python - 如何使 Networkx 生成具有排序节点的 GML 文件

Question

我有以下代码:

#!/usr/bin/env python
import networkx as nx
def main():
    """docstring for main"""
    outerdict = {"A":["a1","a2","a3"], "B":["b1","b2","b3","b5","b6", "b7"], "C":["c2","c3"], "D":["d1","d2","d3"]}
    keynode = "Z"

    colorlist = [ "#beaed4", "#fdc086", "#ffff99", "#386cb0","#f0027f"]
    G = nx.Graph()
    G.add_node(keynode,graphics={"fill":"#7fc97f","w":27,"h":27, "d":27})
    for i,ky in enumerate(outerdict):
        nodes = outerdict[ky]
        nodecol = colorlist[i]
        print ky, nodecol
        for node in nodes:
            G.add_node(node,graphics={"fill":nodecol,"w":27,"h":27,"d":27})
            G.add_edge(keynode, node, value = 10)

    outfile = "test.gml"
    nx.write_gml(G,outfile)


if __name__ == '__main__':
    main()

它生成以下 GML 文件:

graph [
  node [
    id 0
    label "b6"
    graphics [ 
      h 27
      d 27
      w 27
      fill "#ffff99"
    ]
  ]
  node [
    id 1
    label "a1"
    graphics [ 
      h 27
      d 27
      w 27
      fill "#beaed4"
    ]
  ]
  node [
    id 2
    label "b5"
    graphics [ 
      h 27
      d 27
      w 27
      fill "#ffff99"
    ]
  ]
  node [
    id 3
    label "a3"
    graphics [ 
      h 27
      d 27
      w 27
      fill "#beaed4"
    ]
  ]
  node [
    id 4
    label "a2"
    graphics [ 
      h 27
      d 27
      w 27
      fill "#beaed4"
    ]
  ]
  node [
    id 5
    label "b7"
    graphics [ 
      h 27
      d 27
      w 27
      fill "#ffff99"
    ]
  ]
  node [
    id 6
    label "b1"
    graphics [ 
      h 27
      d 27
      w 27
      fill "#ffff99"
    ]
  ]
  node [
    id 7
    label "b2"
    graphics [ 
      h 27
      d 27
      w 27
      fill "#ffff99"
    ]
  ]
  node [
    id 8
    label "b3"
    graphics [ 
      h 27
      d 27
      w 27
      fill "#ffff99"
    ]
  ]
  node [
    id 9
    label "c3"
    graphics [ 
      h 27
      d 27
      w 27
      fill "#fdc086"
    ]
  ]
  node [
    id 10
    label "c2"
    graphics [ 
      h 27
      d 27
      w 27
      fill "#fdc086"
    ]
  ]
  node [
    id 11
    label "Z"
    graphics [ 
      h 27
      d 27
      w 27
      fill "#7fc97f"
    ]
  ]
  node [
    id 12
    label "d2"
    graphics [ 
      h 27
      d 27
      w 27
      fill "#386cb0"
    ]
  ]
  node [
    id 13
    label "d3"
    graphics [ 
      h 27
      d 27
      w 27
      fill "#386cb0"
    ]
  ]
  node [
    id 14
    label "d1"
    graphics [ 
      h 27
      d 27
      w 27
      fill "#386cb0"
    ]
  ]
  edge [
    source 0
    target 11
    value 10
  ]
  edge [
    source 1
    target 11
    value 10
  ]
  edge [
    source 2
    target 11
    value 10
  ]
  edge [
    source 3
    target 11
    value 10
  ]
  edge [
    source 4
    target 11
    value 10
  ]
  edge [
    source 5
    target 11
    value 10
  ]
  edge [
    source 6
    target 11
    value 10
  ]
  edge [
    source 7
    target 11
    value 10
  ]
  edge [
    source 8
    target 11
    value 10
  ]
  edge [
    source 9
    target 11
    value 10
  ]
  edge [
    source 10
    target 11
    value 10
  ]
  edge [
    source 11
    target 12
    value 10
  ]
  edge [
    source 11
    target 13
    value 10
  ]
  edge [
    source 11
    target 14
    value 10
  ]
]

注意节点没有按顺序排列。例如 a1 位于 b1 和 b5 之间。这使得情节看起来像这样:

我期望图形是根据循环和初始数据结构 outderdict 按顺序排序。这样黄色节点将与其他黄色节点依次排列在一起。

如何使用 Networkx 对 GML 文件进行排序？其他解决方案(例如 Igraph)，只要在 Python 框架内，都欢迎。

Answer 1

自 2015 年 1 月 1 日起，NetworkX 中提供了有序图数据结构。OrderedGraph 类将按照添加顺序从 NetworkX 数据结构中输出节点和边。
您需要在 https://github.com/networkx/networkx/ 获取最新的开发版本为以下工作。

import networkx as nx
outerdict = {"A":["a1","a2","a3"], "B":["b1","b2","b3","b5","b6", "b7"], "C":["c2","c3"], "D":["d1","d2","d3"]}
keynode = "Z"
colorlist = [ "#beaed4", "#fdc086", "#ffff99", "#386cb0","#f0027f"]
G = nx.OrderedGraph()
G.add_node(keynode,graphics={"fill":"#7fc97f","w":27,"h":27, "d":27})
for i,ky in enumerate(outerdict):
    nodes = outerdict[ky]
    nodecol = colorlist[i]
    print ky, nodecol
    for node in nodes:
        G.add_node(node,graphics={"fill":nodecol,"w":27,"h":27,"d":27})
        G.add_edge(keynode, node, value = 10)
outfile = "test.gml"
nx.write_gml(G,outfile)

请注意，当您遍历“enumerate(outerdict)”时，您的“outerdict”数据结构的出现顺序可能与您初始化它的顺序不同。如果节点“A”、“B”、“C”和“D”的顺序对您很重要，那么您将需要更改将它们添加到图表中的方式，以确保它们按该顺序插入。