Python Networkx和Plotly边不匹配

我正在尝试使用Networkx 2.1和Plotly 2.7.0生成一个最小生成树的图形，使用距离矩阵作为输入。我正在使用Python 2.7

问题是Plotly图中显示的节点的边与Networkx最小生成树的边列表不匹配

距离矩阵（csv文件）的格式如下：

ST0_1,0,0,1109,1109,1091,1091,1125,1126,1126,1125,1127,1126,1127,1127,1125,1125,1125,1126,1126,1127,1127,1127,1127,1122,1130,1126,1127
ST0_2,0,0,1109,1109,1091,1091,1125,1126,1126,1125,1127,1126,1127,1127,1125,1125,1125,1126,1126,1127,1127,1127,1127,1122,1130,1126,1127
ST1_3,1109,1109,0,0,1107,1107,1047,1048,1048,1047,1049,1048,1049,1049,1049,1049,1049,1047,1049,1049,1047,1047,1047,1050,1050,1049,1049
ST1_4,1109,1109,0,0,1107,1107,1047,1048,1048,1047,1049,1048,1049,1049,1049,1049,1049,1047,1049,1049,1047,1047,1047,1050,1050,1049,1049
ST22_5,1091,1091,1107,1107,0,0,1100,1101,1101,1100,1102,1101,1102,1102,1101,1101,1101,1101,1100,1102,1101,1101,1102,1099,1103,1102,1102
ST22_6,1091,1091,1107,1107,0,0,1100,1101,1101,1100,1102,1101,1102,1102,1101,1101,1101,1101,1100,1102,1101,1101,1102,1099,1103,1102,1102
ST2,1125,1125,1047,1047,1100,1100,0,5,6,8,8,9,8,10,7,7,8,11,16,12,8,7,11,72,43,11,17
ST7,1126,1126,1048,1048,1101,1101,5,0,1,7,3,4,3,5,6,6,7,10,15,13,7,6,10,72,43,6,16
ST9,1126,1126,1048,1048,1101,1101,6,1,0,8,2,3,2,4,7,7,8,11,16,14,8,7,11,73,44,5,17
ST5,1125,1125,1047,1047,1100,1100,8,7,8,0,10,11,10,12,7,7,8,7,16,16,10,9,13,73,44,13,17
ST13,1127,1127,1049,1049,1102,1102,8,3,2,10,0,3,2,4,9,9,10,13,18,16,10,9,13,75,46,7,19
ST11,1126,1126,1048,1048,1101,1101,9,4,3,11,3,0,3,1,10,10,11,14,19,17,11,10,14,76,47,8,20
ST10,1127,1127,1049,1049,1102,1102,8,3,2,10,2,3,0,4,9,9,10,13,18,16,10,9,13,75,46,7,19
ST12,1127,1127,1049,1049,1102,1102,10,5,4,12,4,1,4,0,11,11,12,15,20,18,12,11,15,77,48,9,21
ST16_7,1125,1125,1049,1049,1101,1101,7,6,7,7,9,10,9,11,0,0,3,10,15,15,9,8,12,72,43,12,16
ST16_8,1125,1125,1049,1049,1101,1101,7,6,7,7,9,10,9,11,0,0,3,10,15,15,9,8,12,72,43,12,16
ST15,1125,1125,1049,1049,1101,1101,8,7,8,8,10,11,10,12,3,3,0,11,16,16,10,9,13,73,44,13,17
ST6,1126,1126,1047,1047,1101,1101,11,10,11,7,13,14,13,15,10,10,11,0,17,15,11,12,12,70,43,14,18
ST18,1126,1126,1049,1049,1100,1100,16,15,16,16,18,19,18,20,15,15,16,17,0,22,16,17,18,77,49,21,7
ST17,1127,1127,1049,1049,1102,1102,12,13,14,16,16,17,16,18,15,15,16,15,22,0,14,15,15,75,50,15,23
ST4,1127,1127,1047,1047,1101,1101,8,7,8,10,10,11,10,12,9,9,10,11,16,14,0,1,3,73,44,13,17
ST3,1127,1127,1047,1047,1101,1101,7,6,7,9,9,10,9,11,8,8,9,12,17,15,1,0,4,74,45,12,18
ST8,1127,1127,1047,1047,1102,1102,11,10,11,13,13,14,13,15,12,12,13,12,18,15,3,4,0,72,47,14,20
ST21,1122,1122,1050,1050,1099,1099,72,72,73,73,75,76,75,77,72,72,73,70,77,75,73,74,72,0,83,74,79
ST20,1130,1130,1050,1050,1103,1103,43,43,44,44,46,47,46,48,43,43,44,43,49,50,44,45,47,83,0,49,50
ST14,1126,1126,1049,1049,1102,1102,11,6,5,13,7,8,7,9,12,12,13,14,21,15,13,12,14,74,49,0,22
ST19,1127,1127,1049,1049,1102,1102,17,16,17,17,19,20,19,21,16,16,17,18,7,23,17,18,20,79,50,22,0

以下是Python脚本：

import csv
import numpy as np
import networkx as nx
from plotly.offline import plot
import plotly.graph_objs as go
from networkx.drawing.nx_agraph import graphviz_layout

def read_dist_matrix(file_name):
    """ Reads a distance matrix in PHYLIP format.

        Requires: file_name is the name of a file that has the distance matrix
        in PHYLIP format.
        Ensures: distance matrix as numpy array and a list with the names/ids of
        each sequence.
    """

    with open(file_name) as f:
        #first_line = f.readline().strip()
        reader = csv.reader(f, delimiter=',')
        names = list(zip(*reader))[0]

    cols = tuple(list(range(1,len(names)+1)))

    dist_matrix = np.loadtxt(file_name, delimiter=',',
                             usecols=cols)

    return [dist_matrix, names]


def dist_to_graph(matrix, names):
    """ Converts numpy array representing distance matrix to graph.

        Requires: matrix as a numpy array. names as a list with the names
        of each row/column.
        Ensures: networkx graph labeled with the right names.
    """

    G = nx.from_numpy_matrix(matrix)

    nodes = list(G.nodes())

    names_dict = {}
    for n in range(len(nodes)):
        names_dict[nodes[n]] = names[n]

    G = nx.relabel_nodes(G, names_dict)

    return G

ola = read_dist_matrix("out.csv")
ola_g = dist_to_graph(ola[0], ola[1])

mst = nx.minimum_spanning_tree(ola_g, algorithm='prim')
pos = graphviz_layout(mst, prog='neato')
labels = list(mst.nodes.keys())

X = []
Y = []

for k in pos:
    X.append(pos[k][0])
    Y.append(pos[k][1])


tracer = go.Scatter(x=X, y=Y,
                    mode='lines',
                    line=go.Line(color='#888', width=2),
                    hoverinfo = 'none',
                    showlegend=False)

tracer_marker = go.Scatter(x=X, y=Y,
                    mode='markers+text',
                    text=labels,
                    textposition='top',
                    marker = go.Marker(size= 15,
                                       line = dict(width = 2)),
                    hoverinfo = 'none',
                    showlegend=False)

layout = dict(title='Test', showlegend=False, 
              xaxis=dict(title='', 
                         titlefont=dict(size=20), 
                         showgrid=False, 
                         zeroline=False, 
                         showline=False, 
                         ticks='', 
                         showticklabels=False, 
                         showspikes=False),
              yaxis=dict(title='', 
                         titlefont=dict(size=20), 
                         showgrid=False, 
                         zeroline=False, 
                         showline=False, 
                         ticks='', 
                         showticklabels=False, 
                         showspikes=False)
                           )

fig = dict(data=[tracer, tracer_marker], layout=layout)

plot(fig, filename='./test_plotly.html', auto_open=True, show_link=False)

这是输出HTML的屏幕截图：

如果我们运行命令

mst.edges（data=True）

我们会看到节点ST7和ST5是连接的，但在绘图图中它们不是

有人问了一个类似的问题，但是关于R：

---

有人能帮我吗？

您正在使用多个DICT。无法准确预测dicts中返回键的顺序

---

我认为您不能保证

列表（mst.nodes.keys（））

的顺序与

X

和

Y

的顺序相同。因此我怀疑标签

ST7

正在应用于不同的节点。

哪里定义了

mst

？在绘图中，这两个节点没有连接。很抱歉，我复制脚本失败。编辑了这篇文章以包含

mst

@Joel的定义，这正是我的问题：它们应该在图中连接，因为mst的边列表显示它们之间存在连接。