Python equivalent of D3 js

Question

Can anyone recommend a Python library that can do interactive graph visualization   I specifically want something like d3 js but for python and ideally it would be 3D as well    I have looked at    NetworkX - it only does Matplotlib plots and those seem to be 2D  I didn t see any sort of interactiveness  like one that d3 js gives  such as pulling nodes around  graph-tool - it does only 2D plots and has very slow interactive graphs

User · Answer

I would suggest using mpld3 which combines D3js javascript visualizations with matplotlib of python.

The installation and usage is really simple and it has some cool plugins and interactive stuffs.

http://mpld3.github.io/

User · Answer

You can also choose to serialize your data and then visualize it in D3 js  as done here  Use Python  amp  Pandas to Create a D3 Force Directed Network Diagram  It comes with a jupyter notebook as well    Here is the gist  You serialize your graph data in this format   import json json data        nodes          name   Myriel   group  1         name   Napoleon   group  1         name   Mlle Baptistine   group  1         name   Mme Magloire   group  1         name   CountessdeLo   group  1           links          source  1  target  0  value  1         source  2  target  0  value  8         source  3  target  0  value  10         source  3  target  2  value  6         source  4  target  0  value  1         source  5  target  0  value  1         filename out    graph data json  json out   open filename out  w   json out write json data  json out close     Then you load the data in with d3 js   d3 json  pcap export json   drawGraph     For the routine drawGraph I refer you to the link  however

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One recipe that I have used  described here  Co-Director Network Data Files in GEXF and JSON from OpenCorporates Data via Scraperwiki and networkx   runs as follows    generate a network representation using networkx export the network as a JSON file import that JSON into to d3 js   networkx can export both the tree and graph network representations that d3 js can import     The networkx JSON exporter takes the form   from networkx readwrite import json graph import json print json dumps json graph node link data G     Alternatively you can export the network as a GEXF XML file and then import this representation into the sigma js Javascript visualisation library   from xml etree cElementTree import tostring writer gf GEXFWriter encoding  utf-8  prettyprint True version  1 1draft   writer add graph G  print tostring writer xml

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Plotly can do some cool stuffs for you   https   plot ly   Produces highly interactive graphs that can be easily embedded withing the HTML pages for your private server or website using its off line API    Update  I am note sure about its 3D plotting capabilities  for 2D graphs is awesome Thanks

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Another option is bokeh which just went to version 0 3

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The library d3graph will build a force-directed d3-graph from within python  You can  quot break quot  the network based on the edge weight  and hover over the nodes for more information  Double click on a node will focus on the node and its connected edges  pip install d3graph  Example  source     node A   node F   node B   node B   node B   node A   node C   node Z   target     node F   node B   node J   node F   node F   node M   node M   node A   weight    5 56  0 5  0 64  0 23  0 9 3 28 0 5 0 45     Import library from d3graph import d3graph  vec2adjmat    Convert to adjacency matrix adjmat   vec2adjmat source  target  weight weight  print adjmat    target  node A  node B  node F  node J  node M  node C  node Z   source                                                           node A    0 00     0 0    5 56    0 00    3 28     0 0     0 0   node B    0 00     0 0    1 13    0 64    0 00     0 0     0 0   node F    0 00     0 5    0 00    0 00    0 00     0 0     0 0   node J    0 00     0 0    0 00    0 00    0 00     0 0     0 0   node M    0 00     0 0    0 00    0 00    0 00     0 0     0 0   node C    0 00     0 0    0 00    0 00    0 50     0 0     0 0   node Z    0 45     0 0    0 00    0 00    0 00     0 0     0 0    Example A  simple interactive network out   d3graph adjmat     Example B  Color nodes out   d3graph adjmat  node color adjmat columns values     Example C  include node size node size    10 20 10 10 15 10 5  out   d3graph adjmat  node color adjmat columns values  node size node size     Example D  include node-edge-size out   d3graph adjmat  node color adjmat columns values  node size node size  node size edge node size   -1   cmap  Set2      Example E  include node-edge color out   d3graph adjmat  node color adjmat columns values  node size node size  node size edge node size   -1   node color edge   00FFFF      Example F  Change colormap out   d3graph adjmat  node color adjmat columns values  node size node size  node size edge node size   -1   node color edge   00FFFF   cmap  Set2      Example H  Include directed links  Arrows are set from source - gt  target out   d3graph adjmat  node color adjmat columns values  node size node size  node size edge node size   -1   node color edge   00FFFF   cmap  Set2   directed True    Interactive example from the titanic-case can be found here  https   erdogant github io docs d3graph titanic example index html https   erdogant github io hnet pages html Use 20Cases html

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Plotly supports interactive 2D and 3D graphing  Graphs are rendered with D3 js and can be created with a Python API  matplotlib  ggplot for Python  Seaborn  prettyplotlib  and pandas  You can zoom  pan  toggle traces on and off  and see data on the hover  Plots can be embedded in HTML  apps  dashboards  and IPython Notebooks  Below is a temperature graph showing interactivity  See the gallery of IPython Notebooks tutorials for more examples             The docs provides examples of supported plot types and code snippets        Specifically to your question  you can also make interactive plots from NetworkX        For 3D plotting with Python  you can make 3D scatter  line  and surface plots that are similarly interactive  Plots are rendered with WebGL  For example  see a 3D graph of UK Swap rates        Disclosure  I m on the Plotly team

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For those who recommended pyd3  it is no longer under active development and points you to vincent  vincent is also no longer under active development and recommends using altair   So if you want a pythonic d3  use altair

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Have you looked at vincent   Vincent takes Python data objects and converts them to Vega visualization grammar   Vega is a higher-level visualization tool built on top of D3   As compared to D3py  the vincent repo has been updated more recently   Though the examples are all static D3   more info    https   github com wrobstory vincent https   pypi python org pypi vincent 0 1 6     The graphs can be viewed in Ipython  just add this code  vincent core initialize notebook     Or output to JSON where you can view the JSON output graph in the Vega online editor  http   trifacta github io vega editor   or view them on your Python server locally   More info on viewing can be found in the pypi link above   Not sure when  but the Pandas package should have D3 integration at some point   http   pandas pydata org developers html  Bokeh is a Python visualization library that supports interactive visualization  Its primary output backend is HTML5 Canvas and uses client server model   examples  http   continuumio github io bokehjs

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Check out python-nvd3  It is a python wrapper for nvd3  Looks cooler than d3 py and also has more chart options

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Try https   altair-viz github io  - the successor of d3py and vincent  See also    https   altair-viz github io gallery index html  https   speakerdeck com jakevdp bespoke-visualizations-with-a-declarative-twist

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There is an interesting port of NetworkX to Javascript that might do what you want   See http   felix-kling de JSNetworkX

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See   Is there a good interactive 3D graph library out there   The accepted answer suggests the following program  which apparently has python bindings  http   ubietylab net ubigraph   Edit  I m not sure about the interactivity of NetworkX  but you can definitely make 3D graphs  There is at least one example in the gallery   http   networkx lanl gov examples drawing edge colormap html  And another example in the  examples   This one  however  requires that you have Mayavi   http   networkx lanl gov examples 3d drawing mayavi2 spring html

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I ve got a good example of automatically generating D3 js network diagrams using Python here  http   brandonrose org ner2sna  The cool thing is that you end up with auto-generated HTML and JS and can embed the interactive D3 chart in a notebook with an IFrame

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You could use d3py a python module that generate xml pages embedding d3 js script  For example    import d3py import networkx as nx  import logging logging basicConfig level logging DEBUG   G   nx Graph   G add edge 1 2  G add edge 1 3  G add edge 3 2  G add edge 3 4  G add edge 4 2     use  with  if you are writing a script and want to serve this up forever with d3py NetworkXFigure G  width 500  height 500  as p      p    d3py ForceLayout       p show

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