## ----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( '

Figure 1: RCX data structure.

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.

' ) 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, '

Legend:

Legend

' ) } 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()