Merge pull request #258 from vaniisgh/master

add constructor to main widget

examples/Graph Initialization.ipynb

@@ -0,0 +1,210 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "everyday-colonial",
+   "metadata": {},
+   "source": [
+    "# Some examples of how to initialise the Graph Widget\n",
+    "The CytoscapeWidget accepts an optional graph parameter, using this we can pass the graph's data and initialise a graph. We can pass data as:\n",
+    "- A json file (wither the filename or the json object itself)\n",
+    "- A networkx graph\n",
+    "- A pandas Dataframe\n",
+    "- A neo4j graph\n",
+    "- A ipycytoscape Graph"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "nominated-closing",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import ipycytoscape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "waiting-brunswick",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "385ac265c37a4b35ada50b5f39c54028",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "CytoscapeWidget(cytoscape_layout={'name': 'cola'}, cytoscape_style=[{'selector': 'node', 'css': {'background-c…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "# 1. a cytoscape graph from json file\n",
+    "json_from_filename = ipycytoscape.CytoscapeWidget(\"concentricData.json\")\n",
+    "json_from_filename"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "dominant-locking",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "4c7176cff03b45c9b587e810b1bda8fe",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "CytoscapeWidget(cytoscape_layout={'name': 'cola'}, cytoscape_style=[{'selector': 'node', 'css': {'background-c…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "# 1. a cytoscape graph from json object\n",
+    "\n",
+    "import json\n",
+    "with open(\"concentricData.json\") as fi:\n",
+    "    json_file = json.load(fi)\n",
+    "\n",
+    "json_from_object = ipycytoscape.CytoscapeWidget(json_file)\n",
+    "json_from_object"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "stupid-mayor",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "3ccae77ecfac48ab90b110b0aff16960",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "CytoscapeWidget(cytoscape_layout={'name': 'cola'}, cytoscape_style=[{'selector': 'node', 'css': {'background-c…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "# A networkx graph\n",
+    "import networkx as nx\n",
+    "\n",
+    "G = nx.complete_graph(5)\n",
+    "graph_from_nx = ipycytoscape.CytoscapeWidget(G)\n",
+    "graph_from_nx"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "conceptual-sunday",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "cc1f647957b140d1ba6bfbcd5d7c7132",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "CytoscapeWidget(cytoscape_layout={'name': 'cola'}, cytoscape_style=[{'selector': 'node', 'css': {'background-c…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "# A pandas Dataframe\n",
+    "\n",
+    "import pandas as pd\n",
+    "\n",
+    "graphFrame = pd.read_csv(\"https://raw.githubusercontent.com/nextstrain/ncov/fe5a7ed1f92af63d6d1d43d0307e4b2620108aaa/data/metadata.tsv\", sep = '\\t')\n",
+    "ipycytoscape.CytoscapeWidget(graphFrame[:30], groupby_cols=['country'], attribute_list=['age', 'virus'])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "undefined-store",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# A neo4j graph\n",
+    "\n",
+    "from py2neo import Graph, Node, Relationship\n",
+    "\n",
+    "g = graph = Graph(\"bolt://132.249.238.185:7687\", user=\"reader\", password=\"demo\")\n",
+    "\n",
+    "ipycytoscape.CytoscapeWidget(g)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "instrumental-aggregate",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "1b636bbf760c435a896967b2b9736884",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "CytoscapeWidget(cytoscape_layout={'name': 'cola'}, cytoscape_style=[{'selector': 'node', 'css': {'background-c…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "# A ipycytoscape graph\n",
+    "ipycytoscape.CytoscapeWidget(json_from_object.graph)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

ipycytoscape/cytoscape.py

@@ -7,7 +7,10 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 
+from os import path
+
 import copy
+import json
 
 from spectate import mvc
 from traitlets import TraitType, TraitError
@@ -28,6 +31,19 @@
 
 import networkx as nx
 
+try:
+    import pandas as pd
+
+except ImportError:
+    pd = None
+
+try:
+    import py2neo
+
+except ImportError:
+    py2neo = None
+
+
 """TODO: Remove this after this is somewhat done"""
 import logging
 
@@ -507,11 +523,19 @@ def add_graph_from_json(self, json_file, directed=False, multiple_edges=False):
 
         Parameters
         ----------
-        json_file : dict
+        json_file : dict or string
+            If a dict is passed, it will be parsed as a JSON object,
+            a file path (to the json graph file) can also be passed as a
+            string, the file will be loaded it's content parsed as JSON an
+            object.
         directed : bool
             If True all edges will be given 'directed' as a class if
             they do not already have it.
         """
+        if path.isfile(str(json_file)):
+            with open(json_file) as f:
+                json_file = json.load(f)
+
         node_list = list()
         for node in json_file["nodes"]:
             node_instance = Node()
@@ -814,12 +838,33 @@ class CytoscapeWidget(DOMWidget):
 
     graph = Instance(Graph, args=tuple()).tag(sync=True, **widget_serialization)
 
-    def __init__(self, **kwargs):
+    def __init__(self, graph=None, **kwargs):
+        """
+        Initializes the graph widget.
+
+        Parameters
+        ----------
+        graph: graph: string, dict, pandas.DataFrame, networkx.Graph,
+               neo4j.Graph, Graph object, optional
+               The graph to initialize with. Equivalent to calling the
+               appropriate ``CytoscapeWidget.graph.add_graph_from_` method.
+        """
         super(CytoscapeWidget, self).__init__(**kwargs)
 
         self.on_msg(self._handle_interaction)
         self.graph = Graph()
 
+        if isinstance(graph, nx.Graph):
+            self.graph.add_graph_from_networkx(graph)
+        elif isinstance(graph, (dict, str)):
+            self.graph.add_graph_from_json(graph)
+        elif pd and isinstance(graph, pd.DataFrame):
+            self.graph.add_graph_from_df(graph, **kwargs)
+        elif isinstance(graph, Graph):
+            self.graph = graph
+        elif py2neo and isinstance(graph, py2neo.Graph):
+            self.graph.add_graph_from_neo4j(graph)
+
     # Make sure we have a callback dispatcher for this widget and event type;
     # since _interaction_handlers is synced with the frontend and changes to
     # mutable values don't automatically propagate, we need to explicitly set

setup.py

@@ -101,7 +101,9 @@
     extras_require={
         "test": ["pytest>4.6", "pytest-cov", "nbval", "pandas", "nbclassic>=0.2.8"],
         "examples": [
-            "pandas"
+            "pandas",
+            "py2neo",
+            "neotime",
             # Any requirements for the examples to run
         ],
         "docs": [