{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "a6b3d201",
   "metadata": {},
   "source": [
    "# gJGF\n",
    "\n",
    "This Jupyter notebook provides an example of using the Python package [gravis](https://pypi.org/project/gravis) and its custom format called [gravis JSON Graph Format (gJGF)](../../rst/format_specification.html). The .ipynb file can be found [here](https://github.com/robert-haas/gravis/tree/master/examples)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ac99a969",
   "metadata": {},
   "outputs": [],
   "source": [
    "import gravis as gv"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f837fd5c",
   "metadata": {},
   "source": [
    "## Empty graph"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "28175f45",
   "metadata": {},
   "outputs": [],
   "source": [
    "graph1 = {\n",
    "    'graph': {}\n",
    "}\n",
    "\n",
    "gv.d3(graph1, graph_height=150)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ae172fa5",
   "metadata": {},
   "source": [
    "## Directed graph\n",
    "\n",
    "Reproduced from [Wikipedia: Directed graph](https://en.wikipedia.org/wiki/Directed_graph)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "49824542",
   "metadata": {},
   "outputs": [],
   "source": [
    "graph2 = {\n",
    "    'graph': {\n",
    "        'label': 'Directed graph',\n",
    "        'nodes': {\n",
    "            'a': {},\n",
    "            'b': {},\n",
    "            'c': {},\n",
    "        },\n",
    "        'edges': [\n",
    "            {'source': 'a', 'target': 'b'},\n",
    "            {'source': 'b', 'target': 'c'},\n",
    "            {'source': 'c', 'target': 'a'},\n",
    "        ],\n",
    "        'metadata': {\n",
    "            'node_color': '#007fff',\n",
    "            'node_border_size': 1.5,\n",
    "            'node_size': 16,\n",
    "        }\n",
    "    }\n",
    "}\n",
    "\n",
    "gv.d3(graph2, graph_height=150, show_node_label=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1f283f52",
   "metadata": {},
   "source": [
    "## Undirected graph\n",
    "\n",
    "Reproduced from [Wikipedia: Graph](https://en.wikipedia.org/wiki/Graph_(discrete_mathematics))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c2485856",
   "metadata": {},
   "outputs": [],
   "source": [
    "graph3 = {\n",
    "    'graph': {\n",
    "        'label': 'Undirected graph',\n",
    "        'directed': False,\n",
    "        'nodes': {\n",
    "            1: {},\n",
    "            2: {},\n",
    "            3: {},\n",
    "            4: {},\n",
    "            5: {},\n",
    "            6: {},\n",
    "        },\n",
    "        'edges': [\n",
    "            {'source': 1, 'target': 2},\n",
    "            {'source': 1, 'target': 5},\n",
    "            {'source': 2, 'target': 5},\n",
    "            {'source': 2, 'target': 3},\n",
    "            {'source': 3, 'target': 4},\n",
    "            {'source': 4, 'target': 5},\n",
    "            {'source': 4, 'target': 6},\n",
    "        ],\n",
    "        'metadata': {\n",
    "            'node_color': 'white',\n",
    "            'node_size': 30,\n",
    "            'node_border_size': 2,\n",
    "            'node_label_size': 20\n",
    "        }\n",
    "    }\n",
    "}\n",
    "\n",
    "gv.d3(graph3, graph_height=200)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fcc0a31e",
   "metadata": {},
   "source": [
    "## Multigraph\n",
    "\n",
    "A multigraph with multiedges in red and self-loops in blue, reproduced from [Wikipedia: Multigraph](https://en.wikipedia.org/wiki/Multigraph)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d0ee0c1e",
   "metadata": {},
   "outputs": [],
   "source": [
    "graph4 = {\n",
    "    'graph': {\n",
    "        'label': 'Multigraph',\n",
    "        'directed': False,\n",
    "        'nodes': {\n",
    "            1: {'metadata': {'hover': 'Node 1', 'x': 0, 'y': -60}},\n",
    "            2: {'metadata': {'hover': 'Node 2', 'x': 65, 'y': -20}},\n",
    "            3: {'metadata': {'hover': 'Node 3', 'x': 40, 'y': 60}},\n",
    "            4: {'metadata': {'hover': 'Node 4', 'x': -40, 'y': 60}},\n",
    "            5: {'metadata': {'hover': 'Node 5', 'x': -65, 'y': -20}},\n",
    "            6: {'metadata': {'hover': 'Node 6', 'x': 0, 'y': 5}},\n",
    "        },\n",
    "        'edges': [\n",
    "            {'source': 1, 'target': 2},\n",
    "            {'source': 2, 'target': 3},\n",
    "            {'source': 2, 'target': 2, 'metadata': {'color': 'blue'}},\n",
    "            {'source': 3, 'target': 4},\n",
    "            {'source': 3, 'target': 3, 'metadata': {'color': 'blue'}},\n",
    "            {'source': 4, 'target': 5},\n",
    "            {'source': 4, 'target': 4, 'metadata': {'color': 'blue'}},\n",
    "            {'source': 5, 'target': 1, 'metadata': {'color': 'red'}},\n",
    "            {'source': 5, 'target': 1, 'metadata': {'color': 'red'}},\n",
    "            {'source': 1, 'target': 6, 'metadata': {'color': 'red'}},\n",
    "            {'source': 1, 'target': 6, 'metadata': {'color': 'red'}},\n",
    "            {'source': 6, 'target': 1, 'metadata': {'color': 'red'}},\n",
    "            {'source': 2, 'target': 6},\n",
    "            {'source': 3, 'target': 6, 'metadata': {'color': 'red'}},\n",
    "            {'source': 6, 'target': 3, 'metadata': {'color': 'red'}},\n",
    "            {'source': 4, 'target': 6, 'metadata': {'color': 'red'}},\n",
    "            {'source': 6, 'target': 4, 'metadata': {'color': 'red'}},\n",
    "            {'source': 5, 'target': 6},\n",
    "        ],\n",
    "        'metadata': {'node_color': '#aaa', 'node_border_size': 1.2, 'edge_size': 1.2}\n",
    "    }\n",
    "}\n",
    "\n",
    "gv.d3(graph4, graph_height=200, edge_curvature=0.3, show_node_label=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "297a415f",
   "metadata": {},
   "source": [
    "## Annotated graph\n",
    "\n",
    "- Enzyme image [Protein ADH5 PDB 1m6h.png](https://commons.wikimedia.org/wiki/File:Protein_ADH5_PDB_1m6h.png) with [CC BY 3.0 license](https://creativecommons.org/licenses/by-sa/3.0/) from [Wikipedia: Alcoholdehydrogenase](https://en.wikipedia.org/wiki/Alcohol_dehydrogenase)\n",
    "- Molecule images with [CC BY 4.0 license](https://creativecommons.org/licenses/by/4.0/) from [RHEA:25290](https://www.rhea-db.org/rhea/25290)\n",
    "  \n",
    "  - Bansal et al., Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. Epub:gkab1016 (2021). [PMID:34755880](https://pubmed.ncbi.nlm.nih.gov/34755880/), [DOI:10.1093/nar/gkab1016](https://doi.org/10.1093/nar/gkab1016)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "36781563",
   "metadata": {},
   "outputs": [],
   "source": [
    "img_alcoholdehydrogenase = gv.convert.image_to_data_url(\n",
    "    'https://upload.wikimedia.org/wikipedia/commons/thumb/a/a5/Protein_ADH5_PDB_1m6h.png/320px-Protein_ADH5_PDB_1m6h.png')\n",
    "img_ethanol = gv.convert.image_to_data_url(\n",
    "    'https://www.rhea-db.org/chebi/CHEBI:16236', 'svg')\n",
    "img_nad = gv.convert.image_to_data_url(\n",
    "    'https://www.rhea-db.org/chebi/CHEBI:57540', 'svg')\n",
    "img_acetaldehyde = gv.convert.image_to_data_url(\n",
    "    'https://www.rhea-db.org/chebi/CHEBI:15343', 'svg')\n",
    "img_proton = gv.convert.image_to_data_url(\n",
    "    'https://www.rhea-db.org/chebi/CHEBI:15378', 'svg')\n",
    "img_nadh = gv.convert.image_to_data_url(\n",
    "    'https://www.rhea-db.org/chebi/CHEBI:57945', 'svg')\n",
    "\n",
    "default_color = 'black'\n",
    "highlight_color = 'blue'\n",
    "highlight_size = 1.5\n",
    "background_color = '#f5f5f5'\n",
    "\n",
    "graph5 = {\n",
    "    'graph': {\n",
    "        'label': 'Annotated graph',\n",
    "        'directed': True,\n",
    "        'metadata': {\n",
    "            'arrow_color': 'black',\n",
    "            'arrow_size': 5,\n",
    "            'background_color': background_color,\n",
    "            'node_color': background_color,\n",
    "            'node_opacity': 0.8,\n",
    "            'node_size': 25,\n",
    "            'node_shape': 'hexagon',\n",
    "            'node_border_color': default_color,\n",
    "            'node_border_size': 0.8,\n",
    "            'node_label_color': default_color,\n",
    "            'node_label_size': 6,\n",
    "            'node_hover': 'Molecule: $label',\n",
    "            'node_click': '$hover',\n",
    "            'node_x': 0,\n",
    "            'node_y': 0,\n",
    "            'node_z': 0,\n",
    "            'edge_color': default_color,\n",
    "            'edge_opacity': 0.8,\n",
    "            'edge_size': 1,\n",
    "            'edge_label_color': 'black',\n",
    "            'edge_label_size': 5,\n",
    "            'edge_hover': '$label',\n",
    "            'edge_click': '$label',\n",
    "        },\n",
    "        'nodes': {\n",
    "            1: {\n",
    "                'label': 'Alcohol dehydrogenase',\n",
    "                'metadata': {\n",
    "                    'color': 'white',\n",
    "                    'opacity': 1.0,\n",
    "                    'size': 50,\n",
    "                    'shape': 'circle',\n",
    "                    'border_color': highlight_color,\n",
    "                    'border_size': highlight_size,\n",
    "                    'label_color': highlight_color,\n",
    "                    'label_size': 7,\n",
    "                    'hover': 'Enzyme: $label',\n",
    "                    'click': '$hover',\n",
    "                    'image': img_alcoholdehydrogenase,\n",
    "                }\n",
    "            },\n",
    "            2: {\n",
    "                'label': 'Ethanol',\n",
    "                'metadata': {\n",
    "                    'size': 30,\n",
    "                    'color': 'white',\n",
    "                    'shape': 'rectangle',\n",
    "                    'border_color': highlight_color,\n",
    "                    'border_size': highlight_size,\n",
    "                    'label_color': highlight_color,\n",
    "                    'image': img_ethanol,\n",
    "                    'x': -100,\n",
    "                    'y': 50,\n",
    "                }\n",
    "            },\n",
    "            3: {\n",
    "                'label': 'NAD+',\n",
    "                'metadata': {\n",
    "                    'image': img_nad,\n",
    "                    'x': -100,\n",
    "                    'y': 0,\n",
    "                }\n",
    "            },\n",
    "            4: {\n",
    "                'label': 'Acetaldehyde',\n",
    "                'metadata': {\n",
    "                    'size': 30,\n",
    "                    'color': 'white',\n",
    "                    'shape': 'rectangle',\n",
    "                    'border_color': highlight_color,\n",
    "                    'border_size': highlight_size,\n",
    "                    'label_color': highlight_color,\n",
    "                    'image': img_acetaldehyde,\n",
    "                    'x': 100,\n",
    "                    'y': 50,\n",
    "                }\n",
    "            },\n",
    "            5: {\n",
    "                'label': 'NADH',\n",
    "                'metadata': {\n",
    "                    'image': img_nadh,\n",
    "                    'x': 100,\n",
    "                    'y': 0,\n",
    "                }\n",
    "            },\n",
    "            6: {\n",
    "                'label': 'Proton',\n",
    "                'metadata': {\n",
    "                    'image': img_proton,\n",
    "                    'x': 100,\n",
    "                    'y': -50,\n",
    "                }\n",
    "            },\n",
    "        },\n",
    "        'edges': [\n",
    "            {\n",
    "                'source': 2,\n",
    "                'target': 1,\n",
    "                'label': '1 mol',\n",
    "                'metadata': {\n",
    "                    'color': highlight_color,\n",
    "                    'opacity': 1.0,\n",
    "                    'size': highlight_size,\n",
    "                    'label_color': highlight_color,\n",
    "                    'label_size': 6,\n",
    "                },\n",
    "            },\n",
    "            {\n",
    "                'source': 3,\n",
    "                'target': 1,\n",
    "                'label': '1 mol',\n",
    "            },\n",
    "            {\n",
    "                'source': 1,\n",
    "                'target': 4,\n",
    "                'label': '1 mol',\n",
    "                'metadata': {\n",
    "                    'color': highlight_color,\n",
    "                    'size': highlight_size,\n",
    "                    'label_color': highlight_color,\n",
    "                    'label_size': 6,\n",
    "                },\n",
    "            },\n",
    "            {\n",
    "                'source': 1,\n",
    "                'target': 5,\n",
    "                'label': '1 mol',\n",
    "            },\n",
    "            {\n",
    "                'source': 1,\n",
    "                'target': 6,\n",
    "                'label': '1 mol',\n",
    "            },\n",
    "        ],\n",
    "    }\n",
    "}\n",
    "\n",
    "gv.d3(graph5, node_label_data_source='label', edge_label_data_source='label', show_edge_label=True, zoom_factor=2)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "db13c5bd",
   "metadata": {},
   "source": [
    "## Multiple graphs\n",
    "\n",
    "gJGF can also be used to define multiple graphs in one dictionary (or JSON object). The visualization shows the first graph, while the other graphs can be selected in the menu on the right side in the category `Data selection`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d324ff1b",
   "metadata": {},
   "outputs": [],
   "source": [
    "graphs = {\n",
    "    'graphs': [\n",
    "        {\n",
    "            'label': 'First graph',\n",
    "            'nodes': {\n",
    "                'a': {},\n",
    "                'b': {},\n",
    "            },\n",
    "            'edges': [\n",
    "                {'source': 'a', 'target': 'b'},\n",
    "            ],\n",
    "        },\n",
    "        {\n",
    "            'label': 'Second graph',\n",
    "            'directed': False,\n",
    "            'nodes': {\n",
    "                1: {},\n",
    "                2: {},\n",
    "            },\n",
    "            'edges': [\n",
    "                {'source': 1, 'target': 2},\n",
    "            ],\n",
    "        },\n",
    "    ]\n",
    "}\n",
    "\n",
    "gv.d3(graphs, graph_height=200)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c96544c6",
   "metadata": {},
   "outputs": [],
   "source": [
    "# reuse previous graphs: remove the \"graph\" key from each one, instead add a \"graphs\" key for the collection\n",
    "graphs = [graph2, graph3, graph4, graph5]\n",
    "gjgf = {'graphs': [g['graph'] for g in graphs]}\n",
    "\n",
    "gv.d3(gjgf, graph_height=200)"
   ]
  }
 ],
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