02. Creating RCX from scratch
2023-10-24
Contents
1 The Cytoscape Exchange (CX) Format
CX is an “aspect-oriented” data structure, which means that the network is divided into several independent modules (“aspects”). Each aspect has its own schema for its contained information, and links between aspects are realized by referencing the unique internal IDs of other aspects.
The CX format comes with some pre-defined aspects, which are divided in three groups:
- core aspects, with which the most properties of the network can be defined
- nodes
- edges
- nodeAttributes
- edgeAttributes
- networkAttributes
- cartesianLayout
- cytoscape aspects, which provide additional information to visualize the networks with Cytoscape
- cyGroups
- cyVisualProperties
- cyHiddenAttributes
- cyNetworkRelations
- cySubnetworks
- cyTableColumn
- meta aspects, which are necessary for data transmission
- metaData
- status
RCX data structure
Legend
This network is available at the NDEx platform at https://www.ndexbio.org/viewer/networks/ebdda4da-2ca5-11ec-b3be-0ac135e8bacf
Aspects are the elemental units composing an RCX object. They hold different properties, some are mandatory to the aspect, some are optional. Being mandatory does not necessary mean, that those properties need to be specified at creation. For example, some aspects hold IDs to be referenced by other aspects. Although those IDs are mandatory for the aspect, they will be automatically created if not provided.
For a full documentation of the differences between the RCX and CX, see the vignette Appendix: The RCX and CX Data Model.
In the following, it will be explained, how to create the above RCX network from scratch and save it as CX file ready to be uploaded to the NDEx platform.
2 Starting with nodes and edges
Every RCX network needs at least one node, but it is a good starting point to begin the construction of a new network with the creation of nodes and edges. Firstly we create the nodes:
nodes <- createNodes(
name = c(
"RCX",
"metaData", "name", "version", "idCounter", "elementCount", "consistencyGroup", "properties",
"nodes", "id", "name", "represents",
"edges", "id", "source", "target", "interaction",
"nodeAttributes", "propertyOf", "name", "value", "dataType", "isList", "subnetworkId",
"edgeAttributes", "propertyOf", "name", "value", "dataType", "isList", "subnetworkId",
"networkAttribute", "name", "value", "dataType", "isList", "subnetworkId",
"cartesianLayout", "node", "x", "y", "z", "view",
"cySubNetworks", "id", "nodes", "edges",
"cyGroups", "id", "name", "nodes", "externalEdges", "internalEdges", "collapsed",
"cyHiddenAttributes", "name", "value", "dataType", "isList", "subnetworkId",
"cyNetworkRelations", "child", "parent", "name", "isView",
"cyTableColum", "appliesTo", "name", "dataType", "isList", "subnetworkId",
"cyVisualProperties", "network", "nodes", "edges", "defaultNodes", "defaultEdges",
"cyVisualProperty", "properties", "dependencies", "mappings", "appliesTo", "view",
"cyVisualPropertyProperties", "value", "name",
"cyVisualPropertyDependencies", "value", "name",
"cyVisualPropertyMappings", "type", "definition", "name",
"status", "sucess", "error"
)
)
head(nodes)## Nodes:
## id name
## 1 0 RCX
## 2 1 metaData
## 3 2 name
## 4 3 version
## 5 4 idCounter
## 6 5 elementCountNext we can create the edges, that link the nodes by its IDs used as source and target of the edge. Additionally, the interaction described by an edge can be specified:
edges <- createEdges(
source = c(
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,
38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54,
55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
72, 73, 74, 75, 76, 78, 79, 80, 81, 82, 84, 85, 87, 88, 90, 91, 92,
93, 94, 95, 14, 15, 18, 23, 25, 30, 36, 38, 42, 45, 46, 50, 51, 52,
59, 61, 62, 70, 72, 73, 74, 75, 76, 78, 79, 80, 81, 82
),
target = c(
0, 1, 1, 1, 1, 1, 1, 0, 8, 8, 8, 0, 12, 12, 12, 12, 0, 17, 17, 17, 17,
17, 17, 0, 24, 24, 24, 24, 24, 24, 0, 31, 31, 31, 31, 31, 0, 37, 37,
37, 37, 37, 0, 43, 43, 43, 0, 47, 47, 47, 47, 47, 47, 0, 54, 54, 54,
54, 54, 0, 60, 60, 60, 60, 0, 65, 65, 65, 65, 65, 0, 71, 71, 71, 71,
71, 77, 77, 77, 77, 77, 83, 83, 86, 86, 89, 89, 89, 0, 93, 93, 9, 9,
9, 44, 13, 44, 44, 9, 44, 9, 13, 9, 13, 13, 44, 44, 44, 44, 77, 77,
77, 77, 77, 83, 86, 89, 44, 44
),
interaction = c(
"aspectOf", "propertyOf", "propertyOf", "propertyOf", "propertyOf",
"propertyOf", "propertyOf", "aspectOf", "propertyOf", "propertyOf",
"propertyOf", "aspectOf", "propertyOf", "propertyOf", "propertyOf",
"propertyOf", "aspectOf", "propertyOf", "propertyOf", "propertyOf",
"propertyOf", "propertyOf", "propertyOf", "aspectOf", "propertyOf",
"propertyOf", "propertyOf", "propertyOf", "propertyOf", "propertyOf",
"aspectOf", "propertyOf", "propertyOf", "propertyOf", "propertyOf",
"propertyOf", "aspectOf", "propertyOf", "propertyOf", "propertyOf",
"propertyOf", "propertyOf", "aspectOf", "propertyOf", "propertyOf",
"propertyOf", "aspectOf", "propertyOf", "propertyOf", "propertyOf",
"propertyOf", "propertyOf", "propertyOf", "aspectOf", "propertyOf",
"propertyOf", "propertyOf", "propertyOf", "propertyOf", "aspectOf",
"propertyOf", "propertyOf", "propertyOf", "propertyOf", "aspectOf",
"propertyOf", "propertyOf", "propertyOf", "propertyOf", "propertyOf",
"aspectOf", "propertyOf", "propertyOf", "propertyOf", "propertyOf",
"propertyOf", "propertyOf", "propertyOf", "propertyOf", "propertyOf",
"propertyOf", "propertyOf", "propertyOf", "propertyOf", "propertyOf",
"propertyOf", "propertyOf", "propertyOf", "aspectOf", "propertyOf",
"propertyOf", "references", "references", "references", "references",
"references", "references", "references", "references", "references",
"references", "references", "references", "references", "references",
"references", "references", "references", "references", "contains",
"contains", "contains", "contains", "contains", "contains", "contains",
"contains", "references", "references"
)
)
head(edges)## Edges:
## id source target interaction
## 1 0 1 0 aspectOf
## 2 1 2 1 propertyOf
## 3 2 3 1 propertyOf
## 4 3 4 1 propertyOf
## 5 4 5 1 propertyOf
## 6 5 6 1 propertyOfWith the nodes and edges, the RCX object can be created:
rcx <- createRCX(nodes = nodes, edges = edges)To investigate the created RCX network, we can simply show the summary of the network:
summary(rcx)## $nodes
## id name
## Total:96 Length:96
## Min. : 0 Class :character
## Max. :95 Mode :character
##
## $metaData
## name version idCounter elementCount
## Length:2 Length:2 Min. : 95.0 Min. : 96.0
## Class :character Class :character 1st Qu.:100.8 1st Qu.:101.8
## Mode :character Mode :character Median :106.5 Median :107.5
## Mean :106.5 Mean :107.5
## 3rd Qu.:112.2 3rd Qu.:113.2
## Max. :118.0 Max. :119.0
## consistencyGroup
## Min. :1
## 1st Qu.:1
## Median :1
## Mean :1
## 3rd Qu.:1
## Max. :1
##
## $edges
## id source target interaction
## Total:119 Total :119 Total :119 Length:119
## Min. : 0 Unique ids: 91 Unique ids: 22 Class :character
## Max. :118 Min. : 1 Min. : 0 Mode :character
## Max. : 95 Max. : 93Here we already see that, additionally to the nodes and edges also the metaData is created. Let’s have a closer look at the meta data:
rcx$metaData## Meta-data:
## name version idCounter elementCount consistencyGroup
## 1 nodes 1.0 95 96 1
## 2 edges 1.0 118 119 1This meta aspect is created and updated automatically when the RCX object is modified and gives an overview of the present aspects, number of elements those contain, and the highest IDs used in the single aspects.
The resulting network already can be visualized, but since no coordinates are set, by default, all nodes would clump together at the same position. To avoid this, we can use a force directed layout to visualize the network:
visualize(rcx, layout = c(name = "cose"))
Force directed layout for RCX network with only nodes and edges
3 Adding attributes to the network
3.1 Node Attributes
The firstly, let’s add the node types. The nodes are either the RCX object, the aspects or the properties of the aspects. Those types are later used to color and size the nodes appropriately.
nodeAttributesType = createNodeAttributes(
propertyOf = nodes$id,
name = rep("type", length(nodes$id)),
value = c(
"object",
"aspect", "property", "property", "property", "property", "property", "property",
"aspect", "property", "property", "property",
"aspect", "property", "property", "property", "property",
"aspect", "property", "property", "property", "property", "property", "property",
"aspect", "property", "property", "property", "property", "property", "property",
"aspect", "property", "property", "property", "property", "property",
"aspect", "property", "property", "property", "property", "property",
"aspect", "property", "property", "property",
"aspect", "property", "property", "property", "property", "property", "property",
"aspect", "property", "property", "property", "property", "property",
"aspect", "property", "property", "property", "property",
"aspect", "property", "property", "property", "property", "property",
"aspect", "property", "property", "property", "property", "property",
"subAspect", "property", "property", "property", "property", "property",
"subAspect", "property", "property",
"subAspect", "property", "property",
"subAspect", "property", "property", "property",
"aspect", "property", "property"
)
)
rcx = updateNodeAttributes(rcx, nodeAttributesType)Next, mark those aspects and properties that are required in creation of the aspect and RCX object. To simplify the creation of the node attributes aspect, firstly only create a vector containing the node IDS.
nodesRequired <- c(
0, # RCX
1, # metaData
2, # metaData:name
8, # metaData:nodes
9, # metaData:id
13, # edge:id
14, # edge:source
15, # edge:target
18, # nodeAttributes:propertyOf
19, # nodeAttributes:name
20, # nodeAttributes:value
25, # edgeAttributes:propertyOf
26, # edgeAttributes:name
27, # edgeAttributes:value
32, # networkAttribute:name
33, # networkAttribute:value
38, # cartesianLayout:node
39, # cartesianLayout:x
40, # cartesianLayout:y
44, # cySubNetworks:id
45, # cySubNetworks:nodes
46, # cySubNetworks:edges
48, # cyGroups:id
49, # cyGroups:name
55, # cyHiddenAttributes:name
56, # cyHiddenAttributes:value
61, # cyNetworkRelations:child
66, # cyTableColum:appliesTo
67, # cyTableColum:name
84, # cyVisualPropertyProperties:value
85, # cyVisualPropertyProperties:name
87, # cyVisualPropertyDependencies:value
88, # cyVisualPropertyDependencies:name
90, # cyVisualPropertyMappings:type
91, # cyVisualPropertyMappings:definition
92, # cyVisualPropertyMappings:name
93, # status
94, # status:sucess
95 # status:error
)Also mark those aspects and properties that are automatically created, when aspects and RCX objects are created. Here also only a vector containing the node IDs is created to keep it simple.
nodesAuto <- c(
1, # metaData
2, # metaData:name
4, # metaData:idCounter
5, # metaData:elementCount
9, # nodes:id
13, # edges:id
44, # cySubNetworks:id
48, # cyGroups:id
93, # status
94, # status:sucess
95 # status:error
)Now create the node attributes, combine them to one node attributes aspect and add the aspect to the RCX object. Of course this would be possible in one combined step, but for demonstration purposes it is done here step by step.
The node attributes to mark are simply set to TRUE.
The remaining node attributes could be set to FALSE, but it is not really needed to do so.
If you want to assign a mapping to node attributes, that are not TRUE you would be required to set them.
With not setting them, they are not accessible for the mapping of values (since no value is defined), so the layout falls back to the default style.
Since boolean values only have two possible values this only makes a difference, where you define the visual styles:
Either in the default style or for both values in the mapping.
The later option, as mentioned before, requires you to include the FALSE values as well, which increases the size of the CX file.
nodeAttributesRequired <- createNodeAttributes(
propertyOf = nodesRequired, name = rep("required", length(nodesRequired)),
value = rep(TRUE, length(nodesRequired))
)
nodeAttributesAuto <- createNodeAttributes(
propertyOf = nodesAuto, name = rep("auto", length(nodesAuto)),
value = rep(TRUE, length(nodesAuto))
)
nodeAttributes <- updateNodeAttributes(nodeAttributesRequired, nodeAttributesAuto)
rcx <- updateNodeAttributes(rcx, nodeAttributes)
## nodeAttributesType was already in rcx, so save it all
nodeAttributes <- rcx$nodeAttributesAdding EdgeAttributes would work similarly, but here we have included all needed information already in the interaction property of the edges.
3.2 Network Attributes
Some attributes follow a convention on NDEx, especially in the network attributes. The attributes name, author and description are shown on the NDEx platform along the network or in the list overview of your networks.
Network attributes shown on the NDEx platform
Therefore, it is useful to include those in the network. The description of the network can be formatted using HTML tags. The NDEx platform also includes an editor for the network attributes. Here we also include the image of the legend in the description of the network. Therefore, we have to do some HTML magic and convert the image to a base64 encoding representation of it.
description <- paste0(
'<h3>Figure 1: RCX data structure.</h3>
<p>An RCX object (green) is composed of several aspects (red),
which themself consist different properties (blue).
Some properties contain sub-properties (light red) that also hold properties.
Properties reference ID properties of other aspects.</p>'
)
if(require(base64enc)){
legendImgFile <- "RCX_Data_Structure_Legend.png"
legendImgRaw <- readBin(
legendImgFile,
"raw",
file.info(legendImgFile)[1, "size"]
)
legendImgBase64 <- base64enc::base64encode(legendImgRaw)
description <- paste0(
description,
'<h4>Legend:</h4>
<p>
<img alt="Legend" style="width: 100%;" src="data:image/png;base64,',
legendImgBase64,
'" />
</p>'
)
}## Loading required package: base64encnetworkAttributes <- createNetworkAttributes(
name = c(
"name",
"author",
"description"
),
value = c(
"RCX Data Structure",
"Florian J. Auer",
description
)
)
rcx <- updateNetworkAttributes(rcx, networkAttributes)Now that we have included the node and network attributes, let’s check the network meta-data again to make sure everything worked out fine.
rcx$metaData## Meta-data:
## name version idCounter elementCount consistencyGroup
## 1 nodes 1.0 95 96 1
## 2 edges 1.0 118 119 1
## 3 nodeAttributes 1.0 NA 146 1
## 4 networkAttributes 1.0 NA 3 14 Put the nodes into position
Until now, the nodes don’t have any position yet, which means that the layout of the network did not change and only can be layouted using a visualization together with some layout algorithm. Instead, we can set the position of the nodes manually using the cartesian layout aspect.
posX <- c(
1187, # RCX
219, 430, 540, 650, 760, 870, 980, # metaData
219, 1189, 431, 541, # nodes
219, 1189, 545, 655, 765, # edges
219, 435, 545, 655, 765, 875, 985, # nodeAttributes
219, 435, 545, 655, 765, 875, 985, # edgeAttributes
219, 435, 545, 655, 765, 875, # networkAttribute
219, 435, 545, 655, 765, 875, # cartesianLayout
219, 1201, 545, 655, # cySubNetworks
219, 435, 545, 655, 765, 875, 985, # cyGroups
219, 435, 545, 655, 765, 875, # cyHiddenAttributes
219, 435, 545, 655, 765, # cyNetworkRelations
219, 435, 545, 655, 765, 875, # cyTableColum
219, 435, 545, 655, 765, 875, # cyVisualProperties
655, 326, 656, 986, 1096, 1206, # cyVisualProperty
326, 325, 435, # cyVisualPropertyProperties
656, 655, 765, # cyVisualPropertyDependencies
986, 985, 1095, 1205, # cyVisualPropertyMappings
219, 435, 545 # status
)
posY <- c(
596, # RCX
595, 646, 646, 646, 646, 646, 646, # metaData
692, 743, 743, 743, # nodes
790, 836, 836, 836, 836, # edges
889, 934, 934, 934, 934, 934, 934, # nodeAttributes
985, 1031, 1031, 1031, 1031, 1031, 1031, # edgeAttributes
1081, 1126, 1126, 1126, 1126, 1126, # networkAttribute
1174, 1219, 1219, 1219, 1219, 1219, # cartesianLayout
1270, 1316, 1316, 1316, # cySubNetworks
1364, 1409, 1409, 1409, 1409, 1409, 1409, # cyGroups
1460, 1506, 1506, 1506, 1506, 1506, # cyHiddenAttributes
1557, 1602, 1602, 1602, 1602, # cyNetworkRelations
1653, 1699, 1699, 1699, 1699, 1699, # cyTableColum
1750, 1795, 1795, 1795, 1795, 1795, # cyVisualProperties
1872, 1931, 1931, 1931, 1931, 1931, # cyVisualProperty
2001, 2059, 2059, # cyVisualPropertyProperties
2001, 2059, 2059, # cyVisualPropertyDependencies
2001, 2059, 2059, 2059, # cyVisualPropertyMappings
2136, 2182, 2182 # status
)
cartesianLayout <- createCartesianLayout(
nodes$id,
x=posX,
y=posY)
rcx <- updateCartesianLayout(rcx, cartesianLayout)Now we can visualize the network with the position assigned to the nodes:
visualize(rcx)
RCX network with a cartesian layout for nodes
5 Create visual layout
The visual representation of the network is defined in the CyVisualProperties aspect.
This aspect holds the definitions for the network, nodes and edges in the form of a CyVisualProperty sub-aspect.
In this sub-aspect, the layout is defined by
- properties: static properties of networks, nodes or edges (defined by a
CyVisualPropertyPropertiessub-aspect) - mappings: definition of data dependent discrete, continuous and passthrough mappings (defined by a
CyVisualPropertyMappingssub-aspect) - dependencies: dependencies between visual properties (defined by a
CyVisualPropertyMappingssub-aspect); Currently there are three dependencies supported:- Lock Node with and height:
nodeSizeLocked - Fit Custom Graphics to node:
nodeCustomGraphicsSizeSync - Edge color to arrows:
arrowColorMatchesEdge
- Lock Node with and height:
Each property (element in CyVisualProperty) can be applied to a subnetwork and/or view.
The complete structure of the visual properties looks as follows:
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>In the following we will create the CyVisualProperties aspect and needed sub-aspects to define a proper visual representation.
5.1 Visual properties of the network
For the network visual properties like the background color can be defined.
Here we create the properties for a network and embed it into a new CyVisualProperty sub-aspect.
cyVisualPropertyPropertiesNetwork <- createCyVisualPropertyProperties(
name = c(
"NETWORK_BACKGROUND_PAINT",
"NETWORK_EDGE_SELECTION",
"NETWORK_NODE_SELECTION"
),
value = c(
"#FFFFFF",
"true",
"true"
)
)
cyVisualPropertyNetwork <- createCyVisualProperty(
properties = cyVisualPropertyPropertiesNetwork
)5.2 Visual properties of nodes
First we define the static properties for the nodes. This includes the default node color and size, the border color and with, etc.
cyVisualPropertyPropertiesNodes <- createCyVisualPropertyProperties(
name = c(
"NODE_BORDER_PAINT",
"NODE_BORDER_STROKE",
"NODE_BORDER_TRANSPARENCY",
"NODE_BORDER_WIDTH",
"NODE_DEPTH",
"NODE_FILL_COLOR",
"NODE_HEIGHT",
"NODE_LABEL_COLOR",
"NODE_LABEL_FONT_FACE",
"NODE_LABEL_FONT_SIZE",
"NODE_LABEL_POSITION",
"NODE_LABEL_TRANSPARENCY",
"NODE_LABEL_WIDTH",
"NODE_PAINT",
"NODE_SELECTED",
"NODE_SELECTED_PAINT",
"NODE_SHAPE",
"NODE_SIZE",
"NODE_TRANSPARENCY",
"NODE_VISIBLE",
"NODE_WIDTH"
),
value = c(
"#CCCCCC",
"SOLID",
"255",
"0.0",
"0.0",
"#89D0F5",
"40.0",
"#000000",
"SansSerif.plain,plain,12",
"14",
"C,C,c,0.00,0.00",
"255",
"200.0",
"#1E90FF",
"false",
"#FFFF00",
"ROUND_RECTANGLE",
"35.0",
"255",
"true",
"90.0"
)
)Next we can define the mappings for the nodes.
The node label is simply generated by passing the value of the column name through.
Here, the other property values are discrete mappings, that only take a column by its name and the corresponding data type, and then simply assign new values to the some selected values from the column.
For example the height of the node is set to 50.0pt and 80.0pt for aspect and object values from the node attributes column type.
Here is the full definition of the node mappings:
cyVisualPropertyMappingNodes <- createCyVisualPropertyMappings(
name=c(
"NODE_LABEL",
"NODE_HEIGHT",
"NODE_WIDTH",
"NODE_FILL_COLOR",
"NODE_BORDER_PAINT",
"NODE_BORDER_WIDTH",
"NODE_LABEL_FONT_FACE",
"NODE_LABEL_FONT_SIZE"
),
type = c(
"PASSTHROUGH",
"DISCRETE",
"DISCRETE",
"DISCRETE",
"DISCRETE",
"DISCRETE",
"DISCRETE",
"DISCRETE"
),
definition = c(
"COL=name,T=string",
paste0("COL=type,T=string,",
"K=0=aspect,V=0=50.0,",
"K=1=object,V=1=80.0,"),
paste0("COL=type,T=string,",
"K=0=aspect,V=0=300.0,",
"K=1=object,V=1=150.0,",
"K=2=subAspect,V=2=300.0"),
paste0("COL=type,T=string,",
"K=0=aspect,V=0=#FF3300,",
"K=1=property,V=1=#73A3F0,",
"K=2=object,V=2=#33FF66,",
"K=3=subAspect,V=3=#FF8465"),
paste0("COL=required,T=boolean,",
"K=0=true,V=0=#3F3F3F"),
paste0("COL=required,T=boolean,",
"K=0=true,V=0=10.0"),
paste0("COL=auto,T=boolean,",
"K=0=true,V=0=SansSerif.italic,,plain,,14"),
paste0("COL=type,T=string,",
"K=0=aspect,V=0=30,",
"K=1=object,V=1=50,",
"K=2=subAspect,V=2=20")
)
)As mentioned before, there are only a few dependencies supported. For nodes there are only the following:
cyVisualPropertyDependenciesNodes <- createCyVisualPropertyDependencies(
name = c(
"nodeCustomGraphicsSizeSync",
"nodeSizeLocked"
),
value = c(
"true",
"false"
)
)Finally combine the create sub-aspects to one CyVisualProperty.
By default this is applied to the whole network and not limited to some subnetworks or views.
cyVisualPropertyNodes <- createCyVisualProperty(
properties = cyVisualPropertyPropertiesNodes,
mappings = cyVisualPropertyMappingNodes,
dependencies = cyVisualPropertyDependenciesNodes
)5.3 Visual properties of edges
The definition of visual properties for edges works the same as for nodes. So let’s begin again with the static properties:
cyVisualPropertyPropertiesEdges <- createCyVisualPropertyProperties(
name = c(
"EDGE_CURVED",
"EDGE_LINE_TYPE",
"EDGE_PAINT",
"EDGE_SELECTED",
"EDGE_SELECTED_PAINT",
"EDGE_SOURCE_ARROW_SELECTED_PAINT",
"EDGE_SOURCE_ARROW_SHAPE",
"EDGE_SOURCE_ARROW_SIZE",
"EDGE_SOURCE_ARROW_UNSELECTED_PAINT",
"EDGE_STROKE_SELECTED_PAINT",
"EDGE_STROKE_UNSELECTED_PAINT",
"EDGE_TARGET_ARROW_SELECTED_PAINT",
"EDGE_TARGET_ARROW_SHAPE",
"EDGE_TARGET_ARROW_SIZE",
"EDGE_TARGET_ARROW_UNSELECTED_PAINT",
"EDGE_TRANSPARENCY",
"EDGE_VISIBLE"
),
value = c(
"false",
"SOLID",
"#323232",
"false",
"#FFFF00",
"#FFFF00",
"NONE",
"6.0",
"#000000",
"#FF0000",
"#848484",
"#FFFF00",
"NONE",
"6.0",
"#000000",
"255",
"true"
)
)Add a mapping for the edges:
cyVisualPropertyMappingEdges <- createCyVisualPropertyMappings(
name=c(
"EDGE_LINE_TYPE",
"EDGE_TARGET_ARROW_SHAPE",
"EDGE_UNSELECTED_PAINT",
"EDGE_WIDTH"
),
type = c(
"DISCRETE",
"DISCRETE",
"DISCRETE",
"DISCRETE"
),
definition = c(
paste0("COL=interaction,T=string,",
"K=0=references,V=0=SEPARATE_ARROW"),
paste0("COL=interaction,T=string,",
"K=0=contains,V=0=SQUARE,",
"K=1=references,V=1=DELTA"),
paste0("COL=interaction,T=string,",
"K=0=propertyOf,V=0=#FFAD99,",
"K=1=contains,V=1=#73A3F0,",
"K=2=aspectOf,V=2=#CBFFD8,",
"K=3=references,V=3=#0D377C"),
paste0("COL=interaction,T=string,",
"K=0=partOf,V=0=10.0,",
"K=1=propertyOf,V=1=5.0,",
"K=2=contains,V=2=5.0,",
"K=3=aspectOf,V=3=7.0,",
"K=4=references,V=4=3.0")
)
)And the one remaining dependency:
cyVisualPropertyDependenciesEdges <- createCyVisualPropertyDependencies(
name = c(
"arrowColorMatchesEdge"
),
value = c(
"true"
)
)And combine the sub-aspects to one CyVisualProperty.
cyVisualPropertyEdges <- createCyVisualProperty(
properties=cyVisualPropertyPropertiesEdges,
mappings = cyVisualPropertyMappingEdges,
dependencies = cyVisualPropertyDependenciesEdges
)5.4 Create a visual property aspect
Above we create the CyVisualProperty sub-aspects for the network, nodes and edges.
Finally, we have to combine those to a CyVisualProperties aspect, where usually the default properties are added as defaultNodes or defaultEdges.
The final aspect now can be added to the network:
cyVisualProperties <- createCyVisualProperties(
network = cyVisualPropertyNetwork,
defaultNodes = cyVisualPropertyNodes,
defaultEdges = cyVisualPropertyEdges
)
rcx <- updateCyVisualProperties(rcx, cyVisualProperties)6 Table column
Before we are finished, we can add a table-column aspect to the network as well. This aspect simply holds the information about the node, edge and network attributes, as well as their data type. This seems a little redundant, since the same information can already be found in the network, but Cytoscape seems to depend on it, although it automatically creates this table on import.
Therefore, for completeness, we create the table-column aspect:
cyTableColumn <- createCyTableColumn(
name = c("name", "type", "required", "auto",
"name", "interaction",
"name", "author", "description"),
appliesTo = c("nodes", "nodes", "nodes", "nodes",
"edges", "edges",
"networks", "networks", "networks"),
dataType = c("string", "string", "boolean", "boolean",
"string", "string",
"string", "string", "string")
)
rcx <- updateCyTableColumn(rcx, cyTableColumn)7 Visualize the final network
Now that we are finished, we can visualize the network again, this time with the desired visual representation:
visualize(rcx)Doing this manually might be laborious, but it is a good exercise to understand how visual properties and mappings work in detail.
An easier method would be to the current network as CX file, load it in Cytoscape or the online tool NDExEdit (https://frankkramer-lab.github.io/NDExEdit) to create the desired layout.
Afterwards the created layout could be also re-used in other networks that have the same attributes defined:
newRcx <- updateCyVisualProperties(newRCX, rcx$cyVisualProperties)8 Meta-data
The meta-data of the network is created and updated autimatically.
However, we can also update the meta-data manually, and set its version, consisentcyGroup and properties:
rcx <- updateMetaData(
rcx,
version = c(
nodes="1.1",
edges="1.1",
nodeAttributes="1.1",
networkAttributes="1.1",
cartesianLayout="1.1",
cyVisualProperties="1.1",
cyTableColumn="1.1"
),
consistencyGroup = c(
nodes=2,
edges=2,
nodeAttributes=2,
networkAttributes=2,
cartesianLayout=2,
cyVisualProperties=2,
cyTableColumn=2
))
rcx$metaData## Meta-data:
## name version idCounter elementCount consistencyGroup
## 1 nodes 1.1 95 96 2
## 2 edges 1.1 118 119 2
## 3 nodeAttributes 1.1 NA 146 2
## 4 networkAttributes 1.1 NA 3 2
## 5 cartesianLayout 1.1 NA 96 2
## 6 cyVisualProperties 1.1 NA 3 2
## 7 cyTableColumn 1.1 NA 9 29 Create RCX at once
In the above example, we created the RCX network nearly in the beginning and updated it regularly in the course. Instead, we also could simply create the single aspects one by one, and then create an RCX network with all aspects at once:
rcx <- createRCX(
nodes = nodes,
edges = edges,
nodeAttributes = nodeAttributes,
networkAttributes = networkAttributes,
cartesianLayout = cartesianLayout,
cyVisualProperties = cyVisualProperties,
cyTableColumn = cyTableColumn
)10 Save the network
After spending this much effort on creating a network, we also want to save it for further use. If we only intend to use it within R, saving it simply as RDS would be sufficient:
saveRDS(rcx, "path/to/some-file.rds")For further use of the networks even outside of R, RCX networks can be saved in a similar manner as CX files:
writeCX(rcx, "path/to/some-file.cx")Those files can then be used in other platforms like NDEx, Cytoscape or NDExEdit.
In fact, the create network was uploaded to NDEx and can be accessed at https://www.ndexbio.org/viewer/networks/ebdda4da-2ca5-11ec-b3be-0ac135e8bacf
There it is displayed along with its network information and description:
RCX data structure network displayed on NDEx
11 Session info
sessionInfo()## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] base64enc_0.1-3 RCX_1.6.0 knitr_1.44 BiocStyle_2.30.0
##
## loaded via a namespace (and not attached):
## [1] digest_0.6.33 R6_2.5.1 bookdown_0.36
## [4] fastmap_1.1.1 xfun_0.40 cachem_1.0.8
## [7] htmltools_0.5.6.1 rmarkdown_2.25 cli_3.6.1
## [10] sass_0.4.7 jquerylib_0.1.4 compiler_4.3.1
## [13] plyr_1.8.9 tools_4.3.1 evaluate_0.22
## [16] bslib_0.5.1 Rcpp_1.0.11 yaml_2.3.7
## [19] formatR_1.14 BiocManager_1.30.22 jsonlite_1.8.7
## [22] rlang_1.1.1