Creating network with networkx / plotly from a pandas dataframe
I'd trying to build a network from a pandas dataframe with four columns that look like this:
PTDID | PBDID | BTDID | BDDID
PTD000000 | PBD000024 | BTD000264 | BDD000288
PTD000001 | PBD000025 | BTD000264 | BDD000289
PTD000001 | PBD000025 | BTD000264 | BDD000290
PTD000001 | PBD000025 | BTD000264 | BDD000291
PTD000001 | PBD000025 | BTD000264 | BDD000292
PTD000000 | PBD000024 | BTD000264 | BDD000293
...and so on for 36k rows
I'm trying to recreate this example with my dataframe : https://plot.ly/python/network-graphs/
However, I'm getting a 'KeyError: 0' message.
my current code:
import pandas as pd
import plotly.plotly as py
from plotly.graph_objs import *
import networkx as nx
import numpy as np
df=pd.read_csv('C:UsersnkurdobDocumentsbdh5.csv')
#get node positions
G=nx.from_pandas_dataframe(df, 'BTDID', 'BDDID', ['PTDID', 'PBDID'])
pos=nx.get_node_attributes(G,'pos')
dmin=1
ncenter=0
for n in pos:
x,y=pos[n]
d=(x-0.5)**2+(y-0.5)**2
if d<dmin:
ncenter=n
dmin=d
p=nx.single_source_shortest_path_length(G,ncenter)
Does anyone know how to get past this error? I think this line might be messing it up:
G=nx.from_pandas_dataframe(df, 'BTDID', 'BDDID', ['PTDID', 'PBDID'])
but I'm not sure how to fix it. I got this ^ by following the example shown here: http://networkx.readthedocs.io/en/latest/reference/generated/networkx.convert_matrix.from_pandas_dataframe.html
Thank you in advance!
Nazar
Edit: Traceback error:
runfile('L:/Data/Global ID/Nazar/bdh.py', wdir='L:/Data/Global ID/Nazar') Traceback (most recent call last):
File "", line 1, in runfile('L:/Data/Global ID/Nazar/bdh.py', wdir='L:/Data/Global ID/Nazar')
File "C:UsersnkurdobAppDataLocalContinuumAnaconda2libsite-packagesspyderlibwidgetsexternalshellsitecustomize.py", line 714, in runfile execfile(filename, namespace)
File "C:UsersnkurdobAppDataLocalContinuumAnaconda2libsite-packagesspyderlibwidgetsexternalshellsitecustomize.py", line 74, in execfile exec(compile(scripttext, filename, 'exec'), glob, loc)
File "L:/Data/Global ID/Nazar/bdh.py", line 32, in p=nx.single_source_shortest_path_length(G,ncenter)
File "C:UsersnkurdobAppDataLocalContinuumAnaconda2libsite-packagesnetworkxalgorithmsshortest_pathsunweighted.py", line 63, in single_source_shortest_path_length nextlevel.update(G[v]) # add neighbors of v
File "C:UsersnkurdobAppDataLocalContinuumAnaconda2libsite-packagesnetworkxclassesgraph.py", line 407, in getitem return self.adj[n]
KeyError: 0
It does not look like you have defined pos as a node attribute. So when you do pos = nx.get_node_attributes(G,'pos') , it is made into an empty dict .
Hence the loop for n in pos does nothing. So ncenter is still 0 after the loop. Since your graph doesn't have a node 0 , you're getting a keyerror when you ask it to find the paths from ncenter .