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PyGraphistry: Explore Relationships

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PyGraphistry is a Python visual graph analytics library to extract, transform, and load big graphs into Graphistry end-to-end GPU visual graph analytics sessions.

Graphistry gets used on problems like visually mapping the behavior of devices and users and for analyzing machine learning results. It provides point-and-click features like timebars, search, filtering, clustering, coloring, sharing, and more. Graphistry is the only tool built ground-up for large graphs. The client's custom WebGL rendering engine renders up to 8MM nodes + edges at a time, and most older client GPUs smoothly support somewhere between 100K and 1MM elements. The serverside GPU analytics engine supports even bigger graphs.

The PyGraphistry Python client helps several kinds of usage modes:

  • Data scientists: Go from data to accelerated visual explorations in a couple lines, share live results, build up more advanced views over time, and do it all from notebook environments like Jupyter and Google Colab
  • Developers: Quickly prototype stunning Python solutions with PyGraphistry, embed in a language-neutral way with the REST APIs, and go deep on customizations like colors, icons, layouts, JavaScript, and more
  • Analysts: Every Graphistry session is a point-and-click environment with interactive search, filters, timebars, histograms, and more
  • Dashboarding: Embed into your favorite framework. Additionally, see our sister project Graph-App-Kit for quickly building interactive graph dashboards by launching a stack built on PyGraphistry, StreamLit, Docker, and ready recipes for integrating with common graph libraries

PyGraphistry is a friendly and optimized PyData-native interface to the language-neutral Graphistry REST APIs. You can use PyGraphistry with traditional Python data sources like CSVs, SQL, Neo4j, Splunk, and more (see below). Wrangle data however you want, and with especially good support for Pandas dataframes, Apache Arrow tables, and Nvidia RAPIDS cuDF dataframes.

  1. Interactive Demo
  2. Graph Gallery
  3. Install
  4. Tutorial
  5. Next Steps
  6. Resources

Demo of Friendship Communities on Facebook

Click to open interactive version! (For server-backed interactive analytics, use an API key) Source data: SNAP

PyGraphistry is...

  • Fast & gorgeous: Interactively cluster, filter, inspect large amounts of data, and zip through timebars. It clusters large graphs with a descendant of the gorgeous ForceAtlas2 layout algorithm introduced in Gephi. Our data explorer connects to Graphistry's GPU cluster to layout and render hundreds of thousand of nodes+edges in your browser at unparalleled speeds.

  • Easy to install: pip install the client in your notebook or web app, and then connect to a free Graphistry Hub account or launch your own private GPU server

    # pip install --user graphistry
    import graphistry
    graphistry.register(api=3, username='abc', password='xyz')
    #graphistry.register(..., protocol='http', host='my.site.ngo')
    
  • Notebook-friendly: PyGraphistry plays well with interactive notebooks like Jupyter, Zeppelin, and Databricks. Process, visualize, and drill into with graphs directly within your notebooks:

    graphistry.edges(pd.read_csv('rows.csv'), 'col_a', 'col_b').plot()
    
  • Great for events, CSVs, and more: Not sure if your data is graph-friendly? PyGraphistry's hypergraph transform helps turn any sample data like CSVs, SQL results, and event data into a graph for pattern analysis:

    rows = pandas.read_csv('transactions.csv')[:1000]
    graphistry.hypergraph(rows)['graph'].plot()
    
  • Embeddable: Drop live views into your web dashboards and apps:

    iframe_url = g.plot(render=False)
    print(f'<iframe src="{ iframe_url }"></iframe>')
    
  • Configurable: In-tool or via the declarative APIs, use the powerful encodings systems for tasks like coloring by time, sizing by score, clustering by weight, show icons by type, and more.

Explore any data as a graph

It is easy to turn arbitrary data into insightful graphs. PyGraphistry comes with many built-in connectors, and by supporting Python dataframes (Pandas, Arrow, RAPIDS), it's easy to bring standard Python data libraries. If the data comes as a table instead of a graph, PyGraphistry will help you extract and explore the relationships.

  • Pandas

    edges = pd.read_csv('facebook_combined.txt', sep=' ', names=['src', 'dst'])
    graphistry.edges(edges, 'src', 'dst').plot()
    
    table_rows = pd.read_csv('honeypot.csv')
    graphistry.hypergraph(table_rows, ['attackerIP', 'victimIP', 'victimPort', 'vulnName'])['graph'].plot()
    
    graphistry.hypergraph(table_rows, ['attackerIP', 'victimIP', 'victimPort', 'vulnName'],
        direct=True, 
        opts={'EDGES': {
          'attackerIP': ['victimIP', 'victimPort', 'vulnName'], 
          'victimIP': ['victimPort', 'vulnName'],
          'victimPort': ['vulnName']
    }})['graph'].plot()
    
    ### Override smart defaults with custom settings
    g1 = graphistry.bind(source='src', destination='dst').edges(edges)
    g2 = g1.nodes(nodes).bind(node='col2')
    g3 = g2.bind(point_color='col3')
    g4 = g3.settings(url_params={'edgeInfluence': 1.0, play: 2000})
    url = g4.plot(render=False)
    
    ### Read back data and create modified variants
    enriched_edges = my_function1(g1._edges)
    enriched_nodes = my_function2(g1._nodes)
    g2 = g1.edges(enriched_edges).nodes(enriched_nodes)
    g2.plot()
    
  • GPU RAPIDS.ai

    edges = cudf.read_csv('facebook_combined.txt', sep=' ', names=['src', 'dst'])
    graphistry.edges(edges, 'src', 'dst').plot()
    
  • Apache Arrow

     edges = pa.Table.from_pandas(pd.read_csv('facebook_combined.txt', sep=' ', names=['src', 'dst']))
     graphistry.edges(edges, 'src', 'dst').plot()
    
  • Neo4j (notebook demo)

    NEO4J_CREDS = {'uri': 'bolt://my.site.ngo:7687', 'auth': ('neo4j', 'mypwd')}
    graphistry.register(bolt=NEO4J_CREDS)
    graphistry.cypher("MATCH (n1)-[r1]->(n2) RETURN n1, r1, n2 LIMIT 1000").plot()
    
    graphistry.cypher("CALL db.schema()").plot()
    
    from neo4j import GraphDatabase, Driver
    graphistry.register(bolt=GraphDatabase.driver(**NEO4J_CREDS))
    g = graphistry.cypher("""
      MATCH (a)-[p:PAYMENT]->(b)
      WHERE p.USD > 7000 AND p.USD < 10000
      RETURN a, p, b
      LIMIT 100000""")
    print(g._edges.columns)
    g.plot()
    
  • TigerGaph (notebook demo)

    g = graphistry.tigergraph(protocol='https', ...)
    g2 = g.gsql("...", {'edges': '@@eList'})
    g2.plot()
    print('# edges', len(g2._edges))
    
    g.endpoint('my_fn', {'arg': 'val'}, {'edges': '@@eList'}).plot()
      ```
    
    
  • IGraph

    graph = igraph.read('facebook_combined.txt', format='edgelist', directed=False)
    graphistry.bind(source='src', destination='dst').plot(graph)
    
  • NetworkX (notebook demo)

    graph = networkx.read_edgelist('facebook_combined.txt')
    graphistry.bind(source='src', destination='dst', node='nodeid').plot(graph)
    
  • HyperNetX (notebook demo)

    hg.hypernetx_to_graphistry_nodes(H).plot()
    
    hg.hypernetx_to_graphistry_bipartite(H.dual()).plot()
    
  • Splunk (notebook demo)

    df = splunkToPandas("index=netflow bytes > 100000 | head 100000", {})
    graphistry.edges(df, 'src_ip', 'dest_ip').plot()
    
  • NodeXL (notebook demo)

    graphistry.nodexl('/my/file.xls').plot()
    
    graphistry.nodexl('https://file.xls').plot()
    
    graphistry.nodexl('https://file.xls', 'twitter').plot()
    graphistry.nodexl('https://file.xls', verbose=True).plot()
    graphistry.nodexl('https://file.xls', engine='xlsxwriter').plot()
    graphistry.nodexl('https://file.xls')._nodes
    

Quickly configurable

Set visual attributes through quick data bindings and set all sorts of URL options. Check out the tutorials on colors, sizes, icons, badges, and weighted clustering:

  g
    .edges(df, 'col_a', 'col_b')
    .edges(my_transform1(g._edges))
    .nodes(df, 'col_c')
    .nodes(my_transform2(g._nodes))
    .bind(source='col_a', destination='col_b', node='col_c')
    .bind(
      point_color='col_a',
    point_size='col_b',
    point_title='col_c',
    point_x='col_d',
    point_y='col_e')
    .bind(
      edge_color='col_m',
    edge_weight='col_n',
    edge_title='col_o')
    .encode_edge_color('timestamp', ["blue", "yellow", "red"], as_continuous=True)
    .encode_point_icon('device_type', categorical_mapping={'macbook': 'laptop', ...})
    .encode_point_badge('passport', 'TopRight', categorical_mapping={'Canada': 'flag-icon-ca', ...})
    .addStyle(bg={'color': 'red'}, fg={}, page={'title': 'My Graph'}, logo={})
    .settings(url_params={
      'play': 2000,
    'menu': True, 'info': True,
    'showArrows': True,
    'pointSize': 2.0, 'edgeCurvature': 0.5,
    'edgeOpacity': 1.0, 'pointOpacity': 1.0,
    'lockedX': False, 'lockedY': False, 'lockedR': False,
    'linLog': False, 'strongGravity': False, 'dissuadeHubs': False,
    'edgeInfluence': 1.0, 'precisionVsSpeed': 1.0, 'gravity': 1.0, 'scalingRatio': 1.0,
    'showLabels': True, 'showLabelOnHover': True,
    'showPointsOfInterest': True, 'showPointsOfInterestLabel': True, 'showLabelPropertiesOnHover': True,
    'pointsOfInterestMax': 5
    })
    .plot()

Gallery

Twitter Botnet
Edit Wars on Wikipedia
Source: SNAP
100,000 Bitcoin Transactions
Port Scan Attack
Protein Interactions
Source: BioGRID
Programming Languages
Source: Socio-PLT project

Install

Get

You need to install the PyGraphistry Python client and connect it to a Graphistry GPU server of your choice:

  1. Graphistry server account:

  2. PyGraphistry Python client:

Configure

Most users connect to a Graphistry GPU server account via graphistry.register(api=3, username='abc', password='xyz') (hub.graphistry.com) or graphistry.register(api=3, username='abc', password='xyz', protocol='http', server='my.private_server.org')

For more advanced configuration, read on for:

  • Version: Use protocol api=3, which will soon become the default, or a legacy version

  • Tokens: Connect to a GPU server by providing a username='abc'/password='xyz', or for advanced long-running service account software, a refresh loop using 1-hour-only JWT tokens

  • Private servers: PyGraphistry defaults to using the free Graphistry Hub public API

    • Connect to a private Graphistry server and provide optional settings specific to it via protocol, server, and in some cases, client_protocol_hostname

Non-Python users may want to explore the underlying language-neutral authentication REST API docs.

Advanced Login

  • Recommended for people: Provide your account username/password:
import graphistry
graphistry.register(api=3, username='username', password='your password') # 2.0 API
  • For code: Long-running services may prefer to use 1-hour JWT tokens:
import graphistry
graphistry.register(api=3, username='username', password='your password')
initial_one_hour_token = graphistry.api_token()
graphistry.register(api=3, token=initial_one_hour_token)

# must run every 59min
graphistry.refresh() 
fresh_token = graphistry.api_token()
assert initial_one_hour_token != fresh_token

Alternatively, you can rerun graphistry.register(api=3, username='username', password='your password'), which will also fetch a fresh token.

  • Legacy: 1.0 API (WARNING: DEPRECATED)
#graphistry.register(api=1, key='Your key') # 1.0 API; note parameter name/value 'key' is different from `token`

Optionally, for convenience in the 1.0 API, you may set your API key in your system environment and thereby skip the register step in all your notebooks. In your .profile or .bash_profile, add the following and reload your environment:

export GRAPHISTRY_API_KEY="Your key"

Advanced: Private servers

Specify which Graphistry server to reach:

graphistry.register(protocol='https', server='hub.graphistry.com')

Private Graphistry notebook environments are preconfigured to fill in this data for you:

graphistry.register(protocol='http', server='nginx', client_protocol_hostname='')

Using 'http'/'nginx' ensures uploads stay within the Docker network (vs. going more slowly through an outside network), and client protocol '' ensures the browser URLs do not show http://nginx/, and instead use the server's name. (See immediately following Switch client URL section.)

Advanced: Switch client URL

In cases such as when the notebook server is the same as the Graphistry server, you may want your Python code to upload to a known local Graphistry address without going outside the network (e.g., http://nginx or http://localhost), but for web viewing, generate and embed URLs to a different public address (e.g., https://graphistry.acme.ngo/). In this case, explicitly set a client (browser) location different from protocol / server:

graphistry.register(
    ### fast local notebook<>graphistry upload
    protocol='http', server='nginx', 
  
    ### shareable public URL for browsers
    client_protocol_hostname='https://graphistry.acme.ngo'
)

Prebuilt Graphistry servers are already setup to do this out-of-the-box.

Tutorial: Les Misérables

Let's visualize relationships between the characters in Les Misérables. For this example, we'll choose Pandas to wrangle data and IGraph to run a community detection algorithm. You can view the Jupyter notebook containing this example.

Our dataset is a CSV file that looks like this:

source target value
Cravatte Myriel 1
Valjean Mme.Magloire 3
Valjean Mlle.Baptistine 3

Source and target are character names, and the value column counts the number of time they meet. Parsing is a one-liner with Pandas:

import pandas
links = pandas.read_csv('./lesmiserables.csv')

Quick Visualization

If you already have graph-like data, use this step. Otherwise, try the Hypergraph Transform for creating graphs from rows of data (logs, samples, records, ...).

PyGraphistry can plot graphs directly from Pandas data frames, Arrow tables, cuGraph GPU data frames, IGraph graphs, or NetworkX graphs. Calling plot uploads the data to our visualization servers and return an URL to an embeddable webpage containing the visualization.

To define the graph, we bind source and destination to the columns indicating the start and end nodes of each edges:

import graphistry
graphistry.register(api=3, username='YOUR_ACCOUNT_HERE', password='YOUR_PASSWORD_HERE')

g = graphistry.bind(source="source", destination="target")
g.edges(links).plot()

You should see a beautiful graph like this one: Graph of Miserables

Adding Labels

Let's add labels to edges in order to show how many times each pair of characters met. We create a new column called label in edge table links that contains the text of the label and we bind edge_label to it.

links["label"] = links.value.map(lambda v: "#Meetings: %d" % v)
g = g.bind(edge_title="label")
g.edges(links).plot()

Controlling Node Title, Size, Color, and Position

Let's size nodes based on their PageRank score and color them using their community.

Warmup: IGraph for computing statistics

IGraph already has these algorithms implemented for us for small graphs. (See our cuGraph examples for big graphs.) If IGraph is not already installed, fetch it with pip install python-igraph. Warning: pip install igraph will install the wrong package!

We start by converting our edge dateframe into an IGraph. The plotter can do the conversion for us using the source and destination bindings. Then we compute two new node attributes (pagerank & community).

ig = graphistry.pandas2igraph(links)
ig.vs['pagerank'] = ig.pagerank()
ig.vs['community'] = ig.community_infomap().membership

Bind node data to visual node attributes

We can then bind the node community and pagerank columns to visualization attributes:

g.bind(point_color='community', point_size='pagerank').plot(ig)

See the color palette documentation for specifying color values by using built-in ColorBrewer palettes (int32) or custom RGB values (int64).

To control the position, we can add .bind(point_x='colA', point_y='colB').settings(url_params={'play': 0}) (see demos and additional url parameters]). In api=1, you created columns named x and y.

You may also want to bind point_title: .bind(point_title='colA').

For more in-depth examples, check out the tutorials on colors and sizes.

Second Graph of Miserables

Add edge colors and weights

By default, edges get colored as a gradient between their source/destination node colors. You can override this by setting .bind(edge_color='colA'), similar to how node colors function. (See color documentation.)

Similarly, you can bind the edge weight, where higher weights cause nodes to cluster closer together: .bind(edge_weight='colA'). See tutorial.

For more in-depth examples, check out the tutorials on colors and weighted clustering.

More advanced color and size controls

You may want more controls like using gradients or maping specific values:

g.encode_edge_color('time_col', ["blue", "red"], as_continuous=True)
g.encode_edge_color('type_col', ["#000", "#F00", "#F0F", "#0FF"], as_categorical=True)
g.encode_edge_color('brand',
  categorical_mapping={'toyota': 'red', 'ford': 'blue'},
  default_mapping='#CCC')
g.encode_point_size('criticality',
  categorical_mapping={'critical': 200, 'ok': 100},
  default_mapping=50)

For more in-depth examples, check out the tutorials on colors.

Custom icons and badges

You can add a main icon and multiple peripherary badges to provide more visual information. Use column type for the icon type to appear visually in the legend. The glyph system supports text, icons, flags, and images, as well as multiple mapping and style controls.

Main icon

g.encode_point_icon(
  'some_column',
  shape="circle", #clip excess
  categorical_mapping={
      'macbook': 'laptop', #https://fontawesome.com/v4.7.0/icons/
      'Canada': 'flag-icon-ca', #ISO3611-Alpha-2: https://github.com/datasets/country-codes/blob/master/data/country-codes.csv
      'embedded_smile': 'data:svg...',
      'external_logo': 'http://..../img.png'
  },
  default_mapping="question")
g.encode_point_icon(
  'another_column',
  continuous_binning=[
    [20, 'info'],
    [80, 'exclamation-circle'],
    [None, 'exclamation-triangle']
  ]
)
g.encode_point_icon(
  'another_column',
  as_text=True,
  categorical_mapping={
    'Canada': 'CA',
    'United States': 'US'
    }
)

For more in-depth examples, check out the tutorials on icons.

Badges

# see icons examples for mappings and glyphs
g.encode_point_badge('another_column', 'TopRight', categorical_mapping=...)

g.encode_point_badge('another_column', 'TopRight', categorical_mapping=...,
  shape="circle",
  border={'width': 2, 'color': 'white', 'stroke': 'solid'},
  color={'mapping': {'categorical': {'fixed': {}, 'other': 'white'}}},
  bg={'color': {'mapping': {'continuous': {'bins': [], 'other': 'black'}}}})

For more in-depth examples, check out the tutorials on badges.

Theming

You can customize several style options to match your theme:

g.addStyle(bg={'color': 'red'})
g.addStyle(bg={
  'color': '#333',
  'gradient': {
    'kind': 'radial',
    'stops': [ ["rgba(255,255,255, 0.1)", "10%", "rgba(0,0,0,0)", "20%"] ]}})
g.addStyle(bg={'image': {'url': 'http://site.com/cool.png', 'blendMode': 'multiply'}})
g.addStyle(fg={'blendMode': 'color-burn'})
g.addStyle(page={'title': 'My site'})
g.addStyle(page={'favicon': 'http://site.com/favicon.ico'})
g.addStyle(logo={'url': 'http://www.site.com/transparent_logo.png'})
g.addStyle(logo={
  'url': 'http://www.site.com/transparent_logo.png',
  'dimensions': {'maxHeight': 200, 'maxWidth': 200},
  'style': {'opacity': 0.5}
})

Next Steps

  1. Create a free public data Graphistry Hub account or one-click launch a private Graphistry instance in AWS
  2. Check out the analyst and developer introductions, or try your own CSV
  3. Explore the demos folder for your favorite file format, database, API, use case domain, kind of analysis, and visual analytics feature

Resources


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