large graph visualization with python and networkx
from matplotlib import pylab
import networkx as nx
def save_graph(graph,file_name):
#initialze Figure
plt.figure(num=None, figsize=(20, 20), dpi=80)
plt.axis('off')
fig = plt.figure(1)
pos = nx.spring_layout(graph)
nx.draw_networkx_nodes(graph,pos)
nx.draw_networkx_edges(graph,pos)
nx.draw_networkx_labels(graph,pos)
cut = 1.00
xmax = cut * max(xx for xx, yy in pos.values())
ymax = cut * max(yy for xx, yy in pos.values())
plt.xlim(0, xmax)
plt.ylim(0, ymax)
plt.savefig(file_name,bbox_inches="tight")
pylab.close()
del fig
#Assuming that the graph g has nodes and edges entered
save_graph(g,"my_graph.pdf")
#it can also be saved in .svg, .png. or .ps formats
This answers your first issue. Networkx does not have the facility to zoom into nodes. Use Gephi for this functionality. Gephi accepts an edge list in CSV format and produces a visualization, where zooming can be done interactively.
CodeKingPlusPlus
Updated on July 22, 2022Comments
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CodeKingPlusPlus almost 2 years
I am having trouble with large graph visualization in python and networkx. The graph is wish to visualize is directed, and has an edge and vertex set size of 215,000 From the documenation (which is linked at the top page) it is clear that networkx supports plotting with
matplotlib
and GraphViz. Inmatplotlib
and networkx the drawing is done as follows:import networkx as nx import matplotlib.pyplot as plt #Let g be a graph that I created nx.draw(g)
I get a memory error after
nx.draw(g)
, afterwards you would normally doplt.show()
or plt.[some_function] to save the file in a format for efficient and so forth.Next I tried GraphViz. From the wikipedia page the
dot
format is used for directed graphs and I created a dot file:nx.write_dot(g, "g.dot")
This worked well and I had a dot file in my current directory that is 12 megabytes. Next I ran the
dot
program (part of graphviz to create a postscript file):dot -Tps g.dot -o g.ps
This slows down my computer, runs for a few minutes and then display
Killed
in the terminal. So it never could execute... While reading the documentation for graphviz it seems that only undirected graphs were supported for large graph visualization.Question: With these two unsuccessful attempts can anyone show me how to visualize my large graph using python and networkx with about 215,000 vertices and 215,000 edges? I suspect as with Graphviz I will have to output into an intermediate format (although this shouldn't be that hard it won't be as easy as a builtin function) and then use another tool to read the intermediate format and then output a visualization.
So, I am looking for the following:
- Output graph from networkx into an intermediate format
- With new package/software/tool (ideally python-interactive) read intermediate format and visualize the large graph
If you need more information let me know!
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CodeKingPlusPlus almost 11 yearsI just used a networkx function to save the graph in an edgelist format and was able to read it into Gephi!