Python equivalent of D3.js

2022-11-10 08:25:29

Python equivalent of D3.js

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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.

python graph d3.js graph-tool improve this question edited Dec 12 '16 at 12:03

akaihola 21.9k55 gold badges5151 silver badges6060 bronze badges asked Oct 19 '12 at 15:26

Eiyrioü von Kauyf 3,07044 gold badges2626 silver badges3737 bronze badges

1 You would want to generate a graph in networkx and then manipulate in d3.js, if you're looking for a browser based version. – kreativitea Oct 19 '12 at 15:45
@kreativitea ok .... how would I do that o-o ideally: Graph Data (via API Calls in Python) -> Python (Machine Learning Stuffs) -> Django / Something + D3.js (visualization) -> Pretty pictures and website :) – Eiyrioü von Kauyf Oct 21 '12 at 20:50

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14 Answers

active oldest votes 68

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()

improve this answer edited Dec 1 '13 at 20:34

Eric O Lebigot 70.7k3838 gold badges179179 silver badges229229 bronze badges answered Jan 5 '13 at 23:59

Vincent Agnus 91677 silver badges99 bronze badges

Worked for me, but I had to edit one of the lines to with d3py.NetworkXFigure(G, width=500, height=500, host="localhost") as p:. I checked out the latest commit of d3py at github (SHA: 4e92a90f4003370bc086e0f57b19fca1bd4e8fba) – xb. Jan 4 '14 at 18:57
7 Unfortunately d3py isn't being actively developed any more - Vincent is the modern equivalent (a Python interface to Vega/d3.js) but psychemedia's answer below (export networkx to json then render in d3.js) might be the cleanest. – A.Wan Nov 20 '14 at 0:27
2 Try altair-viz.github.io - the successor of d3py and vincent. See also *.com/a/49695472/179014 . – asmaier Jan 23 at 13:42

add a comment 38

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.

improve this answer edited Jun 3 '15 at 8:48 answered Nov 6 '13 at 2:13

Mateo Sanchez 1,3111212 silver badges1515 bronze badges

6 Clearly the question aims at graphs in the sense of nodes connected by edges. This answer needlessly includes other visualization capabilities of plotly. – Lutz Büch Jul 23 '18 at 5:47
@mateo-sanchez it is very unfortunate that Plotly has decided to terminate all academic and individual subscriptions to focus on corporate clients – Andreuccio Aug 20 at 12:41

add a comment 20

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:

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/

improve this answer edited Nov 20 '13 at 17:44 answered Oct 10 '13 at 19:28

sk8asd123 1,2351111 silver badges1111 bronze badges

2 Vincent is on the way out - looks like there are some replacements, but I'm not sure how closely tied to ipython they will be.. – naught101 Aug 13 '15 at 6:48

add a comment 17

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)

improve this answer answered Mar 16 '13 at 23:56

psychemedia 3,77944 gold badges3737 silver badges6969 bronze badges add a comment 16

Another option is bokeh which just went to version 0.3.

improve this answer answered Nov 21 '13 at 18:37

MrDrFenner 68088 silver badges1010 bronze badges add a comment 7

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.

improve this answer answered Nov 11 '16 at 14:54

Wes 38844 silver badges1212 bronze badges add a comment 5

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

improve this answer answered Aug 23 '13 at 13:07

richie 8,46888 gold badges3939 silver badges5858 bronze badges add a comment 4

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/

improve this answer answered Feb 9 '15 at 11:45

Ram 54466 silver badges1818 bronze badges add a comment 4

Try https://altair-viz.github.io/ - the successor of d3py and vincent. See also

improve this answer edited Jan 23 at 13:39 answered Apr 6 '18 at 14:50

asmaier 8,09977 gold badges5858 silver badges8888 bronze badges add a comment 2

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

improve this answer answered May 17 '17 at 5:26

jax 2,05544 gold badges2020 silver badges4343 bronze badges

2 Note that this is chart visualization... The question requests graph visualization. (I appreciate these phrases are commonly conflated!) – j6m8 Mar 3 '18 at 22:18

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You can also choose to serialize your data and then visualize it in D3.js, as done here: Use Python & 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.

improve this answer edited Jun 14 '18 at 21:59

Pearly Spencer 19.7k2121 gold badges5454 silver badges101101 bronze badges answered Jun 13 '18 at 9:06

Lutz Büch 18811 silver badge99 bronze badges

I edited it now, but I didn't include the drawGraph routine which itself calls drawLinks and drawNodes. It would just be too cumbersome and the elements only make sense in the context of the whole html file. – Lutz Büch Jun 13 '18 at 10:18

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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/

improve this answer answered Oct 24 '12 at 22:31

Aric 18.1k44 gold badges4949 silver badges6262 bronze badges

this might work.... can you refer me to documentation please? How would I output a graph from python into it this javascript library...? I want to generate it in python first ... or how would i load it? – Eiyrioü von Kauyf Oct 25 '12 at 1:57
I've actually never used JSNetworkX so I'm not sure how it works. – Aric Oct 25 '12 at 16:35
@EiyrioüvonKauyf: The input is the same as in Python, e.g. a list of lists or a dict of dicts. You could build the graph in Python, convert it to a list of lists and convert it to JSON. – Felix Kling Oct 28 '12 at 4:00
Yes, definitely easy. The examples here are simple and beautiful:felix-kling.de/JSNetworkX/examples – Aric Oct 29 '12 at 21:58

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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

improve this answer edited May 23 '17 at 12:03

Community♦ 111 silver badge answered Oct 19 '12 at 15:33

juniper- 4,41655 gold badges2727 silver badges4848 bronze badges add a comment 0

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

improve this answer answered Jul 11 '17 at 1 <style></style>

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Python equivalent of D3.js

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