In [4]:
import numpy as np
from ete3 import Tree, TreeStyle
from bionlp.util import io, plot, func, bintree
# Load the tree data
lbid = 0
t = io.read_obj('../data/gesgnext/cnsrnn0.5_hrc_tree_%i.pkl' % lbid)
gsm_X = io.read_df('../data/gesgnext/gsm_X_%i.npz' % lbid, with_idx=True, sparse_fmt='csr')
gsm_y = io.read_df('../data/gesgnext/gsm_y_%i.npz' % lbid, with_idx=True)
# Layout design
def layout(node):
if (node.data.has_key('clt')):
if (node.is_leaf()):
node.img_style['size'] = 10
node.img_style['vt_line_type'] = 0
node.img_style['vt_line_width'] = 5
node.img_style['hz_line_width'] = 5
node.img_style['vt_line_color'] = '#0000FF'
node.img_style['hz_line_color'] = '#0000FF'
else:
node.img_style['size'] = 15
node.img_style['vt_line_type'] = 0
node.img_style['vt_line_width'] = 3
node.img_style['hz_line_width'] = 3
node.img_style['vt_line_color'] = '#00FFFF'
node.img_style['hz_line_color'] = '#00FFFF'
ctrl_num, pert_num = gsm_y['ctrl'].iloc[np.array(node.data['clt'])].sum(), gsm_y['pert'].iloc[np.array(node.data['clt'])].sum()
if (ctrl_num > pert_num):
node.img_style['fgcolor'] = 'green'
elif (pert_num > ctrl_num):
node.img_style['fgcolor'] = 'red'
else:
node.img_style['fgcolor'] = 'grey'
else:
node.img_style['size'] = 8
node.img_style['shape'] = 'square'
node.img_style['fgcolor'] = 'grey'
node.img_style['vt_line_type'] = 1
node.img_style['hz_line_type'] = 1
node.img_style['vt_line_width'] = 2
node.img_style['hz_line_width'] = 2
node.img_style['vt_line_color'] = '#C6C6C6'
node.img_style['hz_line_color'] = '#C6C6C6'
# Modify the leaf name
vertices = bintree.preorder_getnode(t)
for v in vertices:
v.name = '|'.join(gsm_X.index[np.array(v.data['clt'])])
# Add level info
def in_lev(node, val):
node.data['level'] = val['lev']
val['lev'] += 1
def out_lev(node, val):
val['lev'] -= 1
bintree.preorder_modify(t, in_lev, out_lev, val=dict(lev=0))
# Prune the tree
remain_nodes = bintree.preorder_search(t, lambda x: x.data['cond'] > 100, stop_found=True)
levs = [node.data['level'] for node in remain_nodes]
nodes_inlev = {}
for k, v in zip(levs, remain_nodes):
nodes_inlev.setdefault(k, []).append(v)
for k, v in nodes_inlev.iteritems():
node = bintree.ETENode(data=dict(data={}))
node.children.extend(v)
nodes_inlev[k] = node
lev_nodes = func.sorted_tuples(nodes_inlev.items(), key_idx=0)[::-1]
# t = bintree.ETENode()
# t.left, t.right = lev_nodes[0][1], lev_nodes[1][1]
# t.post_build()
# for k, v in lev_nodes[2:]:
# node = bintree.ETENode()
# node.left, node.right = t, v
# node.post_build()
# t = node
cur_lev, next_lev = [v for k, v in lev_nodes], []
while (len(cur_lev) != 1):
for i in range(0, len(cur_lev), 2):
try:
node = bintree.ETENode()
node.left, node.right = cur_lev[i], cur_lev[i+1]
node.post_build()
next_lev.append(node)
except:
next_lev.append(cur_lev[i])
cur_lev = next_lev
next_lev = []
t = cur_lev[0]
t.name = 'root'
# Set the tree style
ts = TreeStyle()
ts.layout_fn = layout
ts.show_leaf_name = True
# ts.branch_vertical_margin = 10
ts.mode = "c"
ts.arc_start = 0
ts.arc_span = 360
t.render("circular_tree_%i.pdf" % lbid, w=600, dpi=400, tree_style=ts)
Out[4]:
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In [ ]:
from bionlp.util import io, func
clt_mdl_0=io.read_obj('../../../workspace/gesgnext/kallima_clusters_0.pkl')
gsm_X_0=io.read_df('../data/gesgnext/udt200/gsm_X_0.npz', with_idx=True, sparse_fmt='csr')
print gsm_X_0.shape[0], len(set(func.flatten_list(clt_mdl_0)))
ndp = list(set(range(gsm_X_0.shape[0]))-set(func.flatten_list(clt_mdl_0)))
print gsm_X_0.index[ndp]
In [ ]:
from bionlp.util import io, func
clt_mdl_1=io.read_obj('../../../workspace/gesgnext/kallima_clusters_1.pkl')
gsm_X_1=io.read_df('../data/gesgnext/udt200/gsm_X_1.npz', with_idx=True, sparse_fmt='csr')
print gsm_X_1.shape[0], len(set(func.flatten_list(clt_mdl_1)))
ndp = list(set(range(gsm_X_1.shape[0]))-set(func.flatten_list(clt_mdl_1)))
print gsm_X_1.index[ndp]
In [ ]:
from bionlp.util import io, func
clt_mdl_2=io.read_obj('../../../workspace/gesgnext/kallima_clusters_2.pkl')
gsm_X_2=io.read_df('../data/gesgnext/udt200/gsm_X_2.npz', with_idx=True, sparse_fmt='csr')
print gsm_X_2.shape[0], len(set(func.flatten_list(clt_mdl_2)))
ndp = list(set(range(gsm_X_2.shape[0]))-set(func.flatten_list(clt_mdl_2)))
print gsm_X_2.index[ndp]
Content source: cskyan/gesgnext
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