def showTreeStructure(inputfile):
t = ClusterTree(
"./OUTPUT/%s/NWK/HIER_CLUST_%s.nwk" %
((inputfile.split("_")[0]).upper(), inputfile.split(".")[0]))
def mylayout(node):
global flag
#print node.left
# print "node",len(node )
#if len(node)!=1:# and flag == 1:
# if flag == 1:
# pidlist= getpid(node)
#print pidlist
# dcs=DoCS(pidlist,PRO_pfam)
#print dcs
# if dcs>=0.5:
# flag=0
# print pidlist,len(node),dcs
# print "_____________________"
if node.is_leaf():
node.img_style["shape"] = "sphere"
node.img_style["size"] = 10
node.img_style["fgcolor"] = 'purple'
t.dist = 0
t.convert_to_ultrametric(1, strategy="fixed")
ts = TreeStyle()
ts.scale = 230
ts.root_opening_factor = 5.0
ts.mode = "c"
ts.layout_fn = mylayout
#print mylayout
t.show(tree_style=ts)
print("--------------------------------")
print("completed")
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")
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")
# 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)
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)
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)