[英]Networkx Multigraph from_pandas_dataframe
Update: 更新:
The question, as written, is relevant to Networkx version < 2.0. 所写的问题与Networkx版本<2.0有关。 The
from_pandas_dataframe
method has been dropped . from_pandas_dataframe
方法已删除 。
To accomplish the same task in Networkx >= 2.0, see the update to the accepted answer. 要在Networkx> = 2.0中完成相同的任务,请参见已接受答案的更新。
Trying to create a MultiGraph()
instance from a pandas DataFrame using networkx's from_pandas_dataframe
. 尝试使用networkx的
from_pandas_dataframe
从pandas DataFrame创建MultiGraph()
实例。 What am I doing wrong in the example below? 在下面的示例中我在做什么错?
In [1]: import pandas as pd
import networkx as nx
df = pd.DataFrame([['geneA', 'geneB', 0.05, 'method1'],
['geneA', 'geneC', 0.45, 'method1'],
['geneA', 'geneD', 0.35, 'method1'],
['geneA', 'geneB', 0.45, 'method2']],
columns = ['gene1','gene2','conf','type'])
First try with the default nx.Graph(): 首先尝试使用默认的nx.Graph():
In [2]: G= nx.from_pandas_dataframe(df, 'gene1', 'gene2', edge_attr=['conf','type'],
create_using=nx.Graph())
As a non-MultiGraph(), I'm missing one of the duplicate edges: 作为非MultiGraph(),我缺少重复的边缘之一:
In [3]: G.edges(data=True)
Out[3]: [('geneA', 'geneB', {'conf': 0.45, 'type': 'method2'}),
('geneA', 'geneC', {'conf': 0.45, 'type': 'method1'}),
('geneA', 'geneD', {'conf': 0.35, 'type': 'method1'})]
With MultiGraph()
: 使用
MultiGraph()
:
In [4]: MG= nx.from_pandas_dataframe(df, 'gene1', 'gene2', edge_attr=['conf','type'],
create_using=nx.MultiGraph())
This: 这个:
TypeError Traceback (most recent call last)
<ipython-input-49-d2c7b8312ea7> in <module>()
----> 1 MG= nx.from_pandas_dataframe(df, 'gene1', 'gene2', ['conf','type'], create_using=nx.MultiGraph())
/usr/lib/python2.7/site-packages/networkx-1.10-py2.7.egg/networkx/convert_matrix.pyc in from_pandas_dataframe(df, source, target, edge_attr, create_using)
209 # Iteration on values returns the rows as Numpy arrays
210 for row in df.values:
--> 211 g.add_edge(row[src_i], row[tar_i], {i:row[j] for i, j in edge_i})
212
213 # If no column names are given, then just return the edges.
/usr/lib/python2.7/site-packages/networkx-1.10-py2.7.egg/networkx/classes/multigraph.pyc in add_edge(self, u, v, key, attr_dict, **attr)
340 datadict.update(attr_dict)
341 keydict = self.edge_key_dict_factory()
--> 342 keydict[key] = datadict
343 self.adj[u][v] = keydict
344 self.adj[v][u] = keydict
TypeError: unhashable type: 'dict'
Question How do I instantiate a MultiGraph()
from a pandas dataframe? 问题如何从熊猫数据帧实例化
MultiGraph()
?
Networkx < 2.0: Networkx <2.0:
It's was a bug, I opened an issue on GitHub, once I made the suggested edit : 这是一个错误,完成建议的编辑后 ,我在GitHub上打开了一个问题:
It changed line 211 of convert_matrix.py
to to read: 它将
convert_matrix.py
第211行更改为:
g.add_edge(row[src_i], row[tar_i], attr_dict={i:row[j] for i, j in edge_i})
Results from that change: (which have since been incorporated) 更改的结果:( 此后已合并)
MG= nx.from_pandas_dataframe(df, 'gene1', 'gene2', edge_attr=['conf','type'],
create_using=nx.MultiGraph())
MG.edges(data=True)
[('geneA', 'geneB', {'conf': 0.05, 'type': 'method1'}),
('geneA', 'geneB', {'conf': 0.45, 'type': 'method2'}),
('geneA', 'geneC', {'conf': 0.45, 'type': 'method1'}),
('geneA', 'geneD', {'conf': 0.35, 'type': 'method1'})]
Networkx >= 2.0: Networkx> = 2.0:
In DataFrames with this format (edge list), use from_pandas_edgelist
在具有这种格式的数据框(边缘列表)中,使用
from_pandas_edgelist
MG= nx.from_pandas_edgelist(df, 'gene1', 'gene2', edge_attr=['conf','type'],
create_using=nx.MultiGraph())
MG.edges(data=True)
MultiEdgeDataView([('geneA', 'geneB', {'conf': 0.05, 'type': 'method1'}),
('geneA', 'geneB', {'conf': 0.45, 'type': 'method2'}),
('geneA', 'geneC', {'conf': 0.45, 'type': 'method1'}),
('geneA', 'geneD', {'conf': 0.35, 'type': 'method1'})])
That's a nice question. 这是一个很好的问题。 I tried to reproduce your problem building your
MultiGraph()
in a different way, using only three/four columns with: 我尝试仅使用三列/四列,并以不同的方式重现您在构建
MultiGraph()
时遇到的问题:
MG = nx.MultiGraph()
MG.add_weighted_edges_from([tuple(d) for d in df[['gene1','gene2','conf']].values])
this correctly returns as MG.edges(data=True)
: 这正确返回为
MG.edges(data=True)
:
[('geneA', 'geneB', {'weight': 0.05}), ('geneA', 'geneB', {'weight': 0.45}), ('geneA', 'geneC', {'weight': 0.45}), ('geneA', 'geneD', {'weight': 0.35})]
I tried also with your from_pandas_dataframe
method using only three columns but it doesn't work: 我也尝试了只使用三列的
from_pandas_dataframe
方法,但是它不起作用:
MG = nx.from_pandas_dataframe(df, 'gene1', 'gene2', edge_attr='conf', create_using=nx.MultiGraph())
this returns the same error you encountered. 这将返回您遇到的相同错误。 I don't know if it is a bug or that method doesn't support more than one weight type for
MultiGraph()
. 我不知道这是一个错误还是该方法不支持
MultiGraph()
多个权重类型。 In the meantime you can use the above workaround to build your MultiGraph, at least with only one weight type. 同时,您可以使用以上解决方法来构建MultiGraph,至少仅使用一种权重类型即可。 Hope that helps.
希望能有所帮助。
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