## ---- include=FALSE-----------------------------------------------------------
library(knitr)
opts_chunk$set(tidy.opts=list(width.cutoff=75,
args.newline = TRUE,
arrow = TRUE),
tidy=TRUE)
## ----eval=FALSE, include=FALSE------------------------------------------------
# output:
# html_vignette:
# toc: true
# output:
# pdf_document:
# latex_engine: xelatex
# toc: true
## ---- echo=FALSE, message=FALSE-----------------------------------------------
library(RCX)
## ----nodes, tidy=FALSE--------------------------------------------------------
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)
## ----edges--------------------------------------------------------------------
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)
## ----rcx----------------------------------------------------------------------
rcx = createRCX(nodes = nodes, edges = edges)
## ----rcxSummary---------------------------------------------------------------
summary(rcx)
## ----rcxMetadata--------------------------------------------------------------
rcx$metaData
## ----visualize1, eval=FALSE---------------------------------------------------
# visualize(rcx, layout = c(name="cose"))
## ----nodeAttributesType, tidy=FALSE-------------------------------------------
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)
## ----nodeAttributesRequired, tidy=FALSE---------------------------------------
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
)
## ----nodeAttributesAuto, tidy=FALSE-------------------------------------------
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
)
## ----nodeAttributesAdd--------------------------------------------------------
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$nodeAttributes
## ----networkAttributes, tidy=FALSE--------------------------------------------
description <- paste0(
'<h3>Figure 1: RCX data structure.</h3>
<p>An RCX object (green) is composed of several aspects (red),
which themself consist different properties (blue).
Some properties contain sub-properties (light red) that also hold properties.
Properties reference ID properties of other aspects.</p>'
)
if(require(base64enc)){
legendImgFile <- "RCX_Data_Structure_Legend.png"
legendImgRaw <- readBin(
legendImgFile,
"raw",
file.info(legendImgFile)[1, "size"]
)
legendImgBase64 <- base64enc::base64encode(legendImgRaw)
description <- paste0(
description,
'<h4>Legend:</h4>
<p>
<img alt="Legend" style="width: 100%;" src="data:image/png;base64,',
legendImgBase64,
'" />
</p>'
)
}
networkAttributes <- createNetworkAttributes(
name = c(
"name",
"author",
"description"
),
value = c(
"RCX Data Structure",
"Florian J. Auer",
description
)
)
rcx <- updateNetworkAttributes(rcx, networkAttributes)
## ----attributesMetadata-------------------------------------------------------
rcx$metaData
## ----cartesianLayout, tidy=FALSE----------------------------------------------
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)
## ----visualizeCartesian, eval=FALSE-------------------------------------------
# visualize(rcx)
## ----visualPropertiesNetwork, tidy=FALSE--------------------------------------
cyVisualPropertyPropertiesNetwork <- createCyVisualPropertyProperties(
name = c(
"NETWORK_BACKGROUND_PAINT",
"NETWORK_EDGE_SELECTION",
"NETWORK_NODE_SELECTION"
),
value = c(
"#FFFFFF",
"true",
"true"
)
)
cyVisualPropertyNetwork <- createCyVisualProperty(
properties = cyVisualPropertyPropertiesNetwork
)
## ----visualPropertiesPropertiesNodes, tidy=FALSE------------------------------
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"
)
)
## ----visualPropertiesMappingsNodes, tidy=FALSE--------------------------------
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")
)
)
## ----visualPropertiesDependenciesNodes, tidy=FALSE----------------------------
cyVisualPropertyDependenciesNodes <- createCyVisualPropertyDependencies(
name = c(
"nodeCustomGraphicsSizeSync",
"nodeSizeLocked"
),
value = c(
"true",
"false"
)
)
## ----visualPropertyNodes, tidy=FALSE------------------------------------------
cyVisualPropertyNodes <- createCyVisualProperty(
properties = cyVisualPropertyPropertiesNodes,
mappings = cyVisualPropertyMappingNodes,
dependencies = cyVisualPropertyDependenciesNodes
)
## ----visualPropertiesPropertiesEdges, tidy=FALSE------------------------------
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"
)
)
## ----visualPropertiesMappingsEdges, tidy=FALSE--------------------------------
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")
)
)
## ----visualPropertiesDependenciesEdges, tidy=FALSE----------------------------
cyVisualPropertyDependenciesEdges <- createCyVisualPropertyDependencies(
name = c(
"arrowColorMatchesEdge"
),
value = c(
"true"
)
)
## ----visualPropertyEdges, tidy=FALSE------------------------------------------
cyVisualPropertyEdges <- createCyVisualProperty(
properties=cyVisualPropertyPropertiesEdges,
mappings = cyVisualPropertyMappingEdges,
dependencies = cyVisualPropertyDependenciesEdges
)
## ----visualProperties, tidy=FALSE---------------------------------------------
cyVisualProperties <- createCyVisualProperties(
network = cyVisualPropertyNetwork,
defaultNodes = cyVisualPropertyNodes,
defaultEdges = cyVisualPropertyEdges
)
rcx <- updateCyVisualProperties(rcx, cyVisualProperties)
## ----tableColumn, tidy=FALSE--------------------------------------------------
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)
## ----visualizeRCX, eval=FALSE-------------------------------------------------
# visualize(rcx)
## ----reuseVisualProperties, eval=FALSE----------------------------------------
# newRcx = updateCyVisualProperties(newRCX, rcx$cyVisualProperties)
## ----metaData, tidy=FALSE-----------------------------------------------------
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
## ----createRCX, tidy=FALSE----------------------------------------------------
rcx <- createRCX(
nodes = nodes,
edges = edges,
nodeAttributes = nodeAttributes,
networkAttributes = networkAttributes,
cartesianLayout = cartesianLayout,
cyVisualProperties = cyVisualProperties,
cyTableColumn = cyTableColumn
)
## ----writeRDS, eval=FALSE-----------------------------------------------------
# saveRDS(rcx, "path/to/some-file.rds")
## ----writeCX, eval=FALSE------------------------------------------------------
# writeCX(rcx, "path/to/some-file.cx")
## ----sessionInfo--------------------------------------------------------------
sessionInfo()