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annotate planemo/lib/python3.7/site-packages/networkx/drawing/nx_pylab.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1
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1 # Copyright (C) 2004-2019 by
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2 # Aric Hagberg <hagberg@lanl.gov>
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3 # Dan Schult <dschult@colgate.edu>
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4 # Pieter Swart <swart@lanl.gov>
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5 # All rights reserved.
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6 # BSD license.
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7 #
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8 # Author: Aric Hagberg (hagberg@lanl.gov)
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9 """
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10 **********
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11 Matplotlib
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12 **********
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13
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14 Draw networks with matplotlib.
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15
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16 See Also
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17 --------
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18
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19 matplotlib: http://matplotlib.org/
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20
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21 pygraphviz: http://pygraphviz.github.io/
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22
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23 """
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24 from numbers import Number
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25 import networkx as nx
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26 from networkx.utils import is_string_like
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27 from networkx.drawing.layout import shell_layout, \
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28 circular_layout, kamada_kawai_layout, spectral_layout, \
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29 spring_layout, random_layout, planar_layout
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30
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31 __all__ = ['draw',
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32 'draw_networkx',
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33 'draw_networkx_nodes',
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34 'draw_networkx_edges',
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35 'draw_networkx_labels',
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36 'draw_networkx_edge_labels',
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37 'draw_circular',
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38 'draw_kamada_kawai',
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39 'draw_random',
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40 'draw_spectral',
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41 'draw_spring',
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42 'draw_planar',
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43 'draw_shell']
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44
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45
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46 def draw(G, pos=None, ax=None, **kwds):
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47 """Draw the graph G with Matplotlib.
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48
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49 Draw the graph as a simple representation with no node
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50 labels or edge labels and using the full Matplotlib figure area
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51 and no axis labels by default. See draw_networkx() for more
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52 full-featured drawing that allows title, axis labels etc.
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53
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54 Parameters
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55 ----------
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56 G : graph
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57 A networkx graph
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58
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59 pos : dictionary, optional
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60 A dictionary with nodes as keys and positions as values.
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61 If not specified a spring layout positioning will be computed.
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62 See :py:mod:`networkx.drawing.layout` for functions that
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63 compute node positions.
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64
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65 ax : Matplotlib Axes object, optional
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66 Draw the graph in specified Matplotlib axes.
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67
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68 kwds : optional keywords
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69 See networkx.draw_networkx() for a description of optional keywords.
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70
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71 Examples
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72 --------
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73 >>> G = nx.dodecahedral_graph()
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74 >>> nx.draw(G)
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75 >>> nx.draw(G, pos=nx.spring_layout(G)) # use spring layout
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76
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77 See Also
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78 --------
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79 draw_networkx()
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80 draw_networkx_nodes()
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81 draw_networkx_edges()
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82 draw_networkx_labels()
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83 draw_networkx_edge_labels()
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84
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85 Notes
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86 -----
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87 This function has the same name as pylab.draw and pyplot.draw
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88 so beware when using `from networkx import *`
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89
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90 since you might overwrite the pylab.draw function.
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91
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92 With pyplot use
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93
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94 >>> import matplotlib.pyplot as plt
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95 >>> import networkx as nx
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96 >>> G = nx.dodecahedral_graph()
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97 >>> nx.draw(G) # networkx draw()
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98 >>> plt.draw() # pyplot draw()
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99
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100 Also see the NetworkX drawing examples at
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101 https://networkx.github.io/documentation/latest/auto_examples/index.html
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102 """
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103 try:
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104 import matplotlib.pyplot as plt
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105 except ImportError:
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106 raise ImportError("Matplotlib required for draw()")
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107 except RuntimeError:
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108 print("Matplotlib unable to open display")
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109 raise
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110
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111 if ax is None:
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112 cf = plt.gcf()
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113 else:
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114 cf = ax.get_figure()
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115 cf.set_facecolor('w')
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116 if ax is None:
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117 if cf._axstack() is None:
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118 ax = cf.add_axes((0, 0, 1, 1))
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119 else:
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120 ax = cf.gca()
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121
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122 if 'with_labels' not in kwds:
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123 kwds['with_labels'] = 'labels' in kwds
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124
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125 draw_networkx(G, pos=pos, ax=ax, **kwds)
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126 ax.set_axis_off()
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127 plt.draw_if_interactive()
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128 return
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129
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130
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131 def draw_networkx(G, pos=None, arrows=True, with_labels=True, **kwds):
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132 """Draw the graph G using Matplotlib.
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133
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134 Draw the graph with Matplotlib with options for node positions,
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135 labeling, titles, and many other drawing features.
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136 See draw() for simple drawing without labels or axes.
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137
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138 Parameters
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139 ----------
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140 G : graph
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141 A networkx graph
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142
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143 pos : dictionary, optional
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144 A dictionary with nodes as keys and positions as values.
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145 If not specified a spring layout positioning will be computed.
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146 See :py:mod:`networkx.drawing.layout` for functions that
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147 compute node positions.
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148
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149 arrows : bool, optional (default=True)
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150 For directed graphs, if True draw arrowheads.
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151 Note: Arrows will be the same color as edges.
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152
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153 arrowstyle : str, optional (default='-|>')
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154 For directed graphs, choose the style of the arrowsheads.
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155 See :py:class: `matplotlib.patches.ArrowStyle` for more
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156 options.
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157
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158 arrowsize : int, optional (default=10)
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159 For directed graphs, choose the size of the arrow head head's length and
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160 width. See :py:class: `matplotlib.patches.FancyArrowPatch` for attribute
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161 `mutation_scale` for more info.
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162
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163 with_labels : bool, optional (default=True)
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164 Set to True to draw labels on the nodes.
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165
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166 ax : Matplotlib Axes object, optional
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167 Draw the graph in the specified Matplotlib axes.
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168
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169 nodelist : list, optional (default G.nodes())
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170 Draw only specified nodes
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171
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172 edgelist : list, optional (default=G.edges())
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173 Draw only specified edges
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174
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175 node_size : scalar or array, optional (default=300)
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176 Size of nodes. If an array is specified it must be the
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177 same length as nodelist.
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178
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179 node_color : color or array of colors (default='#1f78b4')
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180 Node color. Can be a single color or a sequence of colors with the same
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181 length as nodelist. Color can be string, or rgb (or rgba) tuple of
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182 floats from 0-1. If numeric values are specified they will be
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183 mapped to colors using the cmap and vmin,vmax parameters. See
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184 matplotlib.scatter for more details.
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185
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186 node_shape : string, optional (default='o')
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187 The shape of the node. Specification is as matplotlib.scatter
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188 marker, one of 'so^>v<dph8'.
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189
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190 alpha : float, optional (default=None)
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191 The node and edge transparency
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192
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193 cmap : Matplotlib colormap, optional (default=None)
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194 Colormap for mapping intensities of nodes
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195
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196 vmin,vmax : float, optional (default=None)
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197 Minimum and maximum for node colormap scaling
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198
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199 linewidths : [None | scalar | sequence]
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200 Line width of symbol border (default =1.0)
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201
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202 width : float, optional (default=1.0)
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203 Line width of edges
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204
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205 edge_color : color or array of colors (default='k')
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206 Edge color. Can be a single color or a sequence of colors with the same
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207 length as edgelist. Color can be string, or rgb (or rgba) tuple of
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208 floats from 0-1. If numeric values are specified they will be
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209 mapped to colors using the edge_cmap and edge_vmin,edge_vmax parameters.
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210
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211 edge_cmap : Matplotlib colormap, optional (default=None)
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212 Colormap for mapping intensities of edges
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213
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214 edge_vmin,edge_vmax : floats, optional (default=None)
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215 Minimum and maximum for edge colormap scaling
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216
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217 style : string, optional (default='solid')
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218 Edge line style (solid|dashed|dotted,dashdot)
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219
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220 labels : dictionary, optional (default=None)
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221 Node labels in a dictionary keyed by node of text labels
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222
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223 font_size : int, optional (default=12)
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224 Font size for text labels
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225
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226 font_color : string, optional (default='k' black)
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227 Font color string
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228
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229 font_weight : string, optional (default='normal')
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230 Font weight
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231
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232 font_family : string, optional (default='sans-serif')
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233 Font family
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234
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235 label : string, optional
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236 Label for graph legend
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237
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238 Notes
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239 -----
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240 For directed graphs, arrows are drawn at the head end. Arrows can be
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241 turned off with keyword arrows=False.
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242
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243 Examples
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244 --------
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245 >>> G = nx.dodecahedral_graph()
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246 >>> nx.draw(G)
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247 >>> nx.draw(G, pos=nx.spring_layout(G)) # use spring layout
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248
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249 >>> import matplotlib.pyplot as plt
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250 >>> limits = plt.axis('off') # turn of axis
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251
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252 Also see the NetworkX drawing examples at
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253 https://networkx.github.io/documentation/latest/auto_examples/index.html
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254
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255 See Also
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256 --------
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257 draw()
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258 draw_networkx_nodes()
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259 draw_networkx_edges()
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260 draw_networkx_labels()
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261 draw_networkx_edge_labels()
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262 """
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263 try:
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264 import matplotlib.pyplot as plt
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265 except ImportError:
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266 raise ImportError("Matplotlib required for draw()")
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267 except RuntimeError:
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268 print("Matplotlib unable to open display")
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269 raise
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270
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271 if pos is None:
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272 pos = nx.drawing.spring_layout(G) # default to spring layout
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273
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274 node_collection = draw_networkx_nodes(G, pos, **kwds)
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275 edge_collection = draw_networkx_edges(G, pos, arrows=arrows, **kwds)
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276 if with_labels:
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277 draw_networkx_labels(G, pos, **kwds)
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278 plt.draw_if_interactive()
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279
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280
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281 def draw_networkx_nodes(G, pos,
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282 nodelist=None,
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283 node_size=300,
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284 node_color='#1f78b4',
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285 node_shape='o',
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286 alpha=None,
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287 cmap=None,
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288 vmin=None,
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289 vmax=None,
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290 ax=None,
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291 linewidths=None,
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292 edgecolors=None,
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293 label=None,
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294 **kwds):
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295 """Draw the nodes of the graph G.
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296
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297 This draws only the nodes of the graph G.
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298
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299 Parameters
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300 ----------
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301 G : graph
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302 A networkx graph
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303
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304 pos : dictionary
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305 A dictionary with nodes as keys and positions as values.
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306 Positions should be sequences of length 2.
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307
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308 ax : Matplotlib Axes object, optional
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309 Draw the graph in the specified Matplotlib axes.
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310
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311 nodelist : list, optional
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312 Draw only specified nodes (default G.nodes())
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313
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314 node_size : scalar or array
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315 Size of nodes (default=300). If an array is specified it must be the
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316 same length as nodelist.
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317
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318 node_color : color or array of colors (default='#1f78b4')
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319 Node color. Can be a single color or a sequence of colors with the same
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320 length as nodelist. Color can be string, or rgb (or rgba) tuple of
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321 floats from 0-1. If numeric values are specified they will be
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322 mapped to colors using the cmap and vmin,vmax parameters. See
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323 matplotlib.scatter for more details.
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324
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325 node_shape : string
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326 The shape of the node. Specification is as matplotlib.scatter
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327 marker, one of 'so^>v<dph8' (default='o').
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328
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329 alpha : float or array of floats
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330 The node transparency. This can be a single alpha value (default=None),
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331 in which case it will be applied to all the nodes of color. Otherwise,
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332 if it is an array, the elements of alpha will be applied to the colors
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333 in order (cycling through alpha multiple times if necessary).
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334
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335 cmap : Matplotlib colormap
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336 Colormap for mapping intensities of nodes (default=None)
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337
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338 vmin,vmax : floats
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339 Minimum and maximum for node colormap scaling (default=None)
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340
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341 linewidths : [None | scalar | sequence]
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342 Line width of symbol border (default =1.0)
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343
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344 edgecolors : [None | scalar | sequence]
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345 Colors of node borders (default = node_color)
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346
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347 label : [None| string]
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348 Label for legend
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349
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350 min_source_margin : int, optional (default=0)
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351 The minimum margin (gap) at the begining of the edge at the source.
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352
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353 min_target_margin : int, optional (default=0)
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354 The minimum margin (gap) at the end of the edge at the target.
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355
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356 Returns
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357 -------
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358 matplotlib.collections.PathCollection
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359 `PathCollection` of the nodes.
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360
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361 Examples
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362 --------
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363 >>> G = nx.dodecahedral_graph()
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364 >>> nodes = nx.draw_networkx_nodes(G, pos=nx.spring_layout(G))
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365
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366 Also see the NetworkX drawing examples at
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367 https://networkx.github.io/documentation/latest/auto_examples/index.html
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368
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369 See Also
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370 --------
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371 draw()
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372 draw_networkx()
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373 draw_networkx_edges()
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374 draw_networkx_labels()
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375 draw_networkx_edge_labels()
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376 """
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377 from collections.abc import Iterable
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378 try:
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379 import matplotlib.pyplot as plt
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380 import numpy as np
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381 except ImportError:
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382 raise ImportError("Matplotlib required for draw()")
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383 except RuntimeError:
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384 print("Matplotlib unable to open display")
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385 raise
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386
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387 if ax is None:
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388 ax = plt.gca()
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389
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390 if nodelist is None:
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391 nodelist = list(G)
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392
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393 if len(nodelist) == 0: # empty nodelist, no drawing
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394 return
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395
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396 try:
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397 xy = np.asarray([pos[v] for v in nodelist])
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398 except KeyError as e:
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399 raise nx.NetworkXError('Node %s has no position.' % e)
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400 except ValueError:
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401 raise nx.NetworkXError('Bad value in node positions.')
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402
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403 if isinstance(alpha, Iterable):
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404 node_color = apply_alpha(node_color, alpha, nodelist, cmap, vmin, vmax)
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405 alpha = None
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406
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407 node_collection = ax.scatter(xy[:, 0], xy[:, 1],
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408 s=node_size,
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409 c=node_color,
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410 marker=node_shape,
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411 cmap=cmap,
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412 vmin=vmin,
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413 vmax=vmax,
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414 alpha=alpha,
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415 linewidths=linewidths,
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416 edgecolors=edgecolors,
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417 label=label)
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418 ax.tick_params(
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419 axis='both',
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420 which='both',
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421 bottom=False,
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422 left=False,
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423 labelbottom=False,
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424 labelleft=False)
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425
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426 node_collection.set_zorder(2)
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427 return node_collection
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428
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429
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430 def draw_networkx_edges(G, pos,
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431 edgelist=None,
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432 width=1.0,
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433 edge_color='k',
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434 style='solid',
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435 alpha=None,
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436 arrowstyle='-|>',
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437 arrowsize=10,
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438 edge_cmap=None,
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439 edge_vmin=None,
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440 edge_vmax=None,
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441 ax=None,
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442 arrows=True,
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443 label=None,
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444 node_size=300,
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445 nodelist=None,
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446 node_shape="o",
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447 connectionstyle=None,
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448 min_source_margin=0,
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449 min_target_margin=0,
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450 **kwds):
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451 """Draw the edges of the graph G.
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452
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453 This draws only the edges of the graph G.
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454
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455 Parameters
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456 ----------
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457 G : graph
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458 A networkx graph
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459
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460 pos : dictionary
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461 A dictionary with nodes as keys and positions as values.
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462 Positions should be sequences of length 2.
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463
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464 edgelist : collection of edge tuples
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465 Draw only specified edges(default=G.edges())
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466
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467 width : float, or array of floats
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468 Line width of edges (default=1.0)
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469
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470 edge_color : color or array of colors (default='k')
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471 Edge color. Can be a single color or a sequence of colors with the same
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472 length as edgelist. Color can be string, or rgb (or rgba) tuple of
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473 floats from 0-1. If numeric values are specified they will be
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474 mapped to colors using the edge_cmap and edge_vmin,edge_vmax parameters.
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475
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476 style : string
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477 Edge line style (default='solid') (solid|dashed|dotted,dashdot)
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478
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479 alpha : float
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480 The edge transparency (default=None)
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481
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482 edge_ cmap : Matplotlib colormap
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483 Colormap for mapping intensities of edges (default=None)
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484
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485 edge_vmin,edge_vmax : floats
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486 Minimum and maximum for edge colormap scaling (default=None)
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487
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488 ax : Matplotlib Axes object, optional
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489 Draw the graph in the specified Matplotlib axes.
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490
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491 arrows : bool, optional (default=True)
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492 For directed graphs, if True draw arrowheads.
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493 Note: Arrows will be the same color as edges.
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494
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495 arrowstyle : str, optional (default='-|>')
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496 For directed graphs, choose the style of the arrow heads.
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497 See :py:class: `matplotlib.patches.ArrowStyle` for more
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498 options.
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499
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500 arrowsize : int, optional (default=10)
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501 For directed graphs, choose the size of the arrow head head's length and
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502 width. See :py:class: `matplotlib.patches.FancyArrowPatch` for attribute
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503 `mutation_scale` for more info.
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504
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505 connectionstyle : str, optional (default=None)
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506 Pass the connectionstyle parameter to create curved arc of rounding
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507 radius rad. For example, connectionstyle='arc3,rad=0.2'.
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508 See :py:class: `matplotlib.patches.ConnectionStyle` and
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509 :py:class: `matplotlib.patches.FancyArrowPatch` for more info.
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510
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511 label : [None| string]
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512 Label for legend
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513
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514 min_source_margin : int, optional (default=0)
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515 The minimum margin (gap) at the begining of the edge at the source.
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516
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517 min_target_margin : int, optional (default=0)
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518 The minimum margin (gap) at the end of the edge at the target.
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519
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520 Returns
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521 -------
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522 matplotlib.collection.LineCollection
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523 `LineCollection` of the edges
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524
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525 list of matplotlib.patches.FancyArrowPatch
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526 `FancyArrowPatch` instances of the directed edges
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527
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528 Depending whether the drawing includes arrows or not.
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529
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530 Notes
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531 -----
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532 For directed graphs, arrows are drawn at the head end. Arrows can be
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533 turned off with keyword arrows=False. Be sure to include `node_size` as a
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534 keyword argument; arrows are drawn considering the size of nodes.
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535
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536 Examples
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537 --------
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538 >>> G = nx.dodecahedral_graph()
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539 >>> edges = nx.draw_networkx_edges(G, pos=nx.spring_layout(G))
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540
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541 >>> G = nx.DiGraph()
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542 >>> G.add_edges_from([(1, 2), (1, 3), (2, 3)])
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543 >>> arcs = nx.draw_networkx_edges(G, pos=nx.spring_layout(G))
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544 >>> alphas = [0.3, 0.4, 0.5]
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545 >>> for i, arc in enumerate(arcs): # change alpha values of arcs
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546 ... arc.set_alpha(alphas[i])
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547
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548 Also see the NetworkX drawing examples at
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549 https://networkx.github.io/documentation/latest/auto_examples/index.html
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550
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551 See Also
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552 --------
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553 draw()
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554 draw_networkx()
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555 draw_networkx_nodes()
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556 draw_networkx_labels()
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557 draw_networkx_edge_labels()
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558 """
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559 try:
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560 import matplotlib
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561 import matplotlib.pyplot as plt
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562 from matplotlib.colors import colorConverter, Colormap, Normalize
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563 from matplotlib.collections import LineCollection
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564 from matplotlib.patches import FancyArrowPatch
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565 import numpy as np
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566 except ImportError:
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567 raise ImportError("Matplotlib required for draw()")
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568 except RuntimeError:
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569 print("Matplotlib unable to open display")
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570 raise
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571
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572 if ax is None:
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573 ax = plt.gca()
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574
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575 if edgelist is None:
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576 edgelist = list(G.edges())
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577
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578 if not edgelist or len(edgelist) == 0: # no edges!
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579 return None
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580
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581 if nodelist is None:
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582 nodelist = list(G.nodes())
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583
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584 # FancyArrowPatch handles color=None different from LineCollection
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585 if edge_color is None:
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586 edge_color = 'k'
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587
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588 # set edge positions
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589 edge_pos = np.asarray([(pos[e[0]], pos[e[1]]) for e in edgelist])
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590
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591 # Check if edge_color is an array of floats and map to edge_cmap.
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592 # This is the only case handled differently from matplotlib
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593 if np.iterable(edge_color) and (len(edge_color) == len(edge_pos)) \
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594 and np.alltrue([isinstance(c, Number) for c in edge_color]):
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595 if edge_cmap is not None:
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596 assert(isinstance(edge_cmap, Colormap))
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597 else:
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598 edge_cmap = plt.get_cmap()
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599 if edge_vmin is None:
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600 edge_vmin = min(edge_color)
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601 if edge_vmax is None:
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602 edge_vmax = max(edge_color)
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603 color_normal = Normalize(vmin=edge_vmin, vmax=edge_vmax)
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604 edge_color = [edge_cmap(color_normal(e)) for e in edge_color]
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605
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606 if (not G.is_directed() or not arrows):
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607 edge_collection = LineCollection(edge_pos,
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608 colors=edge_color,
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609 linewidths=width,
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610 antialiaseds=(1,),
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611 linestyle=style,
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612 transOffset=ax.transData,
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613 alpha=alpha
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614 )
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615
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616 edge_collection.set_zorder(1) # edges go behind nodes
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617 edge_collection.set_label(label)
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618 ax.add_collection(edge_collection)
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619
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620 return edge_collection
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621
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622 arrow_collection = None
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623
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624 if G.is_directed() and arrows:
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625 # Note: Waiting for someone to implement arrow to intersection with
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626 # marker. Meanwhile, this works well for polygons with more than 4
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627 # sides and circle.
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628
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629 def to_marker_edge(marker_size, marker):
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630 if marker in "s^>v<d": # `large` markers need extra space
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631 return np.sqrt(2 * marker_size) / 2
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632 else:
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633 return np.sqrt(marker_size) / 2
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634
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635 # Draw arrows with `matplotlib.patches.FancyarrowPatch`
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636 arrow_collection = []
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637 mutation_scale = arrowsize # scale factor of arrow head
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638
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639 # FancyArrowPatch doesn't handle color strings
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640 arrow_colors = colorConverter.to_rgba_array(edge_color, alpha)
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641 for i, (src, dst) in enumerate(edge_pos):
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642 x1, y1 = src
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643 x2, y2 = dst
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644 shrink_source = 0 # space from source to tail
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645 shrink_target = 0 # space from head to target
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646 if np.iterable(node_size): # many node sizes
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647 src_node, dst_node = edgelist[i][:2]
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648 index_node = nodelist.index(dst_node)
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649 marker_size = node_size[index_node]
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650 shrink_target = to_marker_edge(marker_size, node_shape)
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651 else:
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652 shrink_target = to_marker_edge(node_size, node_shape)
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653
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654 if shrink_source < min_source_margin:
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655 shrink_source = min_source_margin
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656
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657 if shrink_target < min_target_margin:
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658 shrink_target = min_target_margin
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659
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660 if len(arrow_colors) == len(edge_pos):
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661 arrow_color = arrow_colors[i]
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662 elif len(arrow_colors) == 1:
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663 arrow_color = arrow_colors[0]
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664 else: # Cycle through colors
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665 arrow_color = arrow_colors[i % len(arrow_colors)]
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666
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667 if np.iterable(width):
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668 if len(width) == len(edge_pos):
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669 line_width = width[i]
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670 else:
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671 line_width = width[i % len(width)]
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672 else:
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673 line_width = width
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674
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675 arrow = FancyArrowPatch((x1, y1), (x2, y2),
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676 arrowstyle=arrowstyle,
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677 shrinkA=shrink_source,
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678 shrinkB=shrink_target,
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679 mutation_scale=mutation_scale,
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680 color=arrow_color,
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681 linewidth=line_width,
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682 connectionstyle=connectionstyle,
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683 zorder=1) # arrows go behind nodes
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684
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685 # There seems to be a bug in matplotlib to make collections of
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686 # FancyArrowPatch instances. Until fixed, the patches are added
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687 # individually to the axes instance.
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688 arrow_collection.append(arrow)
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689 ax.add_patch(arrow)
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690
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691 # update view
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692 minx = np.amin(np.ravel(edge_pos[:, :, 0]))
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693 maxx = np.amax(np.ravel(edge_pos[:, :, 0]))
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diff changeset
694 miny = np.amin(np.ravel(edge_pos[:, :, 1]))
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diff changeset
695 maxy = np.amax(np.ravel(edge_pos[:, :, 1]))
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696
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697 w = maxx - minx
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698 h = maxy - miny
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699 padx, pady = 0.05 * w, 0.05 * h
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700 corners = (minx - padx, miny - pady), (maxx + padx, maxy + pady)
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diff changeset
701 ax.update_datalim(corners)
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702 ax.autoscale_view()
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703
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704 ax.tick_params(
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705 axis='both',
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706 which='both',
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707 bottom=False,
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708 left=False,
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709 labelbottom=False,
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710 labelleft=False)
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711
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712 return arrow_collection
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diff changeset
713
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714
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715 def draw_networkx_labels(G, pos,
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716 labels=None,
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717 font_size=12,
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718 font_color='k',
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diff changeset
719 font_family='sans-serif',
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diff changeset
720 font_weight='normal',
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721 alpha=None,
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722 bbox=None,
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723 ax=None,
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724 **kwds):
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725 """Draw node labels on the graph G.
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726
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727 Parameters
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728 ----------
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729 G : graph
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diff changeset
730 A networkx graph
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731
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732 pos : dictionary
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diff changeset
733 A dictionary with nodes as keys and positions as values.
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diff changeset
734 Positions should be sequences of length 2.
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735
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736 labels : dictionary, optional (default=None)
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737 Node labels in a dictionary keyed by node of text labels
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738 Node-keys in labels should appear as keys in `pos`.
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739 If needed use: `{n:lab for n,lab in labels.items() if n in pos}`
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740
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741 font_size : int
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742 Font size for text labels (default=12)
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diff changeset
743
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744 font_color : string
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745 Font color string (default='k' black)
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diff changeset
746
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747 font_family : string
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diff changeset
748 Font family (default='sans-serif')
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diff changeset
749
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750 font_weight : string
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751 Font weight (default='normal')
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752
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753 alpha : float or None
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754 The text transparency (default=None)
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755
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756 ax : Matplotlib Axes object, optional
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757 Draw the graph in the specified Matplotlib axes.
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758
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759 Returns
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760 -------
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761 dict
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762 `dict` of labels keyed on the nodes
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763
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764 Examples
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765 --------
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766 >>> G = nx.dodecahedral_graph()
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767 >>> labels = nx.draw_networkx_labels(G, pos=nx.spring_layout(G))
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768
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769 Also see the NetworkX drawing examples at
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770 https://networkx.github.io/documentation/latest/auto_examples/index.html
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diff changeset
771
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772 See Also
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773 --------
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774 draw()
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775 draw_networkx()
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776 draw_networkx_nodes()
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777 draw_networkx_edges()
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778 draw_networkx_edge_labels()
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779 """
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780 try:
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781 import matplotlib.pyplot as plt
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782 except ImportError:
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diff changeset
783 raise ImportError("Matplotlib required for draw()")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
784 except RuntimeError:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
785 print("Matplotlib unable to open display")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
786 raise
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
787
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
788 if ax is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
789 ax = plt.gca()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
790
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
791 if labels is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
792 labels = dict((n, n) for n in G.nodes())
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
793
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
794 # set optional alignment
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
795 horizontalalignment = kwds.get('horizontalalignment', 'center')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
796 verticalalignment = kwds.get('verticalalignment', 'center')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
797
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
798 text_items = {} # there is no text collection so we'll fake one
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
799 for n, label in labels.items():
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
800 (x, y) = pos[n]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
801 if not is_string_like(label):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
802 label = str(label) # this makes "1" and 1 labeled the same
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
803 t = ax.text(x, y,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
804 label,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
805 size=font_size,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
806 color=font_color,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
807 family=font_family,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
808 weight=font_weight,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
809 alpha=alpha,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
810 horizontalalignment=horizontalalignment,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
811 verticalalignment=verticalalignment,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
812 transform=ax.transData,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
813 bbox=bbox,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
814 clip_on=True,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
815 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
816 text_items[n] = t
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
817
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parents:
diff changeset
818 ax.tick_params(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
819 axis='both',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
820 which='both',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
821 bottom=False,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
822 left=False,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
823 labelbottom=False,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
824 labelleft=False)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
825
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
826 return text_items
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
827
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
828
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
829 def draw_networkx_edge_labels(G, pos,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
830 edge_labels=None,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
831 label_pos=0.5,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
832 font_size=10,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
833 font_color='k',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
834 font_family='sans-serif',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
835 font_weight='normal',
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parents:
diff changeset
836 alpha=None,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
837 bbox=None,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
838 ax=None,
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guerler
parents:
diff changeset
839 rotate=True,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
840 **kwds):
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guerler
parents:
diff changeset
841 """Draw edge labels.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
842
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
843 Parameters
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
844 ----------
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
845 G : graph
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
846 A networkx graph
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
847
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
848 pos : dictionary
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
849 A dictionary with nodes as keys and positions as values.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
850 Positions should be sequences of length 2.
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guerler
parents:
diff changeset
851
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guerler
parents:
diff changeset
852 ax : Matplotlib Axes object, optional
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
853 Draw the graph in the specified Matplotlib axes.
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guerler
parents:
diff changeset
854
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parents:
diff changeset
855 alpha : float or None
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
856 The text transparency (default=None)
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parents:
diff changeset
857
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guerler
parents:
diff changeset
858 edge_labels : dictionary
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guerler
parents:
diff changeset
859 Edge labels in a dictionary keyed by edge two-tuple of text
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
860 labels (default=None). Only labels for the keys in the dictionary
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
861 are drawn.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
862
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
863 label_pos : float
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
864 Position of edge label along edge (0=head, 0.5=center, 1=tail)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
865
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
866 font_size : int
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
867 Font size for text labels (default=12)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
868
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
869 font_color : string
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
870 Font color string (default='k' black)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
871
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
872 font_weight : string
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
873 Font weight (default='normal')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
874
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
875 font_family : string
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
876 Font family (default='sans-serif')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
877
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
878 bbox : Matplotlib bbox
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
879 Specify text box shape and colors.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
880
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
881 clip_on : bool
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
882 Turn on clipping at axis boundaries (default=True)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
883
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
884 Returns
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
885 -------
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
886 dict
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
887 `dict` of labels keyed on the edges
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
888
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
889 Examples
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
890 --------
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
891 >>> G = nx.dodecahedral_graph()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
892 >>> edge_labels = nx.draw_networkx_edge_labels(G, pos=nx.spring_layout(G))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
893
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
894 Also see the NetworkX drawing examples at
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
895 https://networkx.github.io/documentation/latest/auto_examples/index.html
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
896
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
897 See Also
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
898 --------
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
899 draw()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
900 draw_networkx()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
901 draw_networkx_nodes()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
902 draw_networkx_edges()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
903 draw_networkx_labels()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
904 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
905 try:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
906 import matplotlib.pyplot as plt
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
907 import numpy as np
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
908 except ImportError:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
909 raise ImportError("Matplotlib required for draw()")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
910 except RuntimeError:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
911 print("Matplotlib unable to open display")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
912 raise
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
913
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
914 if ax is None:
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guerler
parents:
diff changeset
915 ax = plt.gca()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
916 if edge_labels is None:
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guerler
parents:
diff changeset
917 labels = {(u, v): d for u, v, d in G.edges(data=True)}
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
918 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
919 labels = edge_labels
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
920 text_items = {}
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
921 for (n1, n2), label in labels.items():
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
922 (x1, y1) = pos[n1]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
923 (x2, y2) = pos[n2]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
924 (x, y) = (x1 * label_pos + x2 * (1.0 - label_pos),
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
925 y1 * label_pos + y2 * (1.0 - label_pos))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
926
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
927 if rotate:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
928 # in degrees
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
929 angle = np.arctan2(y2 - y1, x2 - x1) / (2.0 * np.pi) * 360
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
930 # make label orientation "right-side-up"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
931 if angle > 90:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
932 angle -= 180
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
933 if angle < - 90:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
934 angle += 180
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
935 # transform data coordinate angle to screen coordinate angle
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
936 xy = np.array((x, y))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
937 trans_angle = ax.transData.transform_angles(np.array((angle,)),
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
938 xy.reshape((1, 2)))[0]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
939 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
940 trans_angle = 0.0
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
941 # use default box of white with white border
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
942 if bbox is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
943 bbox = dict(boxstyle='round',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
944 ec=(1.0, 1.0, 1.0),
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
945 fc=(1.0, 1.0, 1.0),
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
946 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
947 if not is_string_like(label):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
948 label = str(label) # this makes "1" and 1 labeled the same
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
949
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
950 # set optional alignment
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
951 horizontalalignment = kwds.get('horizontalalignment', 'center')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
952 verticalalignment = kwds.get('verticalalignment', 'center')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
953
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
954 t = ax.text(x, y,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
955 label,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
956 size=font_size,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
957 color=font_color,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
958 family=font_family,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
959 weight=font_weight,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
960 alpha=alpha,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
961 horizontalalignment=horizontalalignment,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
962 verticalalignment=verticalalignment,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
963 rotation=trans_angle,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
964 transform=ax.transData,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
965 bbox=bbox,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
966 zorder=1,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
967 clip_on=True,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
968 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
969 text_items[(n1, n2)] = t
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
970
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
971 ax.tick_params(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
972 axis='both',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
973 which='both',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
974 bottom=False,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
975 left=False,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
976 labelbottom=False,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
977 labelleft=False)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
978
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
979 return text_items
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
980
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
981
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
982 def draw_circular(G, **kwargs):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
983 """Draw the graph G with a circular layout.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
984
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
985 Parameters
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
986 ----------
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
987 G : graph
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
988 A networkx graph
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
989
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
990 kwargs : optional keywords
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
991 See networkx.draw_networkx() for a description of optional keywords,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
992 with the exception of the pos parameter which is not used by this
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
993 function.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
994 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
995 draw(G, circular_layout(G), **kwargs)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
996
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
997
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
998 def draw_kamada_kawai(G, **kwargs):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
999 """Draw the graph G with a Kamada-Kawai force-directed layout.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1000
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1001 Parameters
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1002 ----------
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1003 G : graph
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1004 A networkx graph
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1005
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1006 kwargs : optional keywords
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1007 See networkx.draw_networkx() for a description of optional keywords,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1008 with the exception of the pos parameter which is not used by this
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1009 function.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1010 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1011 draw(G, kamada_kawai_layout(G), **kwargs)
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guerler
parents:
diff changeset
1012
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guerler
parents:
diff changeset
1013
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guerler
parents:
diff changeset
1014 def draw_random(G, **kwargs):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1015 """Draw the graph G with a random layout.
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guerler
parents:
diff changeset
1016
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guerler
parents:
diff changeset
1017 Parameters
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1018 ----------
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1019 G : graph
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1020 A networkx graph
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1021
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1022 kwargs : optional keywords
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1023 See networkx.draw_networkx() for a description of optional keywords,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1024 with the exception of the pos parameter which is not used by this
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1025 function.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1026 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1027 draw(G, random_layout(G), **kwargs)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1028
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1029
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guerler
parents:
diff changeset
1030 def draw_spectral(G, **kwargs):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1031 """Draw the graph G with a spectral 2D layout.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1032
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1033 Using the unnormalized Laplacion, the layout shows possible clusters of
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1034 nodes which are an approximation of the ratio cut. The positions are the
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1035 entries of the second and third eigenvectors corresponding to the
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1036 ascending eigenvalues starting from the second one.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1037
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1038 Parameters
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1039 ----------
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1040 G : graph
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1041 A networkx graph
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1042
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1043 kwargs : optional keywords
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1044 See networkx.draw_networkx() for a description of optional keywords,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1045 with the exception of the pos parameter which is not used by this
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1046 function.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1047 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1048 draw(G, spectral_layout(G), **kwargs)
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1049
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diff changeset
1050
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diff changeset
1051 def draw_spring(G, **kwargs):
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diff changeset
1052 """Draw the graph G with a spring layout.
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diff changeset
1053
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diff changeset
1054 Parameters
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diff changeset
1055 ----------
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diff changeset
1056 G : graph
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diff changeset
1057 A networkx graph
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diff changeset
1058
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diff changeset
1059 kwargs : optional keywords
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diff changeset
1060 See networkx.draw_networkx() for a description of optional keywords,
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diff changeset
1061 with the exception of the pos parameter which is not used by this
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diff changeset
1062 function.
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diff changeset
1063 """
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diff changeset
1064 draw(G, spring_layout(G), **kwargs)
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diff changeset
1065
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diff changeset
1066
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diff changeset
1067 def draw_shell(G, **kwargs):
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diff changeset
1068 """Draw networkx graph with shell layout.
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diff changeset
1069
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1070 Parameters
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1071 ----------
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diff changeset
1072 G : graph
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diff changeset
1073 A networkx graph
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1074
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diff changeset
1075 kwargs : optional keywords
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diff changeset
1076 See networkx.draw_networkx() for a description of optional keywords,
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1077 with the exception of the pos parameter which is not used by this
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diff changeset
1078 function.
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1079 """
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1080 nlist = kwargs.get('nlist', None)
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1081 if nlist is not None:
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diff changeset
1082 del(kwargs['nlist'])
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diff changeset
1083 draw(G, shell_layout(G, nlist=nlist), **kwargs)
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diff changeset
1084
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diff changeset
1085
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diff changeset
1086 def draw_planar(G, **kwargs):
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diff changeset
1087 """Draw a planar networkx graph with planar layout.
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1088
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diff changeset
1089 Parameters
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diff changeset
1090 ----------
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diff changeset
1091 G : graph
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diff changeset
1092 A planar networkx graph
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diff changeset
1093
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diff changeset
1094 kwargs : optional keywords
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diff changeset
1095 See networkx.draw_networkx() for a description of optional keywords,
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1096 with the exception of the pos parameter which is not used by this
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diff changeset
1097 function.
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1098 """
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diff changeset
1099 draw(G, planar_layout(G), **kwargs)
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1100
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1101
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1102 def apply_alpha(colors, alpha, elem_list, cmap=None, vmin=None, vmax=None):
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1103 """Apply an alpha (or list of alphas) to the colors provided.
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diff changeset
1104
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diff changeset
1105 Parameters
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diff changeset
1106 ----------
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diff changeset
1107
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diff changeset
1108 colors : color string, or array of floats
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diff changeset
1109 Color of element. Can be a single color format string (default='r'),
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diff changeset
1110 or a sequence of colors with the same length as nodelist.
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1111 If numeric values are specified they will be mapped to
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1112 colors using the cmap and vmin,vmax parameters. See
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diff changeset
1113 matplotlib.scatter for more details.
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diff changeset
1114
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1115 alpha : float or array of floats
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1116 Alpha values for elements. This can be a single alpha value, in
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1117 which case it will be applied to all the elements of color. Otherwise,
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diff changeset
1118 if it is an array, the elements of alpha will be applied to the colors
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diff changeset
1119 in order (cycling through alpha multiple times if necessary).
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1120
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1121 elem_list : array of networkx objects
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1122 The list of elements which are being colored. These could be nodes,
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diff changeset
1123 edges or labels.
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1124
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1125 cmap : matplotlib colormap
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diff changeset
1126 Color map for use if colors is a list of floats corresponding to points
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diff changeset
1127 on a color mapping.
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diff changeset
1128
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1129 vmin, vmax : float
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diff changeset
1130 Minimum and maximum values for normalizing colors if a color mapping is
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diff changeset
1131 used.
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diff changeset
1132
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1133 Returns
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1134 -------
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1135
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1136 rgba_colors : numpy ndarray
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diff changeset
1137 Array containing RGBA format values for each of the node colours.
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diff changeset
1138
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1139 """
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1140 from itertools import islice, cycle
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diff changeset
1141
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diff changeset
1142 try:
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diff changeset
1143 import numpy as np
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diff changeset
1144 from matplotlib.colors import colorConverter
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diff changeset
1145 import matplotlib.cm as cm
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diff changeset
1146 except ImportError:
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1147 raise ImportError("Matplotlib required for draw()")
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1148
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1149 # If we have been provided with a list of numbers as long as elem_list,
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1150 # apply the color mapping.
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1151 if len(colors) == len(elem_list) and isinstance(colors[0], Number):
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diff changeset
1152 mapper = cm.ScalarMappable(cmap=cmap)
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diff changeset
1153 mapper.set_clim(vmin, vmax)
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diff changeset
1154 rgba_colors = mapper.to_rgba(colors)
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diff changeset
1155 # Otherwise, convert colors to matplotlib's RGB using the colorConverter
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diff changeset
1156 # object. These are converted to numpy ndarrays to be consistent with the
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diff changeset
1157 # to_rgba method of ScalarMappable.
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1158 else:
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1159 try:
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1160 rgba_colors = np.array([colorConverter.to_rgba(colors)])
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1161 except ValueError:
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1162 rgba_colors = np.array([colorConverter.to_rgba(color)
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1163 for color in colors])
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1164 # Set the final column of the rgba_colors to have the relevant alpha values
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1165 try:
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1166 # If alpha is longer than the number of colors, resize to the number of
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diff changeset
1167 # elements. Also, if rgba_colors.size (the number of elements of
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1168 # rgba_colors) is the same as the number of elements, resize the array,
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1169 # to avoid it being interpreted as a colormap by scatter()
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1170 if len(alpha) > len(rgba_colors) or rgba_colors.size == len(elem_list):
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diff changeset
1171 rgba_colors = np.resize(rgba_colors, (len(elem_list), 4))
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1172 rgba_colors[1:, 0] = rgba_colors[0, 0]
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1173 rgba_colors[1:, 1] = rgba_colors[0, 1]
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1174 rgba_colors[1:, 2] = rgba_colors[0, 2]
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1175 rgba_colors[:, 3] = list(islice(cycle(alpha), len(rgba_colors)))
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1176 except TypeError:
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1177 rgba_colors[:, -1] = alpha
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1178 return rgba_colors
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1179
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1180
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1181 # fixture for pytest
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1182 def setup_module(module):
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1183 import pytest
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1184 mpl = pytest.importorskip('matplotlib')
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1185 mpl.use('PS', warn=False)
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1186 plt = pytest.importorskip('matplotlib.pyplot')