A\t-1.23\t-0.81\t1.79\t0.78\t-0.42\t-0.69\t0.58 B\t-1.76\t-0.94\t1.16\t0.36\t0.41\t-0.35\t1.12 C\t-2.19\t0.13\t0.65\t-0.51\t0.52\t1.04\t0.36 D\t-1.22\t-0.98\t0.79\t-0.76\t-0.29\t1.54\t0.93 E\t-1.47\t-0.83\t0.85\t0.07\t-0.81\t1.53\t0.65 F\t-1.04\t-1.11\t0.87\t-0.14\t-0.80\t1.74\t0.48 G\t-1.57\t-1.17\t1.29\t0.23\t-0.20\t1.17\t0.26 H\t-1.53\t-1.25\t0.59\t-0.30\t0.32\t1.41\t0.77 """ print "Example numerical matrix" print matrix # #Names col1 col2 col3 col4 col5 col6 col7 # A -1.23 -0.81 1.79 0.78 -0.42 -0.69 0.58 # B -1.76 -0.94 1.16 0.36 0.41 -0.35 1.12 # C -2.19 0.13 0.65 -0.51 0.52 1.04 0.36 # D -1.22 -0.98 0.79 -0.76 -0.29 1.54 0.93 # E -1.47 -0.83 0.85 0.07 -0.81 1.53 0.65 # F -1.04 -1.11 0.87 -0.14 -0.80 1.74 0.48 # G -1.57 -1.17 1.29 0.23 -0.20 1.17 0.26 # H -1.53 -1.25 0.59 -0.30 0.32 1.41 0.77 # # # We load a tree structure whose leaf nodes correspond to rows in the # numerical matrix. We use the text_array argument to link the tree # with numerical matrix. t = ClusterTree("(((A,B),(C,(D,E))),(F,(G,H)));", text_array=matrix) t.show("heatmap") t.show("cluster_cbars") t.show("cluster_bars") t.show("cluster_lines")
add_face_to_node(nameFace, node, 1, aligned=True) # If node is internal else: # If silhouette is good, creates a green bubble if node.silhouette>0: validationFace = TextFace("Silh=%0.2f" %node.silhouette, "Verdana", 10, "#056600") node.img_style["fgcolor"]="#056600" # Otherwise, use red bubbles else: validationFace = TextFace("Silh=%0.2f" %node.silhouette, "Verdana", 10, "#940000") node.img_style["fgcolor"]="#940000" # Sets node size proportional to the silhouette value. node.img_style["shape"]="sphere" if node.silhouette<=1 and node.silhouette>=-1: node.img_style["size"]= 15+int((abs(node.silhouette)*10)**2) # If node is very internal, draw also a bar diagram # with the average expression of the partition add_face_to_node(validationFace, node, 0) if len(node)>100: add_face_to_node(cbarsFace, node, 1) # Use my layout to visualize the tree ts = TreeStyle() ts.layout_fn = mylayout t.show(tree_style=ts)
if node.is_leaf(): # And a line profile faces.add_face_to_node(profileFace, node, 0, aligned=True) node.img_style["size"]=0 faces.add_face_to_node(nameFace, node, 1, aligned=True) # If node is internal else: # If silhouette is good, creates a green bubble if node.silhouette>0: validationFace = faces.TextFace("Silh=%0.2f" %node.silhouette, "Verdana", 10, "#056600") node.img_style["fgcolor"]="#056600" # Otherwise, use red bubbles else: validationFace = faces.TextFace("Silh=%0.2f" %node.silhouette, "Verdana", 10, "#940000") node.img_style["fgcolor"]="#940000" # Sets node size proportional to the silhouette value. node.img_style["shape"]="sphere" if node.silhouette<=1 and node.silhouette>=-1: node.img_style["size"]= 15+int((abs(node.silhouette)*10)**2) # If node is very internal, draw also a bar diagram # with the average expression of the partition faces.add_face_to_node(validationFace, node, 0) if len(node)>100: faces.add_face_to_node(cbarsFace, node, 1) # Use my layout to visualize the tree t.show(mylayout)
node.img_style["size"] = 0 faces.add_face_to_node(nameFace, node, 1, aligned=True) # If node is internal else: # If silhouette is good, creates a green bubble if node.silhouette > 0: validationFace = faces.TextFace("Silh=%0.2f" % node.silhouette, "Verdana", 10, "#056600") node.img_style["fgcolor"] = "#056600" # Otherwise, use red bubbles else: validationFace = faces.TextFace("Silh=%0.2f" % node.silhouette, "Verdana", 10, "#940000") node.img_style["fgcolor"] = "#940000" # Sets node size proportional to the silhouette value. node.img_style["shape"] = "sphere" if node.silhouette <= 1 and node.silhouette >= -1: node.img_style["size"] = 15 + int((abs(node.silhouette) * 10)**2) # If node is very internal, draw also a bar diagram # with the average expression of the partition faces.add_face_to_node(validationFace, node, 0) if len(node) > 100: faces.add_face_to_node(cbarsFace, node, 1) # Use my layout to visualize the tree t.show(mylayout)