = "id",
  nodeName = "nodeName",
  nodeIgnore = c("name"),
  edgeId = "id",
  edgeInteraction = "edgeInteraction",
  edgeIgnore = c(),
  suppressWarning = FALSE
)

Arguments

Details

In the igraph object the attributes are not separated from the graph like in RCX. Therefore, for converting an RCX object to an igraph object, and back, some adjustments in the naming of the attributes have to be made.

For nodes the name can be present in the nodes aspect, as name in the nodeAttributes aspect. Also name is used in igraph for naming the vertices. To avoid collisions in the conversion, the nodes name is saved in igraph as nodeName, while the nodeAttributes property name is saved as "attribute...name". These names are also used for the conversion back to RCX, but here the name used in the nodes aspect can be changed by the nodeName parameter.

Similar to the node name, if "represents" is present as property in nodeAttributes its name is changed to "attribute...represents".

The conversion of edges works analogously: If "interaction" is present as property in edgeAttributes its name is changed to "attribute...interaction".

Nodes and edges must have IDs in the RCX, but not in the igraph object. To define an vertex or edge attribute to be used as ID, the parameters nodeId and edgeId can be used to define ether an attribute name (default:"id") or set it to NULL to generate ID automatically.

The attributes also may have a special data type assigned. The data type then is saved by adding "...dataType" to the attribute name.

The cartesian layout is also stored in the igraph object. To make those igraph vertex attributes distinguishable from nodeAttributes they are named "cartesianLayout...x", "cartesianLayout...y" and "cartesianLayout...z".

In the RCX attributes it is also possible to define a subnetwork, to which an attribute applies. Those attributes are added with "...123" added to its name, where "123" is the subnetwork id. The subnetwork id itself are added as igraph graph attributes, and are named ⁠subnetwork...123...nodes"⁠ and "subnetwork...123...edges", where "123" is the subnetwork id.

Altogether, the conventions look as follows: "[attribute...]<name>[...<subnetwork>][...dataType]"

Value

igraph or RCX object

See Also

graphNEL

Examples

## Read from a CX file
## reading the provided example network of the package
cxFile <- system.file(
 "extdata", 
 "Imatinib-Inhibition-of-BCR-ABL-66a902f5-2022-11e9-bb6a-0ac135e8bacf.cx", 
 package = "RCX"
)

rcx = readCX(cxFile)

## convert the network to igraph
ig = toIgraph(rcx)

## convert it back
rcxFromIg = fromIgraph(ig)

Description

Functions to handle parsed JSON for the different aspects.

Usage

jsonToRCX(jsonData, verbose)

## Default S3 method:
jsonToRCX(jsonData, verbose)

## S3 method for class 'status'
jsonToRCX(jsonData, verbose)

## S3 method for class 'numberVerification'
jsonToRCX(jsonData, verbose)

## S3 method for class 'metaData'
jsonToRCX(jsonData, verbose)

## S3 method for class 'nodes'
jsonToRCX(jsonData, verbose)

## S3 method for class 'edges'
jsonToRCX(jsonData, verbose)

## S3 method for class 'nodeAttributes'
jsonToRCX(jsonData, verbose)

## S3 method for class 'edgeAttributes'
jsonToRCX(jsonData, verbose)

## S3 method for class 'networkAttributes'
jsonToRCX(jsonData, verbose)

## S3 method for class 'cartesianLayout'
jsonToRCX(jsonData, verbose)

## S3 method for class 'cyGroups'
jsonToRCX(jsonData, verbose)

## S3 method for class 'cyHiddenAttributes'
jsonToRCX(jsonData, verbose)

## S3 method for class 'cyNetworkRelations'
jsonToRCX(jsonData, verbose)

## S3 method for class 'cySubNetworks'
jsonToRCX(jsonData, verbose)

## S3 method for class 'cyTableColumn'
jsonToRCX(jsonData, verbose)

## S3 method for class 'cyVisualProperties'
jsonToRCX(jsonData, verbose)

Arguments

Details

These functions will be used in processCX to process the JSON data for every aspect. Each aspect is accessible in the CX-JSON by a particular accession name (i.e. its aspect name; see NDEx documentation: https://home.ndexbio.org/data-model/). This name is used as class to handle different aspects by method dispatch. This simplifies the extension of RCX for non-standard or self-defined aspects.

The CX-JSON is parsed to R data types using the jsonlite package as follows:

jsonlite::fromJSON(cx, simplifyVector = FALSE)

This results in a list of lists (of lists...) to avoid automatic data type conversions, which affect the correctness and usability of the data. Simplified JSON data for example NodeAttributes would be coerced into a data.frame, therefore the value column looses the format for data types other than string.

The jsonData will be a list with only one element named by the aspect: ⁠jsonData$<accessionName>⁠

To access the parsed data for example nodes, this can be done by jsonData$nodes. The single aspects are then created using the corresponding create functions and combined to an RCX object using the corresponding update functions.

Value

created aspect or NULL

See Also

rcxToJson, toCX, readCX, writeCX

Examples

nodesJD = list(nodes=list(list("@id"=6, name="EGFR"),
                          list("@id"=7, name="CDK3")))
class(nodesJD) = c("nodes", class(nodesJD))

jsonToRCX(nodesJD, verbose=TRUE)

Description

This function returns the highest id used in an aspect, that has ids. As example, the aspect NodesAspect has the property id that must be a unique positive integer.

Usage

maxId(x)

## Default S3 method:
maxId(x)

## S3 method for class 'RCX'
maxId(x)

Arguments

Details

Uses method dispatch, so the default return is NULL and only aspect classes that have ids are implemented. This way it is easier to extend the data model.

Value

integer; Highest id. For RCX objects all highest ids are returned in the vector named by the aspect class.

See Also

hasIds(), idProperty(), refersTo(), referredBy(), maxId()

Examples

nodes = createNodes(name = c("ĆDK1","CDK2","CDK3"))
maxId(nodes)

Description

The meta-data aspect contains meta-data about the aspects in the RCX object. It can be generated automatically based on the aspects present in a RCX object:

• for version and consistencyGroup default values are used

• idCounter is inferred with hasIds and maxId of an aspect

• elementCount is inferred from countElements

• properties is left out by default

Usage

updateMetaData(
  x,
  version = NULL,
  consistencyGroup = NULL,
  properties = NULL,
  aspectClasses = getAspectClasses()
)

## S3 method for class 'RCX'
updateMetaData(
  x,
  version = NULL,
  consistencyGroup = NULL,
  properties = NULL,
  aspectClasses = getAspectClasses()
)

## Default S3 method:
updateMetaData(
  x,
  version = NULL,
  consistencyGroup = NULL,
  properties = NULL,
  aspectClasses = getAspectClasses()
)

Arguments

Details

If version, consistencyGroup or properties should have a different value, they can be set using a named vector (or named list for properties), where the name must be an accession name of that aspect in the RCX-object (e.g. nodes or cyVisualProperties).

Besides being a named list by aspect accession name, properties must also contain the single key-value pairs as a further named list. To remove all key-value pairs for one aspect, an empty list can be provided instead of a list with key-value pairs. To simplify adding of properties to a single aspect, there is the updateMetaDataProperties function available.

Value

MetaDataAspect object or RCX object

Note

The meta-data will always be updated automatically, when an aspect is added to or changed in the RCX object.

See Also

updateMetaDataProperties

Examples

## 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)
cySubNetworks = createCySubNetworks(
  id = c(1,2),
  nodes = list("all", c(1,2,3)),
  edges = list("all", c(0,2))                    
)
rcx = updateCySubNetworks(rcx, cySubNetworks)

## update meta-data manually
rcx = updateMetaData(rcx)

## update meta-data with some values
rcx = updateMetaData(rcx,
                     version=c(edges="2.0"),
                     consistencyGroup=c(nodes=3),
                     properties=list(cySubNetworks=list(some="value",
                                                        another="VALUE"),
                                     edges=list(some="edge",
                                                another="EDGE")))

## remove all properties for edges
rcx = updateMetaData(rcx, properties=list(edges=list()))

Description

This function creates an aspect for attributes of a network.

Usage

createNetworkAttributes(
  name,
  value,
  dataType = NULL,
  isList = NULL,
  subnetworkId = NULL
)

Arguments

Details

Networks may have describing attributes, that are defined in a key-value like manner, with the name of the attribute as key. The same attribute can also be defined for different subnetworks with different values. The values itself may differ in their data types, therefore it is necessary to provide the values as a list of the single values instead of a vector.

With isList it can be set, if a value should be considered as a list. This is of minor significance while working solely with RCX objects, unless it will be transformed to JSON. For some attributes it might be necessary that the values are encoded as lists, even if they contain only one element (or even zero elements). To force an element to be encoded correctly, this parameter can be used, for example: ⁠name="A", value=a, isList=T⁠ will be encoded in JSON as ⁠A=["a"]⁠.

Value

NetworkAttributesAspect object

See Also

updateNetworkAttributes; NodeAttributes, EdgeAttributes

Examples

## a minimal example
networkAttributes = createNetworkAttributes(
  name="A", 
  value="a"
)

## defining several properties at once
networkAttributes = createNetworkAttributes(
  name=c("A", "B"), 
  value=c("a","b")
)

## with characters and numbers mixed
networkAttributes = createNetworkAttributes(
  name=c("A","B"),
  value=list("a",3.14)
)

## force the number to be characters
networkAttributes = createNetworkAttributes(
  name=c("A","B"),
  value=list("a",3.14),
  dataType=c("character","character")
)

## with a list as input for one value
networkAttributes = createNetworkAttributes(
  name=c("A","B"),
  value=list(c("a1","a2"),
             "b")
)

## force "B" to be a list as well
networkAttributes = createNetworkAttributes(
  name=c("A","B"),
  value=list(c("a1","a2"),
             "b"),
  isList=c(TRUE,TRUE)
)

## with a subnetwork
networkAttributes = createNetworkAttributes(
  name=c("A","A"),
  value=c("a","a with subnetwork"),
  subnetworkId=c(NA,1)
)

## with all parameters
networkAttributes = createNetworkAttributes(
  name=c("A","A","B","B"),
  value=list(c("a1","a2"),
             "a with subnetwork",
             "b",
             "b with subnetwork"),
  isList=c(TRUE,FALSE,TRUE,FALSE),
  subnetworkId=c(NA,1,NA,1)
)

Description

This function creates an aspect for additional attributes of nodes.

Usage

createNodeAttributes(
  propertyOf,
  name,
  value,
  dataType = NULL,
  isList = NULL,
  subnetworkId = NULL
)

Arguments

Details

Nodes may have additional attributes besides a name and a representation. Those additional attributes reference a node by its id and are defined in a key-value like manner, with the name of the attribute as key. The same attribute can also be defined for different subnetworks with different values. The values itself may also differ in their data types, therefore it is necessary to provide the values as a list of the single values instead of a vector.

With isList it can be set, if a value should be considered as a list. This is of minor significance while working solely with RCX objects, unless it will be transformed to JSON. For some attributes it might be necessary that the values are encoded as lists, even if they contain only one element (or even zero elements). To force an element to be encoded correctly, this parameter can be used, for example: ⁠name="A", value=a, isList=T⁠ will be encoded in JSON as ⁠A=["a"]⁠.

Value

NodeAttributesAspect object

Note

The propertyOf parameter references the node ids to which the attributes belong to. When adding an NodeAttributesAspect object to an RCX object, those ids must be present in the Nodes aspect, otherwise an error is raised.

See Also

updateNodeAttributes, EdgeAttributes, NetworkAttributes

Examples

## a minimal example
nodeAttributes = createNodeAttributes(
  propertyOf=1, 
  name="A", 
  value="a"
)

## defining several properties at once
nodeAttributes = createNodeAttributes(
  propertyOf=c(1,1), 
  name=c("A", "B"), 
  value=c("a","b")
)

## with characters and numbers mixed
nodeAttributes = createNodeAttributes(
  propertyOf=c(1,1),
  name=c("A","B"),
  value=list("a",3.14)
)

## force the number to be characters
nodeAttributes = createNodeAttributes(
  propertyOf=c(1,1),
  name=c("A","B"),
  value=list("a",3.14),
  dataType=c("string","string")
)

## with a list as input for one value
nodeAttributes = createNodeAttributes(
  propertyOf=c(1,1),
  name=c("A","B"),
  value=list(c("a1","a2"),
             "b")
)

## force "B" to be a list as well
nodeAttributes = createNodeAttributes(
  propertyOf=c(1,1),
  name=c("A","B"),
  value=list(c("a1","a2"),
             "b"),
  isList=c(TRUE,TRUE)
)

## with a subnetwork
nodeAttributes = createNodeAttributes(
  propertyOf=c(1,1),
  name=c("A","A"),
  value=c("a","a with subnetwork"),
  subnetworkId=c(NA,1)
)

## with all parameters
nodeAttributes = createNodeAttributes(
  propertyOf=c(1,1,1,1,1,1),
  name=c("A","A","b","d","i","l"),
  value=list(c("a1","a2"),
             "a with subnetwork",
             TRUE,
             3.14,
             314,
             314),
  dataType=c("string","string","boolean","double","integer","long"), 
  isList=c(TRUE,FALSE,FALSE,FALSE,FALSE,FALSE),
  subnetworkId=c(NA,1,NA,NA,NA,NA)
)

Description

This function creates nodes for networks.

Usage

createNodes(id = NULL, name = NULL, represents = NULL)

Arguments

Details

Nodes are represented by NodesAspect objects. A single node is defined by its unique id, which must be an (positive) integer, which serves as reference to other aspects. Optionally, nodes can have a name and a represents attribute. If no IDs are provided, but either names or representations (or both) IDs are assigned automatically. To be valid, a nodes aspect must contain at least one node. However, if no parameters are set (i.e. id, name and represents = NULL) there is still one node created with neither name nor representation, just an ID. The NodesAspect is the only mandatory aspect for an RCX-object.

Value

NodesAspect object

See Also

updateNodes, RCX-object

Examples

## a minimal example
nodes = createNodes()

## ids will be generated
nodes = createNodes(name = c("a","b","c"))

## with all parameters
nodes = createNodes(id=c(1, 2, 3), 
                    name=c("CDK1", "CDK2", "CDK3"),
                    represents=c("HGNC:CDK1", 
                                 "Uniprot:P24941", 
                                 "Ensembl:ENSG00000250506"))

Description

Create, handle, validate, visualize and convert networks in the Cytoscape exchange (CX) format to standard data types and objects.

Details

The CX format is also used by the NDEx platform, a online commons for biological networks, and the network visualization software Cytocape.

browseVignettes("RCy3")

Author(s)

Florian Auer [email protected]

Description

An RCX object consists of several aspects, but at least one node in the nodes aspect. The network can either created by creating every single aspect first and the create the network with all aspects present, or by creating the aspect only with the nodes and adding the remaining aspects one by one.

Usage

createRCX(
  nodes,
  edges,
  nodeAttributes,
  edgeAttributes,
  networkAttributes,
  cartesianLayout,
  cyGroups,
  cyVisualProperties,
  cyHiddenAttributes,
  cyNetworkRelations,
  cySubNetworks,
  cyTableColumn,
  checkReferences = TRUE
)

Arguments

Details

vignette("01. RCX - an R package implementing the Cytoscape Exchange (CX) format", package = "RCX") vignette("02. Creating RCX from scratch", package = "RCX") vignette("Appendix: The RCX and CX Data Model", package = "RCX")

Value

RCX object

Examples

## minimal example
rcx = createRCX(createNodes())

## create by aspect
nodes = createNodes(name = c("a","b","c"))
edges = createEdges(source=c(0,0), target=c(1,2))

nodeAttributes = createNodeAttributes(
  propertyOf=c(1,1),
  name=c("A","B"),
  value=c("a","b")
)

edgeAttributes = createEdgeAttributes(
  propertyOf=c(0,0), 
  name=c("A", "B"), 
  value=c("a","b")
)

networkAttributes = createNetworkAttributes(
  name=c("A","B"),
  value=list("a",3.14)
)

cartesianLayout = createCartesianLayout(
  node=c(0, 1),
  x=c(5.5, 110.1), 
  y=c(200.3, 210.2)
)

cyGroups = createCyGroups(
  name = c("Group One", "Group Two"),
  nodes = list(c(0,1), 0)                   
)

vpPropertyP = createCyVisualPropertyProperties(c(NODE_BORDER_STROKE="SOLID"))
vpPropertyD = createCyVisualPropertyDependencies(c(nodeSizeLocked="false"))
vpPropertyM = createCyVisualPropertyMappings(c(NODE_FILL_COLOR="CONTINUOUS"), 
                                             "COL=directed,T=boolean,K=0=true,V=0=ARROW")
vpProperty = createCyVisualProperty(properties=vpPropertyP, 
                                    dependencies=vpPropertyD, 
                                    mappings=vpPropertyM)

cyVisualProperties = createCyVisualProperties(nodes=vpProperty)

cyHiddenAttributes = createCyHiddenAttributes(
  name=c("A","B"),
  value=list(c("a1","a2"), "b")
)

cyNetworkRelations = createCyNetworkRelations(
  child = c(0,1),
  name = c("Network A", NA)
)

cySubNetworks = createCySubNetworks(
  nodes = list("all", c(0,1,2)),
  edges = list("all", c(0,1))                    
)

cyTableColumn = createCyTableColumn(
  appliesTo=c("nodes","edges","networks"),
  name=c("weight","weight","collapsed"),
  dataType=c("double","double","boolean")
)

rcx = createRCX(nodes, edges,
                nodeAttributes, edgeAttributes,
                networkAttributes, 
                cartesianLayout,
                cyGroups, 
                cyVisualProperties, 
                cyHiddenAttributes, 
                cyNetworkRelations, 
                cySubNetworks, 
                cyTableColumn)

## create all at once
rcx = createRCX(
  createNodes(name = c("a","b","c")), 
  createEdges(source=c(0,0), target=c(1,2)),
  createNodeAttributes(
    propertyOf=c(1,1),
    name=c("A","B"),
    value=c("a","b")
  ), 
  createEdgeAttributes(
    propertyOf=c(0,0), 
    name=c("A", "B"), 
    value=c("a","b")
  ),
  networkAttributes = createNetworkAttributes(
    name=c("A","B"),
    value=list("a",3.14)
  ), 
  cartesianLayout = createCartesianLayout(
    node=c(0, 1),
    x=c(5.5, 110.1), 
    y=c(200.3, 210.2)
  ),
  createCyGroups(
    name = c("Group One", "Group Two"),
    nodes = list(c(0,1), 0)                   
  ), 
  createCyVisualProperties(
    nodes=createCyVisualProperty(
      properties=createCyVisualPropertyProperties(
        c(NODE_BORDER_STROKE="SOLID")
      ), 
      dependencies=createCyVisualPropertyDependencies(
        c(nodeSizeLocked="false")
      ), 
      mappings=createCyVisualPropertyMappings(
        c(NODE_FILL_COLOR="CONTINUOUS"), 
        "COL=directed,T=boolean,K=0=true,V=0=ARROW")
    )
  ), 
  createCyHiddenAttributes(
    name=c("A","B"),
    value=list(c("a1","a2"), "b")
  ), 
  createCyNetworkRelations(
    child = c(0,1),
    name = c("Network A", NA)
  ), 
  createCySubNetworks(
    nodes = list("all", c(0,1,2)),
    edges = list("all", c(0,1))                    
  ), 
  createCyTableColumn(
    appliesTo=c("nodes","edges","networks"),
    name=c("weight","weight","collapsed"),
    dataType=c("double","double","boolean")
  )
)

Description

Functions for converting the different aspects to JSON following the CX data structure definition (see NDEx documentation: https://home.ndexbio.org/data-model/).

Usage

rcxToJson(aspect, verbose = FALSE, ...)

## Default S3 method:
rcxToJson(aspect, verbose = FALSE, ...)

## S3 method for class 'MetaDataAspect'
rcxToJson(aspect, verbose = FALSE, ...)

## S3 method for class 'NodesAspect'
rcxToJson(aspect, verbose = FALSE, ...)

## S3 method for class 'EdgesAspect'
rcxToJson(aspect, verbose = FALSE, ...)

## S3 method for class 'NodeAttributesAspect'
rcxToJson(aspect, verbose = FALSE, ...)

## S3 method for class 'EdgeAttributesAspect'
rcxToJson(aspect, verbose = FALSE, ...)

## S3 method for class 'NetworkAttributesAspect'
rcxToJson(aspect, verbose = FALSE, ...)

## S3 method for class 'CartesianLayoutAspect'
rcxToJson(aspect, verbose = FALSE, ...)

## S3 method for class 'CyGroupsAspect'
rcxToJson(aspect, verbose = FALSE, ...)

## S3 method for class 'CyHiddenAttributesAspect'
rcxToJson(aspect, verbose = FALSE, ...)

## S3 method for class 'CyNetworkRelationsAspect'
rcxToJson(aspect, verbose = FALSE, ...)

## S3 method for class 'CySubNetworksAspect'
rcxToJson(aspect, verbose = FALSE, ...)

## S3 method for class 'CyTableColumnAspect'
rcxToJson(aspect, verbose = FALSE, ...)

## S3 method for class 'CyVisualPropertiesAspect'
rcxToJson(aspect, verbose = FALSE, ...)

## S3 method for class 'CyVisualProperty'
rcxToJson(aspect, verbose = FALSE, propertyOf = "", ...)

## S3 method for class 'CyVisualPropertyProperties'
rcxToJson(aspect, verbose = FALSE, ...)

## S3 method for class 'CyVisualPropertyDependencies'
rcxToJson(aspect, verbose = FALSE, ...)

## S3 method for class 'CyVisualPropertyMappings'
rcxToJson(aspect, verbose = FALSE, ...)

Arguments

Details

For converting RCX objects to JSON, each aspect is processed by a generic function for its aspect class. Those functions return a character only containing the JSON of this aspect, which is then combined by toCX to be a valid CX data structure.

To support the conversion for non-standard or own-defined aspects, generic functions for those aspect classes have to be implemented.

Value

character; JSON of an aspect

See Also

toCX, writeCX, jsonToRCX, readCX

Examples

nodes = createNodes(name = c("a","b","c","d","e","f"))
rcxToJson(nodes)

Read CX from file, parse the JSON and convert it to an RCX object

Description

The readCX function combines three sub-task:

• read the JSON from file

• parse the JSON

• process the contained aspects to create an RCX object

Usage

readCX(file, verbose = FALSE, aspectClasses = getAspectClasses())

readJSON(file, verbose = FALSE)

parseJSON(json, verbose = FALSE)

processCX(aspectList, verbose = FALSE, aspectClasses = getAspectClasses())

Arguments

Details

If any errors occur during this process, the single steps can be performed individually. This also allows to skip certain steps, for example if the JSON data is already availabe as text, there is no need to save it as file and read it again.

Read the JSON from file

The readJSON function only read the content of a text file and returns it as a simple character vector.

Parse the JSON

The parseJSON function uses the jsonlite package, to parse JSON text:

jsonlite::fromJSON(cx, simplifyVector = FALSE)

The result is a list containing the aspect data as elements. If, for some reason, the JSON is not valid, the jsonlite package raises an error.

Process the contained aspects to create an RCX object

With the processCX function, the single elements from the previous list will be processed with the jsonToRCX functions, which creating objects for the single aspects. The standard CX aspects are processed by generic functions named by the aspect names of the CX data structure, e.g. jsonToRCX.nodeAttributes for the samely named CX aspect the corresponding NodeAttributesAspect in RCX (see also vignette("02. The RCX and CX Data Model") or NDEx documentation: https://home.ndexbio.org/data-model/).

The CX network may contain additional aspects besides the officially defined ones. This includes self defined or deprecated aspects, that sill can be found in the networks at the NDEx platform. By default, those aspects are simply omitted. In those cases, the setting verbose to TRUE is a good idea to see, which aspects cannot be processed this package.

Those not processable aspects can be handled individually, but it is advisable to extend the jsonToRCX functions by implementing own versions for those aspects. Additionally, the update functions have to be implemented to add the newly generated aspect objects to RCX object (see e.g. updateNodes or updateEdges). Therefore, the function also have to be named ⁠"update<aspect-name>⁠, where aspect-name is the capitalized version of the name used in the CX. (see also vignette("03. Extending the RCX Data Model")

Value

RCX object

Functions

• readJSON: Reads the CX/JSON from file and returns the content as text

• parseJSON: Parses the JSON text and returns a list with the aspect data

• processCX: Processes the list of aspect data and creates an RCX

See Also

jsonToRCX, writeCX

Examples

cxFile = system.file(
  "extdata", 
  "Imatinib-Inhibition-of-BCR-ABL-66a902f5-2022-11e9-bb6a-0ac135e8bacf.cx", 
  package = "RCX"
)

rcx = readCX(cxFile)

## OR:

json = readJSON(cxFile)
aspectList = parseJSON(json)
rcx = processCX(aspectList)

Description

This function returns a list of all aspects with all present aspects, that refer to it. As example, the aspect NodesAspect is refered by the property source and target of the EdgesAspect aspect.

Usage

referredBy(rcx, aspectClasses = getAspectClasses())

Arguments

Value

named list; Aspect class names with names of aspect classes, that refer to them.

Note

Uses hasIds() and refersTo() to determine the referring aspects.

See Also

hasIds(), idProperty(), refersTo(), maxId()

Examples

nodes = createNodes(name = c("ĆDK1","CDK2","CDK3"))
edges = createEdges(source = c(0,0), target = c(1,2))
rcx = createRCX(nodes = nodes, edges = edges)

referredBy(rcx)

Description

This function returns the name of the property and the aspect class it refers to. As example, the aspect EdgesAspect has the property source that refers to the ids of the NodesAspect aspect.

Usage

refersTo(aspect)

## Default S3 method:
refersTo(aspect)

## S3 method for class 'EdgesAspect'
refersTo(aspect)

## S3 method for class 'NodeAttributesAspect'
refersTo(aspect)

## S3 method for class 'EdgeAttributesAspect'
refersTo(aspect)

## S3 method for class 'CartesianLayoutAspect'
refersTo(aspect)

## S3 method for class 'CyGroupsAspect'
refersTo(aspect)

## S3 method for class 'CyVisualPropertiesAspect'
refersTo(aspect)

## S3 method for class 'CySubNetworksAspect'
refersTo(aspect)

Arguments

Details

Uses method dispatch, so the default return is NULL and only aspect classes that refer to other aspects are implemented. This way it is easier to extend the data model.

Value

named list; Name of the refering property and aspect class name.

Methods (by class)

• default: of default returns NULL

• EdgesAspect: of EdgesAspect refers to id by source and target

• NodeAttributesAspect: of NodeAttributesAspect refers to id by propertyOf and to id by subnetworkId

• EdgeAttributesAspect: of EdgeAttributesAspect refers to id by propertyOf and to id by subnetworkId

• CartesianLayoutAspect: of CartesianLayoutAspect refers to id by node and to id by view

• CyGroupsAspect: of CyGroupsAspect refers to id by nodes and to id by externalEdges and internalEdges

• CyVisualPropertiesAspect: of CyVisualPropertiesAspect refers to id by appliesTo of the sub-aspects

• CySubNetworksAspect: of refers to id by nodes and to id by edges

See Also

hasIds(), idProperty(), referredBy(), maxId()

Examples

edges = createEdges(source = c(0,0), target = c(1,2))
refersTo(edges)

Description

To simplify the usage of extension of the RCX data model new extensions can easily registered on load with this function. Registered extension then automatically are used for the conversion of CX data containing aspects of these extensions. The accession names and classes then are also added to getAspectClasses.

Usage

setExtension(package, accession, className)

Arguments

Value

options()$RCX.options$extensions

See Also

aspectClasses

Examples

## Not run: 
setExtension("RCXMyRcxExtension", "myRcxExtension", "MyRcxExtensionAspect")

## End(Not run)

Description

summary is a generic function used to produce result summaries of the RCX object. The function invokes particular methods which depend on the class of the first argument.

Usage

## S3 method for class 'RCX'
summary(object, ...)

## S3 method for class 'MetaDataAspect'
summary(object, ...)

## S3 method for class 'NodesAspect'
summary(object, ...)

## S3 method for class 'EdgesAspect'
summary(object, ...)

## S3 method for class 'NodeAttributesAspect'
summary(object, ...)

## S3 method for class 'EdgeAttributesAspect'
summary(object, ...)

## S3 method for class 'NetworkAttributesAspect'
summary(object, ...)

## S3 method for class 'CartesianLayoutAspect'
summary(object, ...)

## S3 method for class 'CyGroupsAspect'
summary(object, ...)

## S3 method for class 'CyHiddenAttributesAspect'
summary(object, ...)

## S3 method for class 'CyNetworkRelationsAspect'
summary(object, ...)

## S3 method for class 'CySubNetworksAspect'
summary(object, ...)

## S3 method for class 'CyTableColumnAspect'
summary(object, ...)

## S3 method for class 'CyVisualPropertiesAspect'
summary(object, ...)

## S3 method for class 'CyVisualProperty'
summary(object, ...)

## S3 method for class 'AspectIdColumn'
summary(object, ...)

## S3 method for class 'AspectRefColumn'
summary(object, ...)

## S3 method for class 'AspectReqRefColumn'
summary(object, ...)

## S3 method for class 'AspectValueColumn'
summary(object, ...)

## S3 method for class 'AspectAttributeColumn'
summary(object, ...)

## S3 method for class 'AspectListLengthColumn'
summary(object, ...)

Arguments

Details

The form of the returned summary depends on the class of its argument, therefore it is possible to summarize RCX objects and their single aspects.

To enhance readability of the summary, some additional classes have summary functions, that are used to show for example ids of an aspect, required and optional references to ids of aspects, or the number of elements in lists.

Value

object summary as list

Methods (by class)

• AspectIdColumn: Summarize an id property

• AspectRefColumn: Summarize an optional property, that references the ids of an other aspect

• AspectReqRefColumn: Summarize a required property, that references the ids of an other aspect

• AspectValueColumn: Summarize the occurrences of the different elements in the property

• AspectAttributeColumn: Summarize the different attributes in the property

• AspectListLengthColumn: The property is a list of vectors, so summarize the length of the vectors

Examples

rcx = createRCX(
  nodes = createNodes(name = c("a","b","c")),
  edges = createEdges(source=1, target=2)
)

summary(rcx)

Convert an RCX object to CX (JSON)

Description

This function converts an RCX object to JSON in a valid CX data structure (see NDEx documentation: https://home.ndexbio.org/data-model/).

Usage

toCX(rcx, verbose = FALSE, pretty = FALSE)

Arguments

Details

The single aspects of the RCX object are processed by generic functions of rcxToJson for each aspect class. Therefore, not only the single aspects are converted to JSON, but also necessary additional aspects are added, so the resulting CX is accepted by the NDEx platform (https://ndexbio.org/):

• numberVerication shows the supported maximal number

• status is needed at the end to show, that no errors have occurred while creation

If the RCX object contains additional aspects besides the officially defined ones, the corresponding rcxToJson functions for those aspect classes have to be implemented in order to include them in the resulting CX.

Value

CX (JSON) text

See Also

toCX, rcxToJson, readCX, writeCX

Examples

rcx = createRCX(
  nodes = createNodes(
    name = LETTERS[seq_len(10)]
  ),
  edges = createEdges(
    source=c(1,2),
    target = c(2,3)
  )
)

json = toCX(rcx, pretty=TRUE)

Description

This functions add a cartesian layout in the form of a CartesianLayout object to an other CartesianLayout or an RCX object.

Usage

updateCartesianLayout(
  x,
  cartesianLayout,
  replace = TRUE,
  stopOnDuplicates = FALSE,
  ...
)

## S3 method for class 'CartesianLayoutAspect'
updateCartesianLayout(
  x,
  cartesianLayout,
  replace = TRUE,
  stopOnDuplicates = FALSE,
  ...
)

## S3 method for class 'RCX'
updateCartesianLayout(
  x,
  cartesianLayout,
  replace = TRUE,
  stopOnDuplicates = FALSE,
  checkReferences = TRUE,
  ...
)

Arguments

Details

Networks, or more precisely its nodes may have a cartesian layout, that is represented as CartesianLayout object. CartesianLayout objects can be added to an RCX or an other CartesianLayout object.

In the case, that a CartesianLayout object is added to an other, or the RCX object already contains a CartesianLayout object, some attributes might be present in both. By default, the properties are updated with the values of the latest one. This can prevented by setting the replace parameter to FALSE, in that case only new properties are added and the existing properties remain untouched.

Furthermore, if duplicated properties are considered as a preventable mistake, an error can be raised by setting stopOnDuplicates to TRUE. This forces the function to stop and raise an error, if duplicated properties are present.

Value

CartesianLayoutAspect or RCX object with added layout

Examples

## For CartesianLayoutAspects: 
## prepare some aspects:
cartesianLayout = createCartesianLayout(
  node=c(0, 1),
  x=c(5.5, 110.1), 
  y=c(200.3, 210.2),
  z=c(-1, 3.1),
)

## node 0 is updated, new view is added 
cartesianLayout2 = createCartesianLayout(
  node=c(0, 0),
  x=c(5.7, 7.2), 
  y=c(98, 13.9),
  view=c(NA, 1476)
)

## Simply update with new values
cartesianLayout3 = updateCartesianLayout(cartesianLayout, cartesianLayout2)

## Ignore already present keys
cartesianLayout3 = updateCartesianLayout(cartesianLayout, cartesianLayout2, 
                                         replace=FALSE)

## Raise an error if duplicate keys are present
try(updateCartesianLayout(cartesianLayout, cartesianLayout2, 
                          stopOnDuplicates=TRUE))
## =>ERROR: 
## Provided IDs (node, view) countain duplicates!

## For RCX:
## prepare RCX object:
nodes = createNodes(name = c("a","b"))
edges = createEdges(source = 0, target = 1)
cySubNetworks = createCySubNetworks(
  id = 1476,
  nodes = "all",
  edges = "all"                    
)
rcx = createRCX(nodes,
                edges = edges,
                cySubNetworks=cySubNetworks)

## add the network attributes
rcx = updateCartesianLayout(rcx, cartesianLayout)

## add additional network attributes and update existing
rcx = updateCartesianLayout(rcx, cartesianLayout2)

Description

This functions add Cytoscape groups in the form of a CyGroups object to an RCX or an other CyGroups object.

Usage

updateCyGroups(x, cyGroups, stopOnDuplicates = FALSE, keepOldIds = TRUE, ...)

## S3 method for class 'CyGroupsAspect'
updateCyGroups(x, cyGroups, stopOnDuplicates = FALSE, keepOldIds = TRUE, ...)

## S3 method for class 'RCX'
updateCyGroups(
  x,
  cyGroups,
  stopOnDuplicates = FALSE,
  keepOldIds = TRUE,
  checkReferences = TRUE,
  ...
)

Arguments

Details

Cytoscape groups allow to group a set of nodes and corresponding internal and external edges together, and represent a group as a single node in the visualization. CyGroups objects can be added to an RCX or an other CyGroups object. The nodes, internalEdges and externalEdges parameters reference the node or edge IDs that belong to a group. When adding an CyGroups object to an RCX object, those IDs must be present in the Nodes or Edges aspect respectively, otherwise an error is raised.

When two groups should be added to each other 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 groups are re-assinged continuing with the next available ID (i.e. maxId(cyGroupsAspect) + 1 and maxId(rcx$cyGroups) + 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 FALSE. Otherwise, if a re-assignment of the IDs is not desired, this can be prevented by setting stopOnDuplicates to TRUE. This forces the function to stop and raise an error, if duplicated IDs are present.

Value

CyGroups or RCX object with added Cytoscape groups

See Also

CyGroups;

Examples

## For CyGroupsAspects: 
## prepare some aspects:
cyGroups1 = createCyGroups(
  name = c("Group One", "Group Two"),
  nodes = list(c(1,2,3), 0),
  internalEdges = list(c(0,1),NA),
  externalEdges = list(NA,c(2,3)),
  collapsed = c(TRUE,NA)                     
)

cyGroups2 = createCyGroups(
  name = "Group Three",
  nodes = list(c(4,5)),
  externalEdges = list(c(4,5))                     
)

## group ids will be kept
cyGroups3 = updateCyGroups(cyGroups1, cyGroups2)

## old group ids will be omitted
cyGroups3 = updateCyGroups(cyGroups1, cyGroups2,
                           keepOldIds=FALSE)

## Raise an error if duplicate keys are present
try(updateCyGroups(cyGroups1, cyGroups2,
                   stopOnDuplicates=TRUE))
## =>ERROR: 
## Elements of "id" (in updateCyGroups) 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 group
rcx = updateCyGroups(rcx, cyGroups1)

## add an additional group
rcx = updateCyGroups(rcx, cyGroups2)

## create a group with a not existing node...
cyGroups3 = createCyGroups(
  name = "Group Three",
  nodes = list(9)                    
)

## ...and try to add them
try(updateCyGroups(rcx, cyGroups3))
## =>ERROR: 
## Provided IDs of "additionalGroups$nodes" (in updateCyGroups) 
## don't exist in "rcx$nodes$id"

## create a group with a not existing edge...
cyGroups4 = createCyGroups(
  name = "Group Four",
  nodes = list(c(1,2)),
  internalEdges = list(c(9))
)

## ...and try to add them
try(updateCyGroups(rcx, cyGroups4))
## =>ERROR: 
## Provided IDs of "additionalGroups$internalEdges" (in updateCyGroups) 
## don't exist in "rcx$edges$id"

Description

This functions add hidden attributes in the form of a CyHiddenAttributes object to an other CyHiddenAttributes or an RCX object.

Usage

updateCyHiddenAttributes(
  x,
  hiddenAttributes,
  replace = TRUE,
  stopOnDuplicates = FALSE,
  ...
)

## S3 method for class 'CyHiddenAttributesAspect'
updateCyHiddenAttributes(
  x,
  hiddenAttributes,
  replace = TRUE,
  stopOnDuplicates = FALSE,
  ...
)

## S3 method for class 'RCX'
updateCyHiddenAttributes(
  x,
  hiddenAttributes,
  replace = TRUE,
  stopOnDuplicates = FALSE,
  checkReferences = TRUE,
  ...
)

Arguments

Details

Cytoscape subnetworks allow to group a set of nodes and corresponding edges together, and network relations define the relations between those networks. CyHiddenAttributes objects can be added to an RCX or an other CyHiddenAttributes object.

In the case, that a CyHiddenAttributes object is added to an other, or the RCX object already contains a CyHiddenAttributes object, some attributes might be present in both. By default, the attributes are updated with the values of the latest one. This can prevented by setting the replace parameter to FALSE, in that case only new attributes are added and the existing attributes remain untouched.

Furthermore, if duplicated attributes are considered as a preventable mistake, an error can be raised by setting stopOnDuplicates to TRUE. This forces the function to stop and raise an error, if duplicated attributes are present.

Value

CyHiddenAttributes or RCX object with added hidden attributes

Examples

## For CyHiddenAttributesAspects: 
## prepare some aspects:
hiddenAttributes1 = createCyHiddenAttributes(
  name=c("A","A","B","B"),
  value=list(c("a1","a2"),
             "a with subnetwork",
             "b",
             "b with subnetwork"),
  isList=c(TRUE,FALSE,TRUE,FALSE),
  subnetworkId=c(NA,1,NA,1)
)

## A is updated, C is new 
hiddenAttributes2 = createCyHiddenAttributes(
  name=c("A","A","C"),
  value=list("new a",
             "new a with subnetwork",
             c(1,2)),
  subnetworkId=c(NA,1,NA)
)

## Simply update with new values
hiddenAttributes3 = updateCyHiddenAttributes(hiddenAttributes1, 
                                             hiddenAttributes2)

## Ignore already present keys
hiddenAttributes3 = updateCyHiddenAttributes(hiddenAttributes1, 
                                             hiddenAttributes2, 
                                             replace=FALSE)

## Raise an error if duplicate keys are present
try(updateCyHiddenAttributes(hiddenAttributes1, hiddenAttributes2, 
                             stopOnDuplicates=TRUE))
## =>ERROR: 
## Elements of "name" and "subnetworkId" (in updateCyHiddenAttributes) 
## 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)
cySubNetworks = createCySubNetworks(
  id = c(1,2),
  nodes = list("all", c(1,2,3)),
  edges = list("all", c(0,2))                    
)
rcx = updateCySubNetworks(rcx, cySubNetworks)

## add a network relation
rcx = updateCyHiddenAttributes(rcx, hiddenAttributes1)

## add an additional relation (update with new values)
rcx = updateCyHiddenAttributes(rcx, hiddenAttributes2)

## create a relation with a not existing subnetwork...
hiddenAttributes3 = createCyHiddenAttributes(
  name="X",
  value="new x",
  subnetworkId=9
)

## ...and try to add them
try(updateCyHiddenAttributes(rcx, hiddenAttributes3))
## =>ERROR: 
## Provided IDs of "additionalAttributes$subnetworkId" (in updateCyHiddenAttributes) 
## don't exist in "rcx$cySubNetworks$id"

Description

This functions add network relations in the form of a CyNetworkRelations object to an other CyNetworkRelations or an RCX object.

Usage

updateCyNetworkRelations(
  x,
  cyNetworkRelations,
  replace = TRUE,
  stopOnDuplicates = FALSE,
  ...
)

## S3 method for class 'CyNetworkRelationsAspect'
updateCyNetworkRelations(
  x,
  cyNetworkRelations,
  replace = TRUE,
  stopOnDuplicates = FALSE,
  ...
)

## S3 method for class 'RCX'
updateCyNetworkRelations(
  x,
  cyNetworkRelations,
  replace = TRUE,
  stopOnDuplicates = FALSE,
  checkReferences = TRUE,
  ...
)

Arguments

Details

Cytoscape subnetworks allow to group a set of nodes and corresponding edges together, and network relations define the relations between those networks. CyNetworkRelations objects can be added to an RCX or an other CyNetworkRelations object.

When network relations are added to a CyNetworkRelations or a RCX object some conflicts may rise, since the aspects might use the same child IDs. If the aspects do not share any child IDs, the two aspects are simply combined, otherwise, the properties of the child are updated. If that is not wanted, the updating can be prevented by setting replace to FALSE. Furthermore, if duplicated properties are considered as a preventable mistake, an error can be raised by setting stopOnDuplicates to TRUE. This forces the function to stop and raise an error, if duplicated child IDs are present.

Value

CyNetworkRelations or RCX object with added network relations

Examples

## For CyNetworkRelationsAspects: 
## prepare some aspects:
cyNetworkRelations1 = createCyNetworkRelations(
  child = c(1,2),
  parent = c(NA,1),
  name = c("Network A",
           "View A"),
  isView = c(FALSE, TRUE)
)

cyNetworkRelations2 = createCyNetworkRelations(
  child = 2,
  name = "View B",
  isView = TRUE
)

## update the duplicated child
cyNetworkRelations3 = updateCyNetworkRelations(cyNetworkRelations1, 
                                               cyNetworkRelations2)

## keep old child values
cyNetworkRelations3 = updateCyNetworkRelations(cyNetworkRelations1, 
                                               cyNetworkRelations2,
                                               replace=FALSE)

## Raise an error if duplicate keys are present
try(updateCyNetworkRelations(cyNetworkRelations1, 
                             cyNetworkRelations2,
                             stopOnDuplicates=TRUE))
## =>ERROR: 
## Elements of "child" (in updateCyNetworkRelations) 
## 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)
cySubNetworks = createCySubNetworks(
  id = c(1,2),
  nodes = list("all", c(1,2,3)),
  edges = list("all", c(0,2))                    
)
rcx = updateCySubNetworks(rcx, cySubNetworks)

## add a network relation
rcx = updateCyNetworkRelations(rcx, cyNetworkRelations1)

## add an additional relation (View A is replaced by B)
rcx = updateCyNetworkRelations(rcx, cyNetworkRelations2)

## create a relation with a not existing subnetwork...
cyNetworkRelations3 = createCyNetworkRelations(
  child = 9
)

## ...and try to add them
try(updateCyNetworkRelations(rcx, cyNetworkRelations3))
## =>ERROR: 
## Provided IDs of "additionalNetworkRelations$child" (in addCyNetworkRelations) 
## don't exist in "rcx$cySubNetworks$id"

## create a relation with a not existing parent subnetwork...
cyNetworkRelations4 = createCyNetworkRelations(
  child = 1,
  parent = 9
)

## ...and try to add them
try(updateCyNetworkRelations(rcx, cyNetworkRelations4))
## =>ERROR: 
## Provided IDs of "additionalNetworkRelations$parent" (in addCyNetworkRelations) 
## don't exist in "rcx$cySubNetworks$id"

Description

This functions add subnetworks in the form of a CySubNetworks object to an other CySubNetworks or an RCX object.

Usage

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,
  ...
)

Arguments

Details

Cytoscape subnetworks allow to group a set of nodes and corresponding edges together. CySubNetworks objects can be added to an RCX or an other CySubNetworks object. 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 Nodes or 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 all.

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 (i.e. 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 FALSE. Otherwise, if a re-assignment of the IDs is not desired, this can be prevented by setting stopOnDuplicates to TRUE. This forces the function to stop and raise an error, if duplicated IDs are present.

Value

CySubNetworks or RCX object with added subnetworks

See Also

CyNetworkRelations;

Examples

## 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"