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    "addGraphFromFile",
    "clearSelection",
    "createTestGraph",
    "dataFramesToJSON",
    "deleteGraph",
    "deleteSelectedNodes",
    "eda",
    "edaNames",
    "fit",
    "fitSelection",
    "getEdgeCount",
    "getJSON",
    "getLayoutStrategies",
    "getNodeCount",
    "getNodes",
    "getPosition",
    "getSelectedNodes",
    "getSupportedEdgeDecoratorShapes",
    "getSupportedNodeShapes",
    "getZoom",
    "graphNELtoJSON.string",
    "hAlign",
    "hideAllEdges",
    "hideEdges",
    "hideNodes",
    "hideSelectedNodes",
    "invertNodeSelection",
    "layout",
    "layoutSelectionInGrid",
    "layoutSelectionInGridInferAnchor",
    "loadStyleFile",
    "noa",
    "noaNames",
    "RCyjs",
    "readAndStandardizeJSONNetworkFile",
    "readAndStandardizeJSONStyleFile",
    "redraw",
    "restoreLayout",
    "saveJPG",
    "saveLayout",
    "savePNG",
    "selectFirstNeighborsOfSelectedNodes",
    "selectNodes",
    "setBackgroundColor",
    "setDefaultEdgeColor",
    "setDefaultEdgeLineColor",
    "setDefaultEdgeLineStyle",
    "setDefaultEdgeSourceArrowColor",
    "setDefaultEdgeSourceArrowShape",
    "setDefaultEdgeTargetArrowColor",
    "setDefaultEdgeTargetArrowShape",
    "setDefaultEdgeWidth",
    "setDefaultNodeBorderColor",
    "setDefaultNodeBorderWidth",
    "setDefaultNodeColor",
    "setDefaultNodeFontColor",
    "setDefaultNodeFontSize",
    "setDefaultNodeHeight",
    "setDefaultNodeShape",
    "setDefaultNodeSize",
    "setDefaultNodeWidth",
    "setDefaultStyle",
    "setEdgeAttributes",
    "setEdgeStyle",
    "setGraph",
    "setNodeAttributes",
    "setNodeBorderColor",
    "setNodeBorderWidth",
    "setNodeColor",
    "setNodeColorRule",
    "setNodeFontColor",
    "setNodeFontSize",
    "setNodeHeight",
    "setNodeLabelAlignment",
    "setNodeLabelRule",
    "setNodeShape",
    "setNodeSize",
    "setNodeSizeRule",
    "setNodeWidth",
    "setPosition",
    "setZoom",
    "sfn",
    "showAll",
    "showEdges",
    "showNodes",
    "simpleDemoGraph",
    "vAlign"
  ],
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    {
      "page": "addGraph",
      "title": "addGraph",
      "topics": [
        "addGraph",
        "addGraph,RCyjs-method"
      ]
    },
    {
      "page": "addGraphFromFile",
      "title": "addGraphFromFile",
      "topics": [
        "addGraphFromFile",
        "addGraphFromFile,RCyjs-method"
      ]
    },
    {
      "page": "clearSelection",
      "title": "clearSelection",
      "topics": [
        "clearSelection",
        "clearSelection,RCyjs-method"
      ]
    },
    {
      "page": "createTestGaph",
      "title": "createTestGraph",
      "topics": [
        "createTestGraph"
      ]
    },
    {
      "page": "dataFramesToJSON",
      "title": "Create a cytoscape.js JSON graph from one or two data.frames.",
      "topics": [
        "dataFramesToJSON"
      ]
    },
    {
      "page": "deleteGraph",
      "title": "deleteGraph",
      "topics": [
        "deleteGraph",
        "deleteGraph,RCyjs-method"
      ]
    },
    {
      "page": "deleteSelectedNodes",
      "title": "deleteSelectedNodes",
      "topics": [
        "deleteSelectedNodes",
        "deleteSelectedNodes,RCyjs-method"
      ]
    },
    {
      "page": "eda",
      "title": "eda",
      "topics": [
        "eda"
      ]
    },
    {
      "page": "edaNames",
      "title": "edaNames",
      "topics": [
        "edaNames"
      ]
    },
    {
      "page": "fit",
      "title": "fit",
      "topics": [
        "fit",
        "fit,RCyjs-method"
      ]
    },
    {
      "page": "fitSelection",
      "title": "fitSelection",
      "topics": [
        "fitSelection",
        "fitSelection,RCyjs-method"
      ]
    },
    {
      "page": "getEdgeCount",
      "title": "getEdgeCount",
      "topics": [
        "getEdgeCount",
        "getEdgeCount,RCyjs-method"
      ]
    },
    {
      "page": "getJSON",
      "title": "getJSON",
      "topics": [
        "getJSON",
        "getJSON,RCyjs-method"
      ]
    },
    {
      "page": "getLayoutStrategies",
      "title": "getLayoutStrategies",
      "topics": [
        "getLayoutStrategies",
        "getLayoutStrategies,RCyjs-method"
      ]
    },
    {
      "page": "getNodeCount",
      "title": "getNodeCount",
      "topics": [
        "getNodeCount",
        "getNodeCount,RCyjs-method"
      ]
    },
    {
      "page": "getNodes",
      "title": "getNodes",
      "topics": [
        "getNodes",
        "getNodes,RCyjs-method"
      ]
    },
    {
      "page": "getPosition",
      "title": "getPosition",
      "topics": [
        "getPosition",
        "getPosition,RCyjs-method"
      ]
    },
    {
      "page": "getSelectedNodes",
      "title": "getSelectedNodes",
      "topics": [
        "getSelectedNodes",
        "getSelectedNodes,RCyjs-method"
      ]
    },
    {
      "page": "getSupportedEdgeDecoratorShapes",
      "title": "getSupportedEdgeDecoratorShapes",
      "topics": [
        "getSupportedEdgeDecoratorShapes",
        "getSupportedEdgeDecoratorShapes,RCyjs-method"
      ]
    },
    {
      "page": "getSupportedNodeShapes",
      "title": "getSupportedNodeShapes",
      "topics": [
        "getSupportedNodeShapes",
        "getSupportedNodeShapes,RCyjs-method"
      ]
    },
    {
      "page": "getZoom",
      "title": "getZoom",
      "topics": [
        "getZoom",
        "getZoom,RCyjs-method"
      ]
    },
    {
      "page": "graphNELtoJSON.string",
      "title": "Convert R graphNEL object to cytoscape.js JSON.",
      "topics": [
        "graphNELtoJSON.string"
      ]
    },
    {
      "page": "hAlign",
      "title": "hAlign",
      "topics": [
        "hAlign",
        "hAlign,RCyjs-method"
      ]
    },
    {
      "page": "hideAllEdges",
      "title": "hideAllEdges",
      "topics": [
        "hideAllEdges",
        "hideAllEdges,RCyjs-method"
      ]
    },
    {
      "page": "hideEdges",
      "title": "hideEdges",
      "topics": [
        "hideEdges",
        "hideEdges,RCyjs-method"
      ]
    },
    {
      "page": "hideNodes",
      "title": "hideNodes",
      "topics": [
        "hideNodes",
        "hideNodes,RCyjs-method"
      ]
    },
    {
      "page": "hideSelectedNodes",
      "title": "hideSelectedNodes",
      "topics": [
        "hideSelectedNodes",
        "hideSelectedNodes,RCyjs-method"
      ]
    },
    {
      "page": "invertNodeSelection",
      "title": "invertNodeSelection",
      "topics": [
        "invertNodeSelection",
        "invertNodeSelection,RCyjs-method"
      ]
    },
    {
      "page": "layout",
      "title": "layout",
      "topics": [
        "layout",
        "layout,RCyjs-method"
      ]
    },
    {
      "page": "layoutSelectionInGrid",
      "title": "layoutSelectionInGrid",
      "topics": [
        "layoutSelectionInGrid",
        "layoutSelectionInGrid,RCyjs-method"
      ]
    },
    {
      "page": "layoutSelectionInGridInferAnchorm",
      "title": "layoutSelectionInGridInferAnchor",
      "topics": [
        "layoutSelectionInGridInferAnchor",
        "layoutSelectionInGridInferAnchor,RCyjs-method"
      ]
    },
    {
      "page": "loadStyleFile",
      "title": "loadStyleFile",
      "topics": [
        "loadStyleFile",
        "loadStyleFile,RCyjs-method"
      ]
    },
    {
      "page": "noa",
      "title": "noa",
      "topics": [
        "noa"
      ]
    },
    {
      "page": "noaNames",
      "title": "noaNames",
      "topics": [
        "noaNames"
      ]
    },
    {
      "page": "RCyjs-class",
      "title": "Create an RCyjs object",
      "topics": [
        ".RCyjs",
        "RCyjs",
        "RCyjs-class"
      ]
    },
    {
      "page": "readAndStandardizeJSONNetworkFile",
      "title": "Read in a JSON network file, identify (or add) elements field return JSON",
      "topics": [
        "readAndStandardizeJSONNetworkFile"
      ]
    },
    {
      "page": "readAndStandardizeJSONStyleFile",
      "title": "Read in a JSON file, extract the selector elements, return JSON",
      "topics": [
        "readAndStandardizeJSONStyleFile"
      ]
    },
    {
      "page": "redraw",
      "title": "redraw",
      "topics": [
        "redraw",
        "redraw,RCyjs-method"
      ]
    },
    {
      "page": "restoreLayout",
      "title": "restoreLayout",
      "topics": [
        "restoreLayout",
        "restoreLayout,RCyjs-method"
      ]
    },
    {
      "page": "saveJPG",
      "title": "saveJPG",
      "topics": [
        "saveJPG",
        "saveJPG,RCyjs-method"
      ]
    },
    {
      "page": "saveLayout",
      "title": "saveLayout",
      "topics": [
        "saveLayout",
        "saveLayout,RCyjs-method"
      ]
    },
    {
      "page": "savePNG",
      "title": "savePNG",
      "topics": [
        "savePNG",
        "savePNG,RCyjs-method"
      ]
    },
    {
      "page": "selectFirstNeighborsOfSelectedNodes",
      "title": "selectFirstNeighborsOfSelectedNodes",
      "topics": [
        "selectFirstNeighborsOfSelectedNodes",
        "selectFirstNeighborsOfSelectedNodes,RCyjs-method"
      ]
    },
    {
      "page": "selectNodes",
      "title": "selectNodes",
      "topics": [
        "selectNodes",
        "selectNodes,RCyjs-method"
      ]
    },
    {
      "page": "setBackgroundColor",
      "title": "setBackgroundColor",
      "topics": [
        "setBackgroundColor",
        "setBackgroundColor,RCyjs-method"
      ]
    },
    {
      "page": "setDefaultEdgeColor",
      "title": "setDefaultEdgeColor",
      "topics": [
        "setDefaultEdgeColor",
        "setDefaultEdgeColor,RCyjs-method"
      ]
    },
    {
      "page": "setDefaultEdgeLineColor",
      "title": "setDefaultEdgeLineColor",
      "topics": [
        "setDefaultEdgeLineColor",
        "setDefaultEdgeLineColor,RCyjs-method"
      ]
    },
    {
      "page": "setDefaultEdgeLineStyle",
      "title": "setDefaultEdgeLineStyle",
      "topics": [
        "setDefaultEdgeLineStyle",
        "setDefaultEdgeLineStyle,RCyjs-method"
      ]
    },
    {
      "page": "setDefaultEdgeSourceArrowColor",
      "title": "setDefaultEdgeSourceArrowColor",
      "topics": [
        "setDefaultEdgeSourceArrowColor",
        "setDefaultEdgeSourceArrowColor,RCyjs-method"
      ]
    },
    {
      "page": "setDefaultEdgeSourceArrowShape",
      "title": "setDefaultEdgeSourceArrowShape",
      "topics": [
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        "setDefaultEdgeSourceArrowShape,RCyjs-method"
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    },
    {
      "page": "setDefaultEdgeTargetArrowColor",
      "title": "setDefaultEdgeTargetArrowColor",
      "topics": [
        "setDefaultEdgeTargetArrowColor",
        "setDefaultEdgeTargetArrowColor,RCyjs-method"
      ]
    },
    {
      "page": "setDefaultEdgeTargetArrowShape",
      "title": "setDefaultEdgeTargetArrowShape",
      "topics": [
        "setDefaultEdgeTargetArrowShape",
        "setDefaultEdgeTargetArrowShape,RCyjs-method"
      ]
    },
    {
      "page": "setDefaultEdgeWidth",
      "title": "setDefaultEdgeWidth",
      "topics": [
        "setDefaultEdgeWidth",
        "setDefaultEdgeWidth,RCyjs-method"
      ]
    },
    {
      "page": "setDefaultNodeBorderColor",
      "title": "setDefaultNodeBorderColor",
      "topics": [
        "setDefaultNodeBorderColor",
        "setDefaultNodeBorderColor,RCyjs-method"
      ]
    },
    {
      "page": "setDefaultNodeBorderWidth",
      "title": "setDefaultNodeBorderWidth",
      "topics": [
        "setDefaultNodeBorderWidth",
        "setDefaultNodeBorderWidth,RCyjs-method"
      ]
    },
    {
      "page": "setDefaultNodeColor",
      "title": "setDefaultNodeColor",
      "topics": [
        "setDefaultNodeColor",
        "setDefaultNodeColor,RCyjs-method"
      ]
    },
    {
      "page": "setDefaultNodeFontColor",
      "title": "setDefaultNodeFontColor",
      "topics": [
        "setDefaultNodeFontColor",
        "setDefaultNodeFontColor,RCyjs-method"
      ]
    },
    {
      "page": "setDefaultNodeFontSize",
      "title": "setDefaultNodeFontSize",
      "topics": [
        "setDefaultNodeFontSize",
        "setDefaultNodeFontSize,RCyjs-method"
      ]
    },
    {
      "page": "setDefaultNodeHeight",
      "title": "setDefaultNodeHeight",
      "topics": [
        "setDefaultNodeHeight",
        "setDefaultNodeHeight,RCyjs-method"
      ]
    },
    {
      "page": "setDefaultNodeShape",
      "title": "setDefaultNodeShape",
      "topics": [
        "setDefaultNodeShape",
        "setDefaultNodeShape,RCyjs-method"
      ]
    },
    {
      "page": "setDefaultNodeSize",
      "title": "setDefaultNodeSize",
      "topics": [
        "setDefaultNodeSize",
        "setDefaultNodeSize,RCyjs-method"
      ]
    },
    {
      "page": "setDefaultNodeWidth",
      "title": "setDefaultNodeWidth",
      "topics": [
        "setDefaultNodeWidth",
        "setDefaultNodeWidth,RCyjs-method"
      ]
    },
    {
      "page": "setDefaultStyle",
      "title": "setDefaultStyle",
      "topics": [
        "setDefaultStyle",
        "setDefaultStyle,RCyjs-method"
      ]
    },
    {
      "page": "setEdgeAttributes",
      "title": "setEdgeAttributes",
      "topics": [
        "setEdgeAttributes",
        "setEdgeAttributes,RCyjs-method"
      ]
    },
    {
      "page": "setEdgeStyle",
      "title": "setEdgeStyle",
      "topics": [
        "setEdgeStyle",
        "setEdgeStyle,RCyjs-method"
      ]
    },
    {
      "page": "setGraph",
      "title": "setGraph",
      "topics": [
        "setGraph",
        "setGraph,RCyjs-method"
      ]
    },
    {
      "page": "setNodeAttributes",
      "title": "setNodeAttributes",
      "topics": [
        "setNodeAttributes",
        "setNodeAttributes,RCyjs-method"
      ]
    },
    {
      "page": "setNodeBorderColor",
      "title": "setNodeBorderColor",
      "topics": [
        "setNodeBorderColor",
        "setNodeBorderColor,RCyjs-method"
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    },
    {
      "page": "setNodeBorderWidth",
      "title": "setNodeBorderWidth",
      "topics": [
        "setNodeBorderWidth",
        "setNodeBorderWidth,RCyjs-method"
      ]
    },
    {
      "page": "setNodeColor",
      "title": "setNodeColor",
      "topics": [
        "setNodeColor",
        "setNodeColor,RCyjs-method"
      ]
    },
    {
      "page": "setNodeColorRule",
      "title": "setNodeColorRule",
      "topics": [
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        "setNodeColorRule,RCyjs-method"
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    {
      "page": "setNodeFontColor",
      "title": "setNodeFontColor",
      "topics": [
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        "setNodeFontColor,RCyjs-method"
      ]
    },
    {
      "page": "setNodeFontSize",
      "title": "setNodeFontSize",
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      "page": "setNodeHeight",
      "title": "setNodeHeight",
      "topics": [
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    },
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    },
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    },
    {
      "page": "setNodeShape",
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      "topics": [
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    },
    {
      "page": "setNodeSize",
      "title": "setNodeSize",
      "topics": [
        "setNodeSize",
        "setNodeSize,RCyjs-method"
      ]
    },
    {
      "page": "setNodeSizeRule",
      "title": "setNodeSizeRule",
      "topics": [
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        "setNodeSizeRule,RCyjs-method"
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    },
    {
      "page": "setNodeWidth",
      "title": "setNodeWidth",
      "topics": [
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        "setNodeWidth,RCyjs-method"
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    },
    {
      "page": "setPosition",
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    },
    {
      "page": "setZoom",
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      "page": "sfn",
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    },
    {
      "page": "showAll",
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    {
      "page": "simpleDemoGraph",
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      "title": "vAlign",
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    "cli",
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      "source": "RCyjs.Rmd",
      "filename": "RCyjs.html",
      "title": "RCyjs: interactive network visualization using cytoscape.js",
      "author": "Paul Shannon",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Overview",
        "Load the RCyjs package and its dependencies",
        "Create the graph: two nodes, one edge between them",
        "Set up default node and edge attributes on the graph",
        "Add the actual initial attributes",
        "Controlling Visual Attributes",
        "Methods for mapping data attributes to visual attributes",
        "Builtin shapes",
        "Change some of the default styling",
        "Assign visual properties directly to specific nodes",
        "Reset to the default style",
        "Motivating visual mapping rules",
        "Node positioning",
        "Layout by algorithm",
        "Layout by ad hoc calculation",
        "Interactive placement on the cytoscape.js canvas",
        "Programmitc layout assists",
        "Convenience functions for edge and node attributes",
        "A two node Activator-Target example: data-driven node size, color, position"
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      "created": "2018-04-20 23:01:14",
      "modified": "2024-04-30 19:31:59",
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