Customized Network Graph for Detailed Analysis

library(canvasXpress)
nodes=read.table("https://www.canvasxpress.org/data/r/cX-networkbasic-nodes.txt", header=TRUE, sep="\t", quote="", fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
edges=read.table("https://www.canvasxpress.org/data/r/cX-networkbasic-edges.txt", header=TRUE, sep="\t", quote="", fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
canvasXpress(
nodeData=nodes,
edgeData=edges,
calculateLayout=FALSE,
decorations=list("exp1", "exp2", "exp3"),
decorationsPosition="top",
decorationsType="bar",
graphType="Network",
networkFreezeOnLoad=TRUE,
nodeFontColor="rgb(29,34,43)",
showAnimation=TRUE,
showDecorations=TRUE
)

from canvasxpress.canvas import CanvasXpress
from canvasxpress.plot import show_in_browser

if __name__ == "__main__":
  # Define the chart with its data and configuration
  chart: CanvasXpress = CanvasXpress(
    render_to = "network15",
    data = {
      "edges": [
        {
          "color": "rgb(51,12,255)",
          "endArrow": "arrow",
          "id1": "Gene1",
          "id2": "Gene2",
          "startArrow": "square",
          "type": "curved",
          "width": "3"
        },
        {
          "color": "rgb(51,12,255)",
          "endArrow": "arrow",
          "id1": "Gene4",
          "id2": "Gene3",
          "startArrow": "square",
          "type": "dashedCurved",
          "width": "3"
        },
        {
          "color": "rgb(51,12,255)",
          "endArrow": "arrow",
          "id1": "Gene5",
          "id2": "Met",
          "type": "line",
          "width": "3"
        },
        {
          "color": "rgb(51,12,255)",
          "endArrow": "round",
          "id1": "Gene3",
          "id2": "DNA",
          "startArrow": "square",
          "type": "bezier",
          "width": "3"
        },
        {
          "color": "rgb(51,12,255)",
          "endArrow": "square",
          "id1": "Gene7",
          "id2": "Gene1",
          "startArrow": "arrow",
          "type": "dashedBezier",
          "width": "3"
        },
        {
          "color": "rgb(51,12,255)",
          "elbows": [
            [235, 100],
            [50, 100],
            [50, 230]
          ],
          "endArrow": "square",
          "id1": "Gene5",
          "id2": "Gene7",
          "type": "dotted",
          "width": "3"
        },
        {
          "color": "rgb(51,12,255)",
          "elbows": [
            [275, 100, 325, 100, 325, 165],
            [325, 165, 325, 270, 425, 270]
          ],
          "endArrow": "square",
          "id1": "Gene5",
          "id2": "DNA",
          "type": "bezier",
          "width": "3"
        }
      ],
      "legend": {
        "edges": [
          {
            "id": "edgesLegendId0",
            "text": "Activate",
            "type": "arrowHeadLine"
          }
        ],
        "nodes": [
          {
            "color": "rgb(255,0,0)",
            "id": "nodesLegendId0",
            "shape": "sphere",
            "text": "Gene"
          }
        ],
        "pos": {
          "decorations": {
            "x": 450,
            "y": 360
          },
          "edges": {
            "x": 360,
            "y": -5
          },
          "nodes": {
            "x": -5,
            "y": -5
          }
        },
        "text": [
          {
            "id": "textLegendId0",
            "text": "Cool Pathway",
            "x": 150,
            "y": 460
          }
        ]
      },
      "nodes": [
        {
          "eventless": True,
          "height": 400,
          "hideLabel": True,
          "id": "Cell",
          "imagePath": "https://www.canvasxpress.org/assets/images/cell.png",
          "shape": "image",
          "width": 525,
          "x": 250,
          "y": 250
        },
        {
          "exp1": 1,
          "exp2": 2,
          "exp3": 4,
          "exp4": {
            "cl1": 2,
            "cl2": 4,
            "cl3": 3
          },
          "exp5": {
            "cl1": 12,
            "cl2": 1,
            "cl3": 5
          },
          "height": 40,
          "id": "Gene1",
          "imagePath": "https://www.canvasxpress.org/assets/images/prot.png",
          "shape": "image",
          "width": 40,
          "x": 155,
          "y": 160
        },
        {
          "color": "rgb(255,0,0)",
          "exp1": 2,
          "exp2": 4,
          "exp3": 1,
          "exp4": {
            "cl1": 7,
            "cl2": 1,
            "cl3": 8
          },
          "exp5": {
            "cl1": 1,
            "cl2": 11,
            "cl3": 8
          },
          "id": "Gene2",
          "shape": "sphere",
          "size": 1,
          "x": 155,
          "y": 340
        },
        {
          "color": "rgb(255,0,0)",
          "exp1": 1,
          "exp2": 5,
          "exp3": 1,
          "exp4": {
            "cl1": 12,
            "cl2": 4,
            "cl3": 8
          },
          "exp5": {
            "cl1": 3,
            "cl2": 7,
            "cl3": 5
          },
          "id": "Gene3",
          "shape": "sphere",
          "size": 1,
          "x": 355,
          "y": 160
        },
        {
          "color": "rgb(255,0,0)",
          "exp1": 4,
          "exp2": 2,
          "exp3": 1,
          "exp4": {
            "cl1": 1,
            "cl2": 14,
            "cl3": 7
          },
          "exp5": {
            "cl1": 2,
            "cl2": 1,
            "cl3": 15
          },
          "id": "Gene4",
          "label": "Receptor Gene4",
          "shape": "sphere",
          "size": 1,
          "x": 355,
          "y": 340
        },
        {
          "color": "rgb(255,0,0)",
          "exp1": 1,
          "exp2": 3,
          "exp3": 2,
          "exp4": {
            "cl1": 4,
            "cl2": 4,
            "cl3": 8
          },
          "exp5": {
            "cl1": 6,
            "cl2": 7,
            "cl3": 2
          },
          "height": 20,
          "id": "Gene5",
          "shape": "sphere",
          "width": 20,
          "x": 255,
          "y": 100
        },
        {
          "height": 40,
          "hideLabel": True,
          "id": "Met",
          "imagePath": "https://www.canvasxpress.org/assets/images/met.png",
          "shape": "image",
          "width": 40,
          "x": 255,
          "y": 400
        },
        {
          "exp1": 3,
          "exp2": 3,
          "exp3": 4,
          "exp4": {
            "cl1": 2,
            "cl2": 14,
            "cl3": 1
          },
          "exp5": {
            "cl1": 9,
            "cl2": 3,
            "cl3": 5
          },
          "height": 40,
          "id": "Gene7",
          "imagePath": "https://www.canvasxpress.org/assets/images/prot7.png",
          "shape": "image",
          "width": 40,
          "x": 50,
          "y": 250
        },
        {
          "height": 40,
          "hideLabel": True,
          "id": "DNA",
          "imagePath": "https://www.canvasxpress.org/assets/images/dna1.png",
          "shape": "image",
          "width": 40,
          "x": 450,
          "y": 250
        }
      ]
    },
    config = {
      "calculateLayout": False,
      "decorations": ["exp1", "exp2", "exp3"],
      "decorationsPosition": "top",
      "decorationsType": "bar",
      "graphType": "Network",
      "networkFreezeOnLoad": True,
      "nodeFontColor": "rgb(29,34,43)",
      "showAnimation": True,
      "showDecorations": True
    },
    width = 600,
    height = 600
  )

  # Display the chart in its own Web page
  show_in_browser(chart)

Run this notebook:

from canvasxpress.canvas import CanvasXpress
from canvasxpress.plot import graph

graph(
  CanvasXpress(
    render_to = "network15",
    data = {
      "edges": [
        {
          "color": "rgb(51,12,255)",
          "endArrow": "arrow",
          "id1": "Gene1",
          "id2": "Gene2",
          "startArrow": "square",
          "type": "curved",
          "width": "3"
        },
        {
          "color": "rgb(51,12,255)",
          "endArrow": "arrow",
          "id1": "Gene4",
          "id2": "Gene3",
          "startArrow": "square",
          "type": "dashedCurved",
          "width": "3"
        },
        {
          "color": "rgb(51,12,255)",
          "endArrow": "arrow",
          "id1": "Gene5",
          "id2": "Met",
          "type": "line",
          "width": "3"
        },
        {
          "color": "rgb(51,12,255)",
          "endArrow": "round",
          "id1": "Gene3",
          "id2": "DNA",
          "startArrow": "square",
          "type": "bezier",
          "width": "3"
        },
        {
          "color": "rgb(51,12,255)",
          "endArrow": "square",
          "id1": "Gene7",
          "id2": "Gene1",
          "startArrow": "arrow",
          "type": "dashedBezier",
          "width": "3"
        },
        {
          "color": "rgb(51,12,255)",
          "elbows": [
            [235, 100],
            [50, 100],
            [50, 230]
          ],
          "endArrow": "square",
          "id1": "Gene5",
          "id2": "Gene7",
          "type": "dotted",
          "width": "3"
        },
        {
          "color": "rgb(51,12,255)",
          "elbows": [
            [275, 100, 325, 100, 325, 165],
            [325, 165, 325, 270, 425, 270]
          ],
          "endArrow": "square",
          "id1": "Gene5",
          "id2": "DNA",
          "type": "bezier",
          "width": "3"
        }
      ],
      "legend": {
        "edges": [
          {
            "id": "edgesLegendId0",
            "text": "Activate",
            "type": "arrowHeadLine"
          }
        ],
        "nodes": [
          {
            "color": "rgb(255,0,0)",
            "id": "nodesLegendId0",
            "shape": "sphere",
            "text": "Gene"
          }
        ],
        "pos": {
          "decorations": {
            "x": 450,
            "y": 360
          },
          "edges": {
            "x": 360,
            "y": -5
          },
          "nodes": {
            "x": -5,
            "y": -5
          }
        },
        "text": [
          {
            "id": "textLegendId0",
            "text": "Cool Pathway",
            "x": 150,
            "y": 460
          }
        ]
      },
      "nodes": [
        {
          "eventless": True,
          "height": 400,
          "hideLabel": True,
          "id": "Cell",
          "imagePath": "https://www.canvasxpress.org/assets/images/cell.png",
          "shape": "image",
          "width": 525,
          "x": 250,
          "y": 250
        },
        {
          "exp1": 1,
          "exp2": 2,
          "exp3": 4,
          "exp4": {
            "cl1": 2,
            "cl2": 4,
            "cl3": 3
          },
          "exp5": {
            "cl1": 12,
            "cl2": 1,
            "cl3": 5
          },
          "height": 40,
          "id": "Gene1",
          "imagePath": "https://www.canvasxpress.org/assets/images/prot.png",
          "shape": "image",
          "width": 40,
          "x": 155,
          "y": 160
        },
        {
          "color": "rgb(255,0,0)",
          "exp1": 2,
          "exp2": 4,
          "exp3": 1,
          "exp4": {
            "cl1": 7,
            "cl2": 1,
            "cl3": 8
          },
          "exp5": {
            "cl1": 1,
            "cl2": 11,
            "cl3": 8
          },
          "id": "Gene2",
          "shape": "sphere",
          "size": 1,
          "x": 155,
          "y": 340
        },
        {
          "color": "rgb(255,0,0)",
          "exp1": 1,
          "exp2": 5,
          "exp3": 1,
          "exp4": {
            "cl1": 12,
            "cl2": 4,
            "cl3": 8
          },
          "exp5": {
            "cl1": 3,
            "cl2": 7,
            "cl3": 5
          },
          "id": "Gene3",
          "shape": "sphere",
          "size": 1,
          "x": 355,
          "y": 160
        },
        {
          "color": "rgb(255,0,0)",
          "exp1": 4,
          "exp2": 2,
          "exp3": 1,
          "exp4": {
            "cl1": 1,
            "cl2": 14,
            "cl3": 7
          },
          "exp5": {
            "cl1": 2,
            "cl2": 1,
            "cl3": 15
          },
          "id": "Gene4",
          "label": "Receptor Gene4",
          "shape": "sphere",
          "size": 1,
          "x": 355,
          "y": 340
        },
        {
          "color": "rgb(255,0,0)",
          "exp1": 1,
          "exp2": 3,
          "exp3": 2,
          "exp4": {
            "cl1": 4,
            "cl2": 4,
            "cl3": 8
          },
          "exp5": {
            "cl1": 6,
            "cl2": 7,
            "cl3": 2
          },
          "height": 20,
          "id": "Gene5",
          "shape": "sphere",
          "width": 20,
          "x": 255,
          "y": 100
        },
        {
          "height": 40,
          "hideLabel": True,
          "id": "Met",
          "imagePath": "https://www.canvasxpress.org/assets/images/met.png",
          "shape": "image",
          "width": 40,
          "x": 255,
          "y": 400
        },
        {
          "exp1": 3,
          "exp2": 3,
          "exp3": 4,
          "exp4": {
            "cl1": 2,
            "cl2": 14,
            "cl3": 1
          },
          "exp5": {
            "cl1": 9,
            "cl2": 3,
            "cl3": 5
          },
          "height": 40,
          "id": "Gene7",
          "imagePath": "https://www.canvasxpress.org/assets/images/prot7.png",
          "shape": "image",
          "width": 40,
          "x": 50,
          "y": 250
        },
        {
          "height": 40,
          "hideLabel": True,
          "id": "DNA",
          "imagePath": "https://www.canvasxpress.org/assets/images/dna1.png",
          "shape": "image",
          "width": 40,
          "x": 450,
          "y": 250
        }
      ]
    },
    config = {
      "calculateLayout": False,
      "decorations": ["exp1", "exp2", "exp3"],
      "decorationsPosition": "top",
      "decorationsType": "bar",
      "graphType": "Network",
      "networkFreezeOnLoad": True,
      "nodeFontColor": "rgb(29,34,43)",
      "showAnimation": True,
      "showDecorations": True
    },
    width = 600,
    height = 600
  )
)

using CanvasXpress

canvasxpress(Dict(
  "edges" => [
    Dict(
      "color" => "rgb(51,12,255)",
      "endArrow" => "arrow",
      "id1" => "Gene1",
      "id2" => "Gene2",
      "startArrow" => "square",
      "type" => "curved",
      "width" => "3"
    ),
    Dict(
      "color" => "rgb(51,12,255)",
      "endArrow" => "arrow",
      "id1" => "Gene4",
      "id2" => "Gene3",
      "startArrow" => "square",
      "type" => "dashedCurved",
      "width" => "3"
    ),
    Dict(
      "color" => "rgb(51,12,255)",
      "endArrow" => "arrow",
      "id1" => "Gene5",
      "id2" => "Met",
      "type" => "line",
      "width" => "3"
    ),
    Dict(
      "color" => "rgb(51,12,255)",
      "endArrow" => "round",
      "id1" => "Gene3",
      "id2" => "DNA",
      "startArrow" => "square",
      "type" => "bezier",
      "width" => "3"
    ),
    Dict(
      "color" => "rgb(51,12,255)",
      "endArrow" => "square",
      "id1" => "Gene7",
      "id2" => "Gene1",
      "startArrow" => "arrow",
      "type" => "dashedBezier",
      "width" => "3"
    ),
    Dict(
      "color" => "rgb(51,12,255)",
      "elbows" => [
        [235, 100],
        [50, 100],
        [50, 230]
      ],
      "endArrow" => "square",
      "id1" => "Gene5",
      "id2" => "Gene7",
      "type" => "dotted",
      "width" => "3"
    ),
    Dict(
      "color" => "rgb(51,12,255)",
      "elbows" => [
        [275, 100, 325, 100, 325, 165],
        [325, 165, 325, 270, 425, 270]
      ],
      "endArrow" => "square",
      "id1" => "Gene5",
      "id2" => "DNA",
      "type" => "bezier",
      "width" => "3"
    )
  ],
  "legend" => Dict(
    "edges" => [
      Dict(
        "id" => "edgesLegendId0",
        "text" => "Activate",
        "type" => "arrowHeadLine"
      )
    ],
    "nodes" => [
      Dict(
        "color" => "rgb(255,0,0)",
        "id" => "nodesLegendId0",
        "shape" => "sphere",
        "text" => "Gene"
      )
    ],
    "pos" => Dict(
      "decorations" => Dict(
        "x" => 450,
        "y" => 360
      ),
      "edges" => Dict(
        "x" => 360,
        "y" => -5
      ),
      "nodes" => Dict(
        "x" => -5,
        "y" => -5
      )
    ),
    "text" => [
      Dict(
        "id" => "textLegendId0",
        "text" => "Cool Pathway",
        "x" => 150,
        "y" => 460
      )
    ]
  ),
  "nodes" => [
    Dict(
      "eventless" => true,
      "height" => 400,
      "hideLabel" => true,
      "id" => "Cell",
      "imagePath" => "https://www.canvasxpress.org/assets/images/cell.png",
      "shape" => "image",
      "width" => 525,
      "x" => 250,
      "y" => 250
    ),
    Dict(
      "exp1" => 1,
      "exp2" => 2,
      "exp3" => 4,
      "exp4" => Dict(
        "cl1" => 2,
        "cl2" => 4,
        "cl3" => 3
      ),
      "exp5" => Dict(
        "cl1" => 12,
        "cl2" => 1,
        "cl3" => 5
      ),
      "height" => 40,
      "id" => "Gene1",
      "imagePath" => "https://www.canvasxpress.org/assets/images/prot.png",
      "shape" => "image",
      "width" => 40,
      "x" => 155,
      "y" => 160
    ),
    Dict(
      "color" => "rgb(255,0,0)",
      "exp1" => 2,
      "exp2" => 4,
      "exp3" => 1,
      "exp4" => Dict(
        "cl1" => 7,
        "cl2" => 1,
        "cl3" => 8
      ),
      "exp5" => Dict(
        "cl1" => 1,
        "cl2" => 11,
        "cl3" => 8
      ),
      "id" => "Gene2",
      "shape" => "sphere",
      "size" => 1,
      "x" => 155,
      "y" => 340
    ),
    Dict(
      "color" => "rgb(255,0,0)",
      "exp1" => 1,
      "exp2" => 5,
      "exp3" => 1,
      "exp4" => Dict(
        "cl1" => 12,
        "cl2" => 4,
        "cl3" => 8
      ),
      "exp5" => Dict(
        "cl1" => 3,
        "cl2" => 7,
        "cl3" => 5
      ),
      "id" => "Gene3",
      "shape" => "sphere",
      "size" => 1,
      "x" => 355,
      "y" => 160
    ),
    Dict(
      "color" => "rgb(255,0,0)",
      "exp1" => 4,
      "exp2" => 2,
      "exp3" => 1,
      "exp4" => Dict(
        "cl1" => 1,
        "cl2" => 14,
        "cl3" => 7
      ),
      "exp5" => Dict(
        "cl1" => 2,
        "cl2" => 1,
        "cl3" => 15
      ),
      "id" => "Gene4",
      "label" => "Receptor Gene4",
      "shape" => "sphere",
      "size" => 1,
      "x" => 355,
      "y" => 340
    ),
    Dict(
      "color" => "rgb(255,0,0)",
      "exp1" => 1,
      "exp2" => 3,
      "exp3" => 2,
      "exp4" => Dict(
        "cl1" => 4,
        "cl2" => 4,
        "cl3" => 8
      ),
      "exp5" => Dict(
        "cl1" => 6,
        "cl2" => 7,
        "cl3" => 2
      ),
      "height" => 20,
      "id" => "Gene5",
      "shape" => "sphere",
      "width" => 20,
      "x" => 255,
      "y" => 100
    ),
    Dict(
      "height" => 40,
      "hideLabel" => true,
      "id" => "Met",
      "imagePath" => "https://www.canvasxpress.org/assets/images/met.png",
      "shape" => "image",
      "width" => 40,
      "x" => 255,
      "y" => 400
    ),
    Dict(
      "exp1" => 3,
      "exp2" => 3,
      "exp3" => 4,
      "exp4" => Dict(
        "cl1" => 2,
        "cl2" => 14,
        "cl3" => 1
      ),
      "exp5" => Dict(
        "cl1" => 9,
        "cl2" => 3,
        "cl3" => 5
      ),
      "height" => 40,
      "id" => "Gene7",
      "imagePath" => "https://www.canvasxpress.org/assets/images/prot7.png",
      "shape" => "image",
      "width" => 40,
      "x" => 50,
      "y" => 250
    ),
    Dict(
      "height" => 40,
      "hideLabel" => true,
      "id" => "DNA",
      "imagePath" => "https://www.canvasxpress.org/assets/images/dna1.png",
      "shape" => "image",
      "width" => 40,
      "x" => 450,
      "y" => 250
    )
  ]
);
  calculateLayout = false,
  decorations = ["exp1", "exp2", "exp3"],
  decorationsPosition = "top",
  decorationsType = "bar",
  graphType = "Network",
  networkFreezeOnLoad = true,
  nodeFontColor = "rgb(29,34,43)",
  showAnimation = true,
  showDecorations = true
)