Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/networkx/drawing/nx_pylab.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """ |
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2 ********** |
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3 Matplotlib |
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4 ********** |
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5 |
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6 Draw networks with matplotlib. |
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7 |
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8 See Also |
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9 -------- |
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10 |
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11 matplotlib: http://matplotlib.org/ |
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12 |
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13 pygraphviz: http://pygraphviz.github.io/ |
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14 |
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15 """ |
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16 from numbers import Number |
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17 import networkx as nx |
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18 from networkx.drawing.layout import ( |
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19 shell_layout, |
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20 circular_layout, |
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21 kamada_kawai_layout, |
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22 spectral_layout, |
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23 spring_layout, |
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24 random_layout, |
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25 planar_layout, |
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26 ) |
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27 |
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28 __all__ = [ |
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29 "draw", |
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30 "draw_networkx", |
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31 "draw_networkx_nodes", |
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32 "draw_networkx_edges", |
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33 "draw_networkx_labels", |
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34 "draw_networkx_edge_labels", |
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35 "draw_circular", |
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36 "draw_kamada_kawai", |
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37 "draw_random", |
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38 "draw_spectral", |
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39 "draw_spring", |
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40 "draw_planar", |
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41 "draw_shell", |
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42 ] |
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43 |
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44 |
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45 def draw(G, pos=None, ax=None, **kwds): |
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46 """Draw the graph G with Matplotlib. |
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47 |
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48 Draw the graph as a simple representation with no node |
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49 labels or edge labels and using the full Matplotlib figure area |
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50 and no axis labels by default. See draw_networkx() for more |
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51 full-featured drawing that allows title, axis labels etc. |
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52 |
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53 Parameters |
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54 ---------- |
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55 G : graph |
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56 A networkx graph |
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57 |
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58 pos : dictionary, optional |
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59 A dictionary with nodes as keys and positions as values. |
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60 If not specified a spring layout positioning will be computed. |
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61 See :py:mod:`networkx.drawing.layout` for functions that |
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62 compute node positions. |
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63 |
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64 ax : Matplotlib Axes object, optional |
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65 Draw the graph in specified Matplotlib axes. |
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66 |
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67 kwds : optional keywords |
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68 See networkx.draw_networkx() for a description of optional keywords. |
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69 |
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70 Examples |
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71 -------- |
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72 >>> G = nx.dodecahedral_graph() |
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73 >>> nx.draw(G) |
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74 >>> nx.draw(G, pos=nx.spring_layout(G)) # use spring layout |
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75 |
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76 See Also |
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77 -------- |
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78 draw_networkx() |
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79 draw_networkx_nodes() |
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80 draw_networkx_edges() |
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81 draw_networkx_labels() |
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82 draw_networkx_edge_labels() |
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83 |
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84 Notes |
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85 ----- |
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86 This function has the same name as pylab.draw and pyplot.draw |
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87 so beware when using `from networkx import *` |
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88 |
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89 since you might overwrite the pylab.draw function. |
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90 |
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91 With pyplot use |
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92 |
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93 >>> import matplotlib.pyplot as plt |
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94 >>> G = nx.dodecahedral_graph() |
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95 >>> nx.draw(G) # networkx draw() |
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96 >>> plt.draw() # pyplot draw() |
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97 |
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98 Also see the NetworkX drawing examples at |
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99 https://networkx.github.io/documentation/latest/auto_examples/index.html |
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100 """ |
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101 try: |
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102 import matplotlib.pyplot as plt |
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103 except ImportError as e: |
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104 raise ImportError("Matplotlib required for draw()") from e |
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105 except RuntimeError: |
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106 print("Matplotlib unable to open display") |
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107 raise |
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108 |
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109 if ax is None: |
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110 cf = plt.gcf() |
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111 else: |
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112 cf = ax.get_figure() |
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113 cf.set_facecolor("w") |
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114 if ax is None: |
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115 if cf._axstack() is None: |
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116 ax = cf.add_axes((0, 0, 1, 1)) |
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117 else: |
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118 ax = cf.gca() |
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119 |
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120 if "with_labels" not in kwds: |
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121 kwds["with_labels"] = "labels" in kwds |
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122 |
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123 draw_networkx(G, pos=pos, ax=ax, **kwds) |
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124 ax.set_axis_off() |
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125 plt.draw_if_interactive() |
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126 return |
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127 |
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128 |
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129 def draw_networkx(G, pos=None, arrows=True, with_labels=True, **kwds): |
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130 """Draw the graph G using Matplotlib. |
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131 |
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132 Draw the graph with Matplotlib with options for node positions, |
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133 labeling, titles, and many other drawing features. |
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134 See draw() for simple drawing without labels or axes. |
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135 |
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136 Parameters |
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137 ---------- |
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138 G : graph |
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139 A networkx graph |
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140 |
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141 pos : dictionary, optional |
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142 A dictionary with nodes as keys and positions as values. |
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143 If not specified a spring layout positioning will be computed. |
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144 See :py:mod:`networkx.drawing.layout` for functions that |
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145 compute node positions. |
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146 |
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147 arrows : bool, optional (default=True) |
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148 For directed graphs, if True draw arrowheads. |
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149 Note: Arrows will be the same color as edges. |
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150 |
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151 arrowstyle : str, optional (default='-|>') |
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152 For directed graphs, choose the style of the arrowsheads. |
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153 See :py:class: `matplotlib.patches.ArrowStyle` for more |
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154 options. |
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155 |
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156 arrowsize : int, optional (default=10) |
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157 For directed graphs, choose the size of the arrow head head's length and |
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158 width. See :py:class: `matplotlib.patches.FancyArrowPatch` for attribute |
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159 `mutation_scale` for more info. |
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160 |
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161 with_labels : bool, optional (default=True) |
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162 Set to True to draw labels on the nodes. |
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163 |
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164 ax : Matplotlib Axes object, optional |
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165 Draw the graph in the specified Matplotlib axes. |
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166 |
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167 nodelist : list, optional (default G.nodes()) |
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168 Draw only specified nodes |
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169 |
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170 edgelist : list, optional (default=G.edges()) |
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171 Draw only specified edges |
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172 |
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173 node_size : scalar or array, optional (default=300) |
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174 Size of nodes. If an array is specified it must be the |
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175 same length as nodelist. |
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176 |
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177 node_color : color or array of colors (default='#1f78b4') |
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178 Node color. Can be a single color or a sequence of colors with the same |
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179 length as nodelist. Color can be string, or rgb (or rgba) tuple of |
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180 floats from 0-1. If numeric values are specified they will be |
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181 mapped to colors using the cmap and vmin,vmax parameters. See |
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182 matplotlib.scatter for more details. |
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183 |
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184 node_shape : string, optional (default='o') |
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185 The shape of the node. Specification is as matplotlib.scatter |
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186 marker, one of 'so^>v<dph8'. |
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187 |
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188 alpha : float, optional (default=None) |
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189 The node and edge transparency |
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190 |
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191 cmap : Matplotlib colormap, optional (default=None) |
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192 Colormap for mapping intensities of nodes |
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193 |
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194 vmin,vmax : float, optional (default=None) |
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195 Minimum and maximum for node colormap scaling |
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196 |
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197 linewidths : [None | scalar | sequence] |
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198 Line width of symbol border (default =1.0) |
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199 |
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200 width : float, optional (default=1.0) |
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201 Line width of edges |
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202 |
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203 edge_color : color or array of colors (default='k') |
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204 Edge color. Can be a single color or a sequence of colors with the same |
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205 length as edgelist. Color can be string, or rgb (or rgba) tuple of |
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206 floats from 0-1. If numeric values are specified they will be |
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207 mapped to colors using the edge_cmap and edge_vmin,edge_vmax parameters. |
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208 |
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209 edge_cmap : Matplotlib colormap, optional (default=None) |
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210 Colormap for mapping intensities of edges |
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211 |
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212 edge_vmin,edge_vmax : floats, optional (default=None) |
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213 Minimum and maximum for edge colormap scaling |
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214 |
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215 style : string, optional (default='solid') |
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216 Edge line style (solid|dashed|dotted,dashdot) |
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217 |
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218 labels : dictionary, optional (default=None) |
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219 Node labels in a dictionary keyed by node of text labels |
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220 |
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221 font_size : int, optional (default=12) |
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222 Font size for text labels |
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223 |
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224 font_color : string, optional (default='k' black) |
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225 Font color string |
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226 |
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227 font_weight : string, optional (default='normal') |
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228 Font weight |
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229 |
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230 font_family : string, optional (default='sans-serif') |
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231 Font family |
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232 |
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233 label : string, optional |
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234 Label for graph legend |
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235 |
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236 kwds : optional keywords |
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237 See networkx.draw_networkx_nodes(), networkx.draw_networkx_edges(), and |
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238 networkx.draw_networkx_labels() for a description of optional keywords. |
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239 |
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240 Notes |
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241 ----- |
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242 For directed graphs, arrows are drawn at the head end. Arrows can be |
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243 turned off with keyword arrows=False. |
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244 |
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245 Examples |
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246 -------- |
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247 >>> G = nx.dodecahedral_graph() |
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248 >>> nx.draw(G) |
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249 >>> nx.draw(G, pos=nx.spring_layout(G)) # use spring layout |
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250 |
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251 >>> import matplotlib.pyplot as plt |
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252 >>> limits = plt.axis("off") # turn of axis |
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253 |
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254 Also see the NetworkX drawing examples at |
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255 https://networkx.github.io/documentation/latest/auto_examples/index.html |
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256 |
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257 See Also |
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258 -------- |
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259 draw() |
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260 draw_networkx_nodes() |
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261 draw_networkx_edges() |
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262 draw_networkx_labels() |
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263 draw_networkx_edge_labels() |
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264 """ |
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265 try: |
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266 import matplotlib.pyplot as plt |
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267 except ImportError as e: |
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268 raise ImportError("Matplotlib required for draw()") from e |
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269 except RuntimeError: |
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270 print("Matplotlib unable to open display") |
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271 raise |
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272 |
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273 valid_node_kwds = ( |
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274 "nodelist", |
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275 "node_size", |
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276 "node_color", |
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277 "node_shape", |
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278 "alpha", |
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279 "cmap", |
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280 "vmin", |
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281 "vmax", |
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282 "ax", |
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283 "linewidths", |
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284 "edgecolors", |
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285 "label", |
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286 ) |
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287 |
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288 valid_edge_kwds = ( |
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289 "edgelist", |
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290 "width", |
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291 "edge_color", |
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292 "style", |
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293 "alpha", |
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294 "arrowstyle", |
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295 "arrowsize", |
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296 "edge_cmap", |
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297 "edge_vmin", |
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298 "edge_vmax", |
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299 "ax", |
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300 "label", |
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301 "node_size", |
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302 "nodelist", |
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303 "node_shape", |
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304 "connectionstyle", |
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305 "min_source_margin", |
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306 "min_target_margin", |
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307 ) |
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308 |
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309 valid_label_kwds = ( |
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310 "labels", |
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311 "font_size", |
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312 "font_color", |
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313 "font_family", |
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314 "font_weight", |
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315 "alpha", |
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316 "bbox", |
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317 "ax", |
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318 "horizontalalignment", |
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319 "verticalalignment", |
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320 ) |
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321 |
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322 valid_kwds = valid_node_kwds + valid_edge_kwds + valid_label_kwds |
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323 |
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324 if any([k not in valid_kwds for k in kwds]): |
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325 invalid_args = ", ".join([k for k in kwds if k not in valid_kwds]) |
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326 raise ValueError(f"Received invalid argument(s): {invalid_args}") |
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327 |
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328 node_kwds = {k: v for k, v in kwds.items() if k in valid_node_kwds} |
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329 edge_kwds = {k: v for k, v in kwds.items() if k in valid_edge_kwds} |
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330 label_kwds = {k: v for k, v in kwds.items() if k in valid_label_kwds} |
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331 |
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332 if pos is None: |
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333 pos = nx.drawing.spring_layout(G) # default to spring layout |
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334 |
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335 draw_networkx_nodes(G, pos, **node_kwds) |
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336 draw_networkx_edges(G, pos, arrows=arrows, **edge_kwds) |
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337 if with_labels: |
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338 draw_networkx_labels(G, pos, **label_kwds) |
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339 plt.draw_if_interactive() |
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340 |
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341 |
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342 def draw_networkx_nodes( |
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343 G, |
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344 pos, |
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345 nodelist=None, |
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346 node_size=300, |
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347 node_color="#1f78b4", |
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348 node_shape="o", |
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349 alpha=None, |
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350 cmap=None, |
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351 vmin=None, |
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352 vmax=None, |
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353 ax=None, |
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354 linewidths=None, |
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355 edgecolors=None, |
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356 label=None, |
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357 ): |
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358 """Draw the nodes of the graph G. |
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359 |
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360 This draws only the nodes of the graph G. |
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361 |
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362 Parameters |
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363 ---------- |
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364 G : graph |
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365 A networkx graph |
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366 |
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367 pos : dictionary |
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368 A dictionary with nodes as keys and positions as values. |
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369 Positions should be sequences of length 2. |
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370 |
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371 ax : Matplotlib Axes object, optional |
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372 Draw the graph in the specified Matplotlib axes. |
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373 |
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374 nodelist : list, optional |
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375 Draw only specified nodes (default G.nodes()) |
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376 |
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377 node_size : scalar or array |
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378 Size of nodes (default=300). If an array is specified it must be the |
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379 same length as nodelist. |
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380 |
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381 node_color : color or array of colors (default='#1f78b4') |
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382 Node color. Can be a single color or a sequence of colors with the same |
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383 length as nodelist. Color can be string, or rgb (or rgba) tuple of |
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384 floats from 0-1. If numeric values are specified they will be |
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385 mapped to colors using the cmap and vmin,vmax parameters. See |
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386 matplotlib.scatter for more details. |
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387 |
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388 node_shape : string |
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389 The shape of the node. Specification is as matplotlib.scatter |
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390 marker, one of 'so^>v<dph8' (default='o'). |
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391 |
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392 alpha : float or array of floats |
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393 The node transparency. This can be a single alpha value (default=None), |
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394 in which case it will be applied to all the nodes of color. Otherwise, |
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395 if it is an array, the elements of alpha will be applied to the colors |
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396 in order (cycling through alpha multiple times if necessary). |
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397 |
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398 cmap : Matplotlib colormap |
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399 Colormap for mapping intensities of nodes (default=None) |
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400 |
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401 vmin,vmax : floats |
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402 Minimum and maximum for node colormap scaling (default=None) |
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403 |
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404 linewidths : [None | scalar | sequence] |
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405 Line width of symbol border (default =1.0) |
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406 |
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407 edgecolors : [None | scalar | sequence] |
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408 Colors of node borders (default = node_color) |
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409 |
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410 label : [None| string] |
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411 Label for legend |
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412 |
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413 Returns |
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414 ------- |
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415 matplotlib.collections.PathCollection |
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416 `PathCollection` of the nodes. |
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417 |
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418 Examples |
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419 -------- |
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420 >>> G = nx.dodecahedral_graph() |
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421 >>> nodes = nx.draw_networkx_nodes(G, pos=nx.spring_layout(G)) |
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422 |
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423 Also see the NetworkX drawing examples at |
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424 https://networkx.github.io/documentation/latest/auto_examples/index.html |
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425 |
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426 See Also |
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427 -------- |
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428 draw() |
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429 draw_networkx() |
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430 draw_networkx_edges() |
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431 draw_networkx_labels() |
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432 draw_networkx_edge_labels() |
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433 """ |
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434 from collections.abc import Iterable |
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435 |
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436 try: |
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437 import matplotlib.pyplot as plt |
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438 from matplotlib.collections import PathCollection |
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439 import numpy as np |
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440 except ImportError as e: |
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441 raise ImportError("Matplotlib required for draw()") from e |
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442 except RuntimeError: |
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443 print("Matplotlib unable to open display") |
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444 raise |
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445 |
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446 if ax is None: |
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447 ax = plt.gca() |
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448 |
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449 if nodelist is None: |
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450 nodelist = list(G) |
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451 |
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452 if len(nodelist) == 0: # empty nodelist, no drawing |
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453 return PathCollection(None) |
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454 |
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455 try: |
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456 xy = np.asarray([pos[v] for v in nodelist]) |
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457 except KeyError as e: |
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458 raise nx.NetworkXError(f"Node {e} has no position.") from e |
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459 except ValueError as e: |
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460 raise nx.NetworkXError("Bad value in node positions.") from e |
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461 |
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462 if isinstance(alpha, Iterable): |
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463 node_color = apply_alpha(node_color, alpha, nodelist, cmap, vmin, vmax) |
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464 alpha = None |
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465 |
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466 node_collection = ax.scatter( |
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467 xy[:, 0], |
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468 xy[:, 1], |
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469 s=node_size, |
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470 c=node_color, |
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471 marker=node_shape, |
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472 cmap=cmap, |
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473 vmin=vmin, |
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474 vmax=vmax, |
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475 alpha=alpha, |
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476 linewidths=linewidths, |
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477 edgecolors=edgecolors, |
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478 label=label, |
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479 ) |
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480 ax.tick_params( |
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481 axis="both", |
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482 which="both", |
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483 bottom=False, |
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484 left=False, |
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485 labelbottom=False, |
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486 labelleft=False, |
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487 ) |
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488 |
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489 node_collection.set_zorder(2) |
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490 return node_collection |
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491 |
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492 |
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493 def draw_networkx_edges( |
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494 G, |
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495 pos, |
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496 edgelist=None, |
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497 width=1.0, |
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498 edge_color="k", |
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499 style="solid", |
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500 alpha=None, |
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501 arrowstyle="-|>", |
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502 arrowsize=10, |
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503 edge_cmap=None, |
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504 edge_vmin=None, |
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505 edge_vmax=None, |
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506 ax=None, |
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507 arrows=True, |
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508 label=None, |
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509 node_size=300, |
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510 nodelist=None, |
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511 node_shape="o", |
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512 connectionstyle=None, |
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513 min_source_margin=0, |
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514 min_target_margin=0, |
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515 ): |
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516 """Draw the edges of the graph G. |
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517 |
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518 This draws only the edges of the graph G. |
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519 |
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520 Parameters |
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521 ---------- |
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522 G : graph |
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523 A networkx graph |
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524 |
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525 pos : dictionary |
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526 A dictionary with nodes as keys and positions as values. |
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527 Positions should be sequences of length 2. |
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528 |
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529 edgelist : collection of edge tuples |
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530 Draw only specified edges(default=G.edges()) |
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531 |
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532 width : float, or array of floats |
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533 Line width of edges (default=1.0) |
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534 |
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535 edge_color : color or array of colors (default='k') |
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536 Edge color. Can be a single color or a sequence of colors with the same |
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537 length as edgelist. Color can be string, or rgb (or rgba) tuple of |
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538 floats from 0-1. If numeric values are specified they will be |
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539 mapped to colors using the edge_cmap and edge_vmin,edge_vmax parameters. |
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540 |
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541 style : string |
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542 Edge line style (default='solid') (solid|dashed|dotted,dashdot) |
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543 |
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544 alpha : float |
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545 The edge transparency (default=None) |
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546 |
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547 edge_ cmap : Matplotlib colormap |
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548 Colormap for mapping intensities of edges (default=None) |
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549 |
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550 edge_vmin,edge_vmax : floats |
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551 Minimum and maximum for edge colormap scaling (default=None) |
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552 |
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553 ax : Matplotlib Axes object, optional |
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554 Draw the graph in the specified Matplotlib axes. |
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555 |
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556 arrows : bool, optional (default=True) |
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557 For directed graphs, if True draw arrowheads. |
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558 Note: Arrows will be the same color as edges. |
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559 |
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560 arrowstyle : str, optional (default='-|>') |
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561 For directed graphs, choose the style of the arrow heads. |
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562 See :py:class: `matplotlib.patches.ArrowStyle` for more |
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563 options. |
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564 |
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565 arrowsize : int, optional (default=10) |
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566 For directed graphs, choose the size of the arrow head head's length and |
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567 width. See :py:class: `matplotlib.patches.FancyArrowPatch` for attribute |
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568 `mutation_scale` for more info. |
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569 |
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570 connectionstyle : str, optional (default=None) |
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571 Pass the connectionstyle parameter to create curved arc of rounding |
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572 radius rad. For example, connectionstyle='arc3,rad=0.2'. |
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573 See :py:class: `matplotlib.patches.ConnectionStyle` and |
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574 :py:class: `matplotlib.patches.FancyArrowPatch` for more info. |
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575 |
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576 label : [None| string] |
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577 Label for legend |
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578 |
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579 min_source_margin : int, optional (default=0) |
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580 The minimum margin (gap) at the begining of the edge at the source. |
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581 |
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582 min_target_margin : int, optional (default=0) |
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583 The minimum margin (gap) at the end of the edge at the target. |
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584 |
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585 Returns |
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586 ------- |
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587 matplotlib.collection.LineCollection |
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588 `LineCollection` of the edges |
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589 |
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590 list of matplotlib.patches.FancyArrowPatch |
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591 `FancyArrowPatch` instances of the directed edges |
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592 |
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593 Depending whether the drawing includes arrows or not. |
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594 |
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595 Notes |
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596 ----- |
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597 For directed graphs, arrows are drawn at the head end. Arrows can be |
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598 turned off with keyword arrows=False. Be sure to include `node_size` as a |
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599 keyword argument; arrows are drawn considering the size of nodes. |
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600 |
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601 Examples |
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602 -------- |
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603 >>> G = nx.dodecahedral_graph() |
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604 >>> edges = nx.draw_networkx_edges(G, pos=nx.spring_layout(G)) |
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605 |
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606 >>> G = nx.DiGraph() |
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607 >>> G.add_edges_from([(1, 2), (1, 3), (2, 3)]) |
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608 >>> arcs = nx.draw_networkx_edges(G, pos=nx.spring_layout(G)) |
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609 >>> alphas = [0.3, 0.4, 0.5] |
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610 >>> for i, arc in enumerate(arcs): # change alpha values of arcs |
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611 ... arc.set_alpha(alphas[i]) |
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612 |
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613 Also see the NetworkX drawing examples at |
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614 https://networkx.github.io/documentation/latest/auto_examples/index.html |
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615 |
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616 See Also |
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617 -------- |
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618 draw() |
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619 draw_networkx() |
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620 draw_networkx_nodes() |
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621 draw_networkx_labels() |
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622 draw_networkx_edge_labels() |
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623 """ |
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624 try: |
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625 import matplotlib.pyplot as plt |
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626 from matplotlib.colors import colorConverter, Colormap, Normalize |
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627 from matplotlib.collections import LineCollection |
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628 from matplotlib.patches import FancyArrowPatch |
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629 import numpy as np |
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630 except ImportError as e: |
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631 raise ImportError("Matplotlib required for draw()") from e |
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632 except RuntimeError: |
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633 print("Matplotlib unable to open display") |
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634 raise |
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635 |
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636 if ax is None: |
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637 ax = plt.gca() |
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638 |
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639 if edgelist is None: |
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640 edgelist = list(G.edges()) |
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641 |
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642 if len(edgelist) == 0: # no edges! |
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643 if not G.is_directed() or not arrows: |
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644 return LineCollection(None) |
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645 else: |
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646 return [] |
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647 |
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648 if nodelist is None: |
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649 nodelist = list(G.nodes()) |
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650 |
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651 # FancyArrowPatch handles color=None different from LineCollection |
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652 if edge_color is None: |
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653 edge_color = "k" |
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654 |
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655 # set edge positions |
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656 edge_pos = np.asarray([(pos[e[0]], pos[e[1]]) for e in edgelist]) |
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657 |
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658 # Check if edge_color is an array of floats and map to edge_cmap. |
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659 # This is the only case handled differently from matplotlib |
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660 if ( |
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661 np.iterable(edge_color) |
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662 and (len(edge_color) == len(edge_pos)) |
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663 and np.alltrue([isinstance(c, Number) for c in edge_color]) |
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664 ): |
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665 if edge_cmap is not None: |
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666 assert isinstance(edge_cmap, Colormap) |
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667 else: |
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668 edge_cmap = plt.get_cmap() |
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669 if edge_vmin is None: |
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670 edge_vmin = min(edge_color) |
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671 if edge_vmax is None: |
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672 edge_vmax = max(edge_color) |
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673 color_normal = Normalize(vmin=edge_vmin, vmax=edge_vmax) |
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674 edge_color = [edge_cmap(color_normal(e)) for e in edge_color] |
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675 |
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676 if not G.is_directed() or not arrows: |
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677 edge_collection = LineCollection( |
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678 edge_pos, |
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679 colors=edge_color, |
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680 linewidths=width, |
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681 antialiaseds=(1,), |
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682 linestyle=style, |
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683 transOffset=ax.transData, |
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684 alpha=alpha, |
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685 ) |
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686 |
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687 edge_collection.set_cmap(edge_cmap) |
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688 edge_collection.set_clim(edge_vmin, edge_vmax) |
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|
689 |
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|
690 edge_collection.set_zorder(1) # edges go behind nodes |
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691 edge_collection.set_label(label) |
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|
692 ax.add_collection(edge_collection) |
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|
693 |
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|
694 return edge_collection |
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|
695 |
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696 arrow_collection = None |
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|
697 |
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698 if G.is_directed() and arrows: |
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|
699 # Note: Waiting for someone to implement arrow to intersection with |
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|
700 # marker. Meanwhile, this works well for polygons with more than 4 |
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|
701 # sides and circle. |
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702 |
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|
703 def to_marker_edge(marker_size, marker): |
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704 if marker in "s^>v<d": # `large` markers need extra space |
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705 return np.sqrt(2 * marker_size) / 2 |
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|
706 else: |
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707 return np.sqrt(marker_size) / 2 |
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708 |
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|
709 # Draw arrows with `matplotlib.patches.FancyarrowPatch` |
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710 arrow_collection = [] |
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711 mutation_scale = arrowsize # scale factor of arrow head |
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712 |
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713 # FancyArrowPatch doesn't handle color strings |
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714 arrow_colors = colorConverter.to_rgba_array(edge_color, alpha) |
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|
715 for i, (src, dst) in enumerate(edge_pos): |
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716 x1, y1 = src |
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717 x2, y2 = dst |
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718 shrink_source = 0 # space from source to tail |
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719 shrink_target = 0 # space from head to target |
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720 if np.iterable(node_size): # many node sizes |
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721 source, target = edgelist[i][:2] |
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|
722 source_node_size = node_size[nodelist.index(source)] |
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723 target_node_size = node_size[nodelist.index(target)] |
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724 shrink_source = to_marker_edge(source_node_size, node_shape) |
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725 shrink_target = to_marker_edge(target_node_size, node_shape) |
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726 else: |
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727 shrink_source = shrink_target = to_marker_edge(node_size, node_shape) |
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|
728 |
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|
729 if shrink_source < min_source_margin: |
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730 shrink_source = min_source_margin |
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731 |
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|
732 if shrink_target < min_target_margin: |
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|
733 shrink_target = min_target_margin |
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|
734 |
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|
735 if len(arrow_colors) == len(edge_pos): |
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|
736 arrow_color = arrow_colors[i] |
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737 elif len(arrow_colors) == 1: |
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|
738 arrow_color = arrow_colors[0] |
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739 else: # Cycle through colors |
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shellac
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740 arrow_color = arrow_colors[i % len(arrow_colors)] |
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|
741 |
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|
742 if np.iterable(width): |
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743 if len(width) == len(edge_pos): |
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744 line_width = width[i] |
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745 else: |
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746 line_width = width[i % len(width)] |
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747 else: |
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748 line_width = width |
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|
749 |
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750 arrow = FancyArrowPatch( |
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shellac
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|
751 (x1, y1), |
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shellac
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|
752 (x2, y2), |
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753 arrowstyle=arrowstyle, |
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|
754 shrinkA=shrink_source, |
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|
755 shrinkB=shrink_target, |
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shellac
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|
756 mutation_scale=mutation_scale, |
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shellac
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|
757 color=arrow_color, |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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|
758 linewidth=line_width, |
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parents:
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|
759 connectionstyle=connectionstyle, |
4f3585e2f14b
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shellac
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|
760 linestyle=style, |
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|
761 zorder=1, |
4f3585e2f14b
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shellac
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|
762 ) # arrows go behind nodes |
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shellac
parents:
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|
763 |
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shellac
parents:
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|
764 # There seems to be a bug in matplotlib to make collections of |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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|
765 # FancyArrowPatch instances. Until fixed, the patches are added |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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|
766 # individually to the axes instance. |
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|
767 arrow_collection.append(arrow) |
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shellac
parents:
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|
768 ax.add_patch(arrow) |
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|
769 |
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|
770 # update view |
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771 minx = np.amin(np.ravel(edge_pos[:, :, 0])) |
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|
772 maxx = np.amax(np.ravel(edge_pos[:, :, 0])) |
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shellac
parents:
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773 miny = np.amin(np.ravel(edge_pos[:, :, 1])) |
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shellac
parents:
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|
774 maxy = np.amax(np.ravel(edge_pos[:, :, 1])) |
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|
775 |
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776 w = maxx - minx |
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parents:
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|
777 h = maxy - miny |
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shellac
parents:
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|
778 padx, pady = 0.05 * w, 0.05 * h |
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shellac
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779 corners = (minx - padx, miny - pady), (maxx + padx, maxy + pady) |
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parents:
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|
780 ax.update_datalim(corners) |
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shellac
parents:
diff
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|
781 ax.autoscale_view() |
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shellac
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|
782 |
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shellac
parents:
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|
783 ax.tick_params( |
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|
784 axis="both", |
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|
785 which="both", |
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|
786 bottom=False, |
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shellac
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|
787 left=False, |
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|
788 labelbottom=False, |
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|
789 labelleft=False, |
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|
790 ) |
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|
791 |
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|
792 return arrow_collection |
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|
793 |
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|
794 |
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|
795 def draw_networkx_labels( |
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|
796 G, |
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|
797 pos, |
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798 labels=None, |
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|
799 font_size=12, |
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|
800 font_color="k", |
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parents:
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801 font_family="sans-serif", |
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802 font_weight="normal", |
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803 alpha=None, |
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804 bbox=None, |
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805 horizontalalignment="center", |
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806 verticalalignment="center", |
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807 ax=None, |
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808 ): |
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809 """Draw node labels on the graph G. |
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810 |
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811 Parameters |
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812 ---------- |
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813 G : graph |
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814 A networkx graph |
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815 |
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816 pos : dictionary |
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817 A dictionary with nodes as keys and positions as values. |
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818 Positions should be sequences of length 2. |
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819 |
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820 labels : dictionary, optional (default=None) |
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821 Node labels in a dictionary keyed by node of text labels |
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822 Node-keys in labels should appear as keys in `pos`. |
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823 If needed use: `{n:lab for n,lab in labels.items() if n in pos}` |
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824 |
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825 font_size : int |
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826 Font size for text labels (default=12) |
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827 |
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828 font_color : string |
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829 Font color string (default='k' black) |
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830 |
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831 font_family : string |
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832 Font family (default='sans-serif') |
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833 |
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834 font_weight : string |
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835 Font weight (default='normal') |
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836 |
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837 alpha : float or None |
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838 The text transparency (default=None) |
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839 |
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840 horizontalalignment : {'center', 'right', 'left'} |
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841 Horizontal alignment (default='center') |
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842 |
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843 verticalalignment : {'center', 'top', 'bottom', 'baseline', 'center_baseline'} |
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844 Vertical alignment (default='center') |
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845 |
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846 ax : Matplotlib Axes object, optional |
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847 Draw the graph in the specified Matplotlib axes. |
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848 |
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849 |
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850 Returns |
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851 ------- |
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852 dict |
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853 `dict` of labels keyed on the nodes |
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854 |
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855 Examples |
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856 -------- |
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857 >>> G = nx.dodecahedral_graph() |
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858 >>> labels = nx.draw_networkx_labels(G, pos=nx.spring_layout(G)) |
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859 |
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860 Also see the NetworkX drawing examples at |
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861 https://networkx.github.io/documentation/latest/auto_examples/index.html |
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862 |
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863 See Also |
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864 -------- |
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865 draw() |
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866 draw_networkx() |
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867 draw_networkx_nodes() |
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868 draw_networkx_edges() |
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869 draw_networkx_edge_labels() |
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870 """ |
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871 try: |
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872 import matplotlib.pyplot as plt |
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873 except ImportError as e: |
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874 raise ImportError("Matplotlib required for draw()") from e |
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875 except RuntimeError: |
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876 print("Matplotlib unable to open display") |
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877 raise |
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878 |
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879 if ax is None: |
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880 ax = plt.gca() |
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881 |
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882 if labels is None: |
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883 labels = {n: n for n in G.nodes()} |
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884 |
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885 text_items = {} # there is no text collection so we'll fake one |
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886 for n, label in labels.items(): |
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887 (x, y) = pos[n] |
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888 if not isinstance(label, str): |
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889 label = str(label) # this makes "1" and 1 labeled the same |
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890 t = ax.text( |
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891 x, |
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892 y, |
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893 label, |
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894 size=font_size, |
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895 color=font_color, |
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896 family=font_family, |
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897 weight=font_weight, |
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898 alpha=alpha, |
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899 horizontalalignment=horizontalalignment, |
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900 verticalalignment=verticalalignment, |
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901 transform=ax.transData, |
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902 bbox=bbox, |
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903 clip_on=True, |
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904 ) |
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905 text_items[n] = t |
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906 |
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907 ax.tick_params( |
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908 axis="both", |
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909 which="both", |
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910 bottom=False, |
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911 left=False, |
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912 labelbottom=False, |
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913 labelleft=False, |
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914 ) |
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915 |
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916 return text_items |
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917 |
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918 |
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|
919 def draw_networkx_edge_labels( |
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|
920 G, |
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|
921 pos, |
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922 edge_labels=None, |
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923 label_pos=0.5, |
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|
924 font_size=10, |
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925 font_color="k", |
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|
926 font_family="sans-serif", |
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927 font_weight="normal", |
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928 alpha=None, |
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929 bbox=None, |
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930 horizontalalignment="center", |
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931 verticalalignment="center", |
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932 ax=None, |
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933 rotate=True, |
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934 ): |
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935 """Draw edge labels. |
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936 |
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|
937 Parameters |
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|
938 ---------- |
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939 G : graph |
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940 A networkx graph |
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941 |
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942 pos : dictionary |
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943 A dictionary with nodes as keys and positions as values. |
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944 Positions should be sequences of length 2. |
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945 |
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946 ax : Matplotlib Axes object, optional |
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947 Draw the graph in the specified Matplotlib axes. |
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948 |
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949 alpha : float or None |
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950 The text transparency (default=None) |
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951 |
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952 edge_labels : dictionary |
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953 Edge labels in a dictionary keyed by edge two-tuple of text |
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954 labels (default=None). Only labels for the keys in the dictionary |
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955 are drawn. |
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956 |
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957 label_pos : float |
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958 Position of edge label along edge (0=head, 0.5=center, 1=tail) |
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959 |
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960 font_size : int |
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961 Font size for text labels (default=12) |
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962 |
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963 font_color : string |
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964 Font color string (default='k' black) |
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965 |
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966 font_weight : string |
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967 Font weight (default='normal') |
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968 |
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969 font_family : string |
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970 Font family (default='sans-serif') |
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971 |
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972 bbox : Matplotlib bbox |
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973 Specify text box shape and colors. |
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974 |
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975 clip_on : bool |
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976 Turn on clipping at axis boundaries (default=True) |
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977 |
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978 horizontalalignment : {'center', 'right', 'left'} |
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979 Horizontal alignment (default='center') |
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980 |
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981 verticalalignment : {'center', 'top', 'bottom', 'baseline', 'center_baseline'} |
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982 Vertical alignment (default='center') |
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983 |
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984 ax : Matplotlib Axes object, optional |
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985 Draw the graph in the specified Matplotlib axes. |
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986 |
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987 Returns |
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988 ------- |
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989 dict |
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990 `dict` of labels keyed on the edges |
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991 |
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992 Examples |
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993 -------- |
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994 >>> G = nx.dodecahedral_graph() |
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995 >>> edge_labels = nx.draw_networkx_edge_labels(G, pos=nx.spring_layout(G)) |
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996 |
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997 Also see the NetworkX drawing examples at |
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998 https://networkx.github.io/documentation/latest/auto_examples/index.html |
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999 |
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1000 See Also |
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1001 -------- |
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1002 draw() |
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1003 draw_networkx() |
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1004 draw_networkx_nodes() |
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1005 draw_networkx_edges() |
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1006 draw_networkx_labels() |
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1007 """ |
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1008 try: |
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1009 import matplotlib.pyplot as plt |
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1010 import numpy as np |
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1011 except ImportError as e: |
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1012 raise ImportError("Matplotlib required for draw()") from e |
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1013 except RuntimeError: |
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1014 print("Matplotlib unable to open display") |
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1015 raise |
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1016 |
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1017 if ax is None: |
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1018 ax = plt.gca() |
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1019 if edge_labels is None: |
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1020 labels = {(u, v): d for u, v, d in G.edges(data=True)} |
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1021 else: |
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1022 labels = edge_labels |
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1023 text_items = {} |
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1024 for (n1, n2), label in labels.items(): |
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1025 (x1, y1) = pos[n1] |
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1026 (x2, y2) = pos[n2] |
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1027 (x, y) = ( |
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1028 x1 * label_pos + x2 * (1.0 - label_pos), |
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1029 y1 * label_pos + y2 * (1.0 - label_pos), |
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1030 ) |
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1031 |
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1032 if rotate: |
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1033 # in degrees |
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1034 angle = np.arctan2(y2 - y1, x2 - x1) / (2.0 * np.pi) * 360 |
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1035 # make label orientation "right-side-up" |
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1036 if angle > 90: |
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1037 angle -= 180 |
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1038 if angle < -90: |
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1039 angle += 180 |
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1040 # transform data coordinate angle to screen coordinate angle |
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1041 xy = np.array((x, y)) |
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1042 trans_angle = ax.transData.transform_angles( |
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1043 np.array((angle,)), xy.reshape((1, 2)) |
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1044 )[0] |
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1045 else: |
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1046 trans_angle = 0.0 |
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1047 # use default box of white with white border |
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1048 if bbox is None: |
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1049 bbox = dict(boxstyle="round", ec=(1.0, 1.0, 1.0), fc=(1.0, 1.0, 1.0)) |
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1050 if not isinstance(label, str): |
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1051 label = str(label) # this makes "1" and 1 labeled the same |
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1052 |
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1053 t = ax.text( |
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1054 x, |
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1055 y, |
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1056 label, |
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1057 size=font_size, |
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1058 color=font_color, |
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1059 family=font_family, |
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1060 weight=font_weight, |
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1061 alpha=alpha, |
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1062 horizontalalignment=horizontalalignment, |
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1063 verticalalignment=verticalalignment, |
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1064 rotation=trans_angle, |
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1065 transform=ax.transData, |
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1066 bbox=bbox, |
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1067 zorder=1, |
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1068 clip_on=True, |
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1069 ) |
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1070 text_items[(n1, n2)] = t |
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1071 |
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1072 ax.tick_params( |
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1073 axis="both", |
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1074 which="both", |
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1075 bottom=False, |
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1076 left=False, |
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1077 labelbottom=False, |
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1078 labelleft=False, |
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1079 ) |
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1080 |
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1081 return text_items |
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1082 |
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1083 |
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1084 def draw_circular(G, **kwargs): |
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1085 """Draw the graph G with a circular layout. |
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1086 |
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1087 Parameters |
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1088 ---------- |
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1089 G : graph |
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1090 A networkx graph |
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1091 |
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1092 kwargs : optional keywords |
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1093 See networkx.draw_networkx() for a description of optional keywords, |
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1094 with the exception of the pos parameter which is not used by this |
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1095 function. |
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1096 """ |
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1097 draw(G, circular_layout(G), **kwargs) |
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1098 |
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1099 |
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1100 def draw_kamada_kawai(G, **kwargs): |
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1101 """Draw the graph G with a Kamada-Kawai force-directed layout. |
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1102 |
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1103 Parameters |
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1104 ---------- |
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1105 G : graph |
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1106 A networkx graph |
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1107 |
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1108 kwargs : optional keywords |
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1109 See networkx.draw_networkx() for a description of optional keywords, |
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1110 with the exception of the pos parameter which is not used by this |
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1111 function. |
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1112 """ |
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1113 draw(G, kamada_kawai_layout(G), **kwargs) |
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1114 |
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1115 |
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1116 def draw_random(G, **kwargs): |
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1117 """Draw the graph G with a random layout. |
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1118 |
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1119 Parameters |
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1120 ---------- |
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1121 G : graph |
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1122 A networkx graph |
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1123 |
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1124 kwargs : optional keywords |
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1125 See networkx.draw_networkx() for a description of optional keywords, |
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1126 with the exception of the pos parameter which is not used by this |
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1127 function. |
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1128 """ |
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1129 draw(G, random_layout(G), **kwargs) |
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1130 |
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1131 |
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1132 def draw_spectral(G, **kwargs): |
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1133 """Draw the graph G with a spectral 2D layout. |
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1134 |
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1135 Using the unnormalized Laplacian, the layout shows possible clusters of |
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1136 nodes which are an approximation of the ratio cut. The positions are the |
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1137 entries of the second and third eigenvectors corresponding to the |
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1138 ascending eigenvalues starting from the second one. |
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1139 |
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1140 Parameters |
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1141 ---------- |
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1142 G : graph |
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1143 A networkx graph |
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1144 |
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1145 kwargs : optional keywords |
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1146 See networkx.draw_networkx() for a description of optional keywords, |
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1147 with the exception of the pos parameter which is not used by this |
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1148 function. |
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1149 """ |
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1150 draw(G, spectral_layout(G), **kwargs) |
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1151 |
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1152 |
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1153 def draw_spring(G, **kwargs): |
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1154 """Draw the graph G with a spring layout. |
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1155 |
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1156 Parameters |
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1157 ---------- |
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1158 G : graph |
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1159 A networkx graph |
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1160 |
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1161 kwargs : optional keywords |
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1162 See networkx.draw_networkx() for a description of optional keywords, |
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1163 with the exception of the pos parameter which is not used by this |
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1164 function. |
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1165 """ |
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1166 draw(G, spring_layout(G), **kwargs) |
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1167 |
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1168 |
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1169 def draw_shell(G, **kwargs): |
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1170 """Draw networkx graph with shell layout. |
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1171 |
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1172 Parameters |
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1173 ---------- |
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1174 G : graph |
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1175 A networkx graph |
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1176 |
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1177 kwargs : optional keywords |
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1178 See networkx.draw_networkx() for a description of optional keywords, |
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1179 with the exception of the pos parameter which is not used by this |
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1180 function. |
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1181 """ |
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1182 nlist = kwargs.get("nlist", None) |
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1183 if nlist is not None: |
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1184 del kwargs["nlist"] |
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1185 draw(G, shell_layout(G, nlist=nlist), **kwargs) |
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1186 |
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1187 |
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1188 def draw_planar(G, **kwargs): |
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1189 """Draw a planar networkx graph with planar layout. |
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1190 |
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1191 Parameters |
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1192 ---------- |
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1193 G : graph |
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1194 A planar networkx graph |
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1195 |
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1196 kwargs : optional keywords |
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1197 See networkx.draw_networkx() for a description of optional keywords, |
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1198 with the exception of the pos parameter which is not used by this |
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1199 function. |
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1200 """ |
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1201 draw(G, planar_layout(G), **kwargs) |
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1202 |
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1203 |
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1204 def apply_alpha(colors, alpha, elem_list, cmap=None, vmin=None, vmax=None): |
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1205 """Apply an alpha (or list of alphas) to the colors provided. |
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1206 |
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1207 Parameters |
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1208 ---------- |
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1209 |
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1210 colors : color string, or array of floats |
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1211 Color of element. Can be a single color format string (default='r'), |
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1212 or a sequence of colors with the same length as nodelist. |
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1213 If numeric values are specified they will be mapped to |
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1214 colors using the cmap and vmin,vmax parameters. See |
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1215 matplotlib.scatter for more details. |
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1216 |
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1217 alpha : float or array of floats |
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1218 Alpha values for elements. This can be a single alpha value, in |
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1219 which case it will be applied to all the elements of color. Otherwise, |
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1220 if it is an array, the elements of alpha will be applied to the colors |
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1221 in order (cycling through alpha multiple times if necessary). |
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1222 |
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1223 elem_list : array of networkx objects |
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1224 The list of elements which are being colored. These could be nodes, |
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1225 edges or labels. |
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1226 |
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1227 cmap : matplotlib colormap |
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1228 Color map for use if colors is a list of floats corresponding to points |
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1229 on a color mapping. |
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1230 |
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1231 vmin, vmax : float |
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1232 Minimum and maximum values for normalizing colors if a color mapping is |
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1233 used. |
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1234 |
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1235 Returns |
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1236 ------- |
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1237 |
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1238 rgba_colors : numpy ndarray |
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1239 Array containing RGBA format values for each of the node colours. |
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1240 |
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1241 """ |
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1242 from itertools import islice, cycle |
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1243 |
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1244 try: |
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1245 import numpy as np |
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1246 from matplotlib.colors import colorConverter |
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1247 import matplotlib.cm as cm |
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1248 except ImportError as e: |
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1249 raise ImportError("Matplotlib required for draw()") from e |
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1250 |
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1251 # If we have been provided with a list of numbers as long as elem_list, |
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1252 # apply the color mapping. |
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1253 if len(colors) == len(elem_list) and isinstance(colors[0], Number): |
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1254 mapper = cm.ScalarMappable(cmap=cmap) |
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1255 mapper.set_clim(vmin, vmax) |
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1256 rgba_colors = mapper.to_rgba(colors) |
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1257 # Otherwise, convert colors to matplotlib's RGB using the colorConverter |
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1258 # object. These are converted to numpy ndarrays to be consistent with the |
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1259 # to_rgba method of ScalarMappable. |
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1260 else: |
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1261 try: |
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1262 rgba_colors = np.array([colorConverter.to_rgba(colors)]) |
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1263 except ValueError: |
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1264 rgba_colors = np.array([colorConverter.to_rgba(color) for color in colors]) |
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1265 # Set the final column of the rgba_colors to have the relevant alpha values |
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1266 try: |
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1267 # If alpha is longer than the number of colors, resize to the number of |
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1268 # elements. Also, if rgba_colors.size (the number of elements of |
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1269 # rgba_colors) is the same as the number of elements, resize the array, |
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1270 # to avoid it being interpreted as a colormap by scatter() |
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1271 if len(alpha) > len(rgba_colors) or rgba_colors.size == len(elem_list): |
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1272 rgba_colors = np.resize(rgba_colors, (len(elem_list), 4)) |
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1273 rgba_colors[1:, 0] = rgba_colors[0, 0] |
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1274 rgba_colors[1:, 1] = rgba_colors[0, 1] |
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1275 rgba_colors[1:, 2] = rgba_colors[0, 2] |
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1276 rgba_colors[:, 3] = list(islice(cycle(alpha), len(rgba_colors))) |
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1277 except TypeError: |
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1278 rgba_colors[:, -1] = alpha |
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1279 return rgba_colors |