@@ -838,6 +838,198 @@ def lab2node(labels, labels_dict):
838838 return [labels_dict [ll ] for ll in labels ]
839839
840840
841+ ### Patched version for networx draw_networkx_edges, sent to Aric.
842+ def draw_networkx_edges (G , pos ,
843+ edgelist = None ,
844+ width = 1.0 ,
845+ edge_color = 'k' ,
846+ style = 'solid' ,
847+ alpha = None ,
848+ edge_cmap = None ,
849+ edge_vmin = None ,
850+ edge_vmax = None ,
851+ ax = None ,
852+ arrows = True ,
853+ ** kwds ):
854+ """Draw the edges of the graph G
855+
856+ This draws only the edges of the graph G.
857+
858+ pos is a dictionary keyed by vertex with a two-tuple
859+ of x-y positions as the value.
860+ See networkx.layout for functions that compute node positions.
861+
862+ edgelist is an optional list of the edges in G to be drawn.
863+ If provided, only the edges in edgelist will be drawn.
864+
865+ edgecolor can be a list of matplotlib color letters such as 'k' or
866+ 'b' that lists the color of each edge; the list must be ordered in
867+ the same way as the edge list. Alternatively, this list can contain
868+ numbers and those number are mapped to a color scale using the color
869+ map edge_cmap. Finally, it can also be a list of (r,g,b) or (r,g,b,a)
870+ tuples, in which case these will be used directly to color the edges. If
871+ the latter mode is used, you should not provide a value for alpha, as it
872+ would be applied globally to all lines.
873+
874+ For directed graphs, 'arrows' (actually just thicker stubs) are drawn
875+ at the head end. Arrows can be turned off with keyword arrows=False.
876+
877+ See draw_networkx for the list of other optional parameters.
878+
879+ """
880+ try :
881+ import matplotlib .pylab as pylab
882+ import matplotlib .cbook as cb
883+ from matplotlib .colors import colorConverter , Colormap
884+ from matplotlib .collections import LineCollection
885+ except ImportError :
886+ raise ImportError ("Matplotlib required for draw()" )
887+ except RuntimeError :
888+ pass # unable to open display
889+
890+ if ax is None :
891+ ax = pylab .gca ()
892+
893+ if edgelist is None :
894+ edgelist = G .edges ()
895+
896+ if not edgelist or len (edgelist ) == 0 : # no edges!
897+ return None
898+
899+ # set edge positions
900+ edge_pos = np .asarray ([(pos [e [0 ]], pos [e [1 ]]) for e in edgelist ])
901+
902+ if not cb .iterable (width ):
903+ lw = (width ,)
904+ else :
905+ lw = width
906+
907+ if not isinstance (edge_color , str ) \
908+ and cb .iterable (edge_color ) \
909+ and len (edge_color ) == len (edge_pos ):
910+ if np .alltrue ([isinstance (c , str )
911+ for c in edge_color ]):
912+ # (should check ALL elements)
913+ # list of color letters such as ['k','r','k',...]
914+ edge_colors = tuple ([colorConverter .to_rgba (c , alpha )
915+ for c in edge_color ])
916+ elif np .alltrue ([not isinstance (c , str )
917+ for c in edge_color ]):
918+ # If color specs are given as (rgb) or (rgba) tuples, we're OK
919+ if np .alltrue ([cb .iterable (c ) and len (c ) in (3 , 4 )
920+ for c in edge_color ]):
921+ edge_colors = tuple (edge_color )
922+ alpha = None
923+ else :
924+ # numbers (which are going to be mapped with a colormap)
925+ edge_colors = None
926+ else :
927+ e_s = 'edge_color must consist of either color names or numbers'
928+ raise ValueError (e_s )
929+ else :
930+ if len (edge_color ) == 1 :
931+ edge_colors = (colorConverter .to_rgba (edge_color , alpha ),)
932+ else :
933+ e_s = 'edge_color must be a single color or list of exactly'
934+ e_s += 'm colors where m is the number or edges'
935+ raise ValueError (e_s )
936+ edge_collection = LineCollection (edge_pos ,
937+ colors = edge_colors ,
938+ linewidths = lw ,
939+ antialiaseds = (1 ,),
940+ linestyle = style ,
941+ transOffset = ax .transData ,
942+ )
943+
944+ # Note: there was a bug in mpl regarding the handling of alpha values for
945+ # each line in a LineCollection. It was fixed in matplotlib in r7184 and
946+ # r7189 (June 6 2009). We should then not set the alpha value globally,
947+ # since the user can instead provide per-edge alphas now. Only set it
948+ # globally if provided as a scalar.
949+ if cb .is_numlike (alpha ):
950+ edge_collection .set_alpha (alpha )
951+
952+ # need 0.87.7 or greater for edge colormaps
953+ if edge_colors is None :
954+ if edge_cmap is not None :
955+ assert (isinstance (edge_cmap , Colormap ))
956+ edge_collection .set_array (np .asarray (edge_color ))
957+ edge_collection .set_cmap (edge_cmap )
958+ if edge_vmin is not None or edge_vmax is not None :
959+ edge_collection .set_clim (edge_vmin , edge_vmax )
960+ else :
961+ edge_collection .autoscale ()
962+ pylab .sci (edge_collection )
963+
964+ # else:
965+ # sys.stderr.write(\
966+ # """matplotlib version >= 0.87.7 required for colormapped edges.
967+ # (version %s detected)."""%matplotlib.__version__)
968+ # raise UserWarning(\
969+ # """matplotlib version >= 0.87.7 required for colormapped edges.
970+ # (version %s detected)."""%matplotlib.__version__)
971+
972+ arrow_collection = None
973+
974+ if G .is_directed () and arrows :
975+
976+ # a directed graph hack
977+ # draw thick line segments at head end of edge
978+ # waiting for someone else to implement arrows that will work
979+ arrow_colors = (colorConverter .to_rgba ('k' , alpha ),)
980+ a_pos = []
981+ p = 1.0 - 0.25 # make head segment 25 percent of edge length
982+ for src , dst in edge_pos :
983+ x1 , y1 = src
984+ x2 , y2 = dst
985+ dx = x2 - x1 # x offset
986+ dy = y2 - y1 # y offset
987+ d = np .sqrt (float (dx ** 2 + dy ** 2 )) # length of edge
988+ if d == 0 : # source and target at same position
989+ continue
990+ if dx == 0 : # vertical edge
991+ xa = x2
992+ ya = dy * p + y1
993+ if dy == 0 : # horizontal edge
994+ ya = y2
995+ xa = dx * p + x1
996+ else :
997+ theta = np .arctan2 (dy , dx )
998+ xa = p * d * np .cos (theta ) + x1
999+ ya = p * d * np .sin (theta ) + y1
1000+
1001+ a_pos .append (((xa , ya ), (x2 , y2 )))
1002+
1003+ arrow_collection = LineCollection (a_pos ,
1004+ colors = arrow_colors ,
1005+ linewidths = [4 * ww for ww in lw ],
1006+ antialiaseds = (1 ,),
1007+ transOffset = ax .transData ,
1008+ )
1009+
1010+ # update view
1011+ minx = np .amin (np .ravel (edge_pos [:, :, 0 ]))
1012+ maxx = np .amax (np .ravel (edge_pos [:, :, 0 ]))
1013+ miny = np .amin (np .ravel (edge_pos [:, :, 1 ]))
1014+ maxy = np .amax (np .ravel (edge_pos [:, :, 1 ]))
1015+
1016+ w = maxx - minx
1017+ h = maxy - miny
1018+ padx , pady = 0.05 * w , 0.05 * h
1019+ corners = (minx - padx , miny - pady ), (maxx + padx , maxy + pady )
1020+ ax .update_datalim (corners )
1021+ ax .autoscale_view ()
1022+
1023+ edge_collection .set_zorder (1 ) # edges go behind nodes
1024+ ax .add_collection (edge_collection )
1025+ if arrow_collection :
1026+ arrow_collection .set_zorder (1 ) # edges go behind nodes
1027+ ax .add_collection (arrow_collection )
1028+
1029+ return ax
1030+
1031+
1032+ > >> >> >> Updating older APIs .
8411033def mkgraph (cmat , threshold = 0.0 , threshold2 = None ):
8421034 """Make a weighted graph object out of an adjacency matrix.
8431035
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