jverma/networkxd3

D3 JavaScript networkx Graphs in Python

networkxd3's Issues

Depricated Package: Fixed Code in the Comment

import networkx as nx 
from rpy2.robjects.packages import importr
import rpy2.robjects as ro
import pandas as p

from rpy2.robjects import pandas2ri
pandas2ri.activate()


def simpleNetworkx(G):
    ro.r('src = c()')
    ro.r('target =c()')
    ro.r('rdf=data.frame()')

    df = p.DataFrame(data=G.edges())
    df_r = pandas2ri.py2rpy(df)  # <------------- use py2rpy

    ro.globalenv['src'] = df_r[0]
    ro.globalenv['target'] = df_r[1]

    ro.r('rdf=data.frame(src,target)')

    utils = importr('utils')
    utils.chooseCRANmirror(ind=1)

    try:
        networkD3 = importr('networkD3')
    except:
        utils.install_packages('networkD3')
        networkD3 = importr('networkD3')

    try:
        magrittr = importr('magrittr')
    except:
        utils.install_packages('magrittr')
        magrittr = importr('magrittr')

    ro.r('''simpleNetwork(rdf) %>% saveNetwork(file = 'Net.html')''')
    return None`

Directory `Data/` missing ?

setup.py is mentioning data in Data/*.txt but the directory appears missing from the repository.

git add Data/*.txt before git commit and git push in the root directory of the original clone might be a way to fix this. An another way would be to remove Data/*.txt from setup.py.

NetworkxD3 issue

[Apologies in advance if it transpires that this issue is due to my newbie-ness.]

After installing NetworkxD3 as described and trying to run the MWE provided (see end), I get the following error: "NameError: name 'simpleNetworkx' is not defined"

Can you help? I am running Python 2.7.10.

Thanks,
Lisa

---

import networkx as nx
from NetworkxD3 import simpleNetworkx

G = nx.Graph()
H = ["A","B","C","D","E","F","G", "H","I","J"]
G.add_nodes_from(H)
G.add_edges_from([("A","B"), ("A","C"), ("A","D"), ("A","J"), ("B","E"), ("B","F"),
("C","G"),("C","H"), ("D","I")])

simpleNetworkx(G)

Unreadable Notebook

I tried to open NetworkxD3example.ipynb, but neither Github, nbviewer nor my local jupyter installation could handle it. Here's jupyter's error message:

Unreadable Notebook: /tmp/NetworkxD3/NetworkxD3example.ipynb NotJSONError('Notebook does not appear to be JSON: u\'{\\n "cells": [\\n {\\n "cell_type": "...',)

PandasError: DataFrame constructor not properly called!

I had to downgrade to Pandas 0.19.1 due to another error. Now I get the following error. Please provide the package versions you used:

import networkx as nx
from NetworkxD3.NetworkxD3 import simpleNetworkx
from IPython.display import IFrame 

G = nx.Graph()
H = ["A","B","C","D","E","F","G", "H","I","J"]
G.add_nodes_from(H)
G.add_edges_from([("A","B"), ("A","C"), ("A","D"), ("A","J"), ("B","E"), ("B","F"),
("C","G"),("C","H"), ("D","I")])

simpleNetworkx(G)
IFrame('Net.html', width=400, height=400)

PandasError Traceback (most recent call last)
in ()
9 ("C","G"),("C","H"), ("D","I")])
10
---> 11 simpleNetworkx(G)
12 IFrame('Net.html', width=400, height=400)

/vagrant/JMB/NetworkxD3/NetworkxD3/NetworkxD3.py in simpleNetworkx(G)
49 ro.r('rdf=data.frame()')
50
---> 51 df = p.DataFrame(G.edges())
52
53 df_r = com.convert_to_r_dataframe(df)

~/anaconda3/envs/normal/lib/python3.6/site-packages/pandas/core/frame.py in init(self, data, index, columns, dtype, copy)
343 copy=False)
344 else:
--> 345 raise PandasError('DataFrame constructor not properly called!')
346
347 NDFrame.init(self, mgr, fastpath=True)

PandasError: DataFrame constructor not properly called!