def createconnectogram(num_out_lbl, heatmap, annot_csv, uniq_lbls, targ, dic):
""" Generates & saves the connectome graph of the connectiviy matrix
"""
print(
"\n Computing & saving the interactive connectivity graph (connectogram) "
)
lgn = Lightning(ipython=True, local=True)
# create circle connectome
connections = np.zeros(((2 * num_out_lbl) + 1, (2 * num_out_lbl) + 1))
connections[1:(num_out_lbl + 1), 0] = uniq_lbls.T
connections[num_out_lbl + 1:, 0] = targ.T
connections[0, 1:(num_out_lbl + 1)] = uniq_lbls.T
connections[0, (num_out_lbl + 1):] = targ.T
# propagate connections
alllbls = connections[1:, 0]
for l, lbl in enumerate(alllbls):
for t, tart in enumerate(alllbls):
iind = heatmap[:-1, 0] == lbl
jind = heatmap[num_out_lbl, :] == tart
val = heatmap[np.where(iind == True), np.where(jind == True)]
connections[l + 1, t + 1] = val if val > 0 else 0
# threshold connections
thr = 0.1
connections[connections < thr] = 0
# lbls abrv
alllbls_abrv = pd.DataFrame(alllbls)
alllbls_abrv = alllbls_abrv.replace(dic)
alllbls_abrv = np.array(alllbls_abrv[0])
# get grand parents ids for groups
ggp_parents = np.array([
annot_csv['parent_structure_id'][annot_csv['id'] == lbl].item()
for l, lbl in enumerate(alllbls)
])
parent_grps = ggp_parents
for i in range(2):
parent_grps = np.array([
annot_csv['parent_structure_id'][annot_csv['id'] == lbl].item() if
(lbl != 997) else 997 for l, lbl in enumerate(parent_grps)
])
# make dic
repl = np.unique(ggp_parents)
np.place(repl, repl > 0, range(len(repl)))
uniq_parents = np.unique(ggp_parents)
parents_dic = dict(zip(uniq_parents, repl))
# replace
ggp_parents = pd.DataFrame(ggp_parents)
groups = ggp_parents.replace(parents_dic)
groups = np.array(groups[0])
# make dic
repl2 = np.unique(parent_grps)
np.place(repl2, repl2 > 0, range(len(repl2)))
uniq_parents2 = np.unique(parent_grps)
parents_dic2 = dict(zip(uniq_parents2, repl2))
parent_grps = pd.DataFrame(parent_grps)
parent_groups = parent_grps.replace(parents_dic2)
parent_groups = np.array(parent_groups[0])
justconn = connections[1:, 1:]
c = lgn.circle(justconn,
labels=alllbls_abrv,
group=[parent_groups, groups],
width=1000,
height=1000)
c.save_html('connectogram_grouped_by_parent_id_%d_labels.html' %
num_out_lbl,
overwrite=True)
from lightning import Lightning
from numpy import random
lgn = Lightning()
connections = random.rand(50,50)
connections[connections<0.98] = 0
g1 = (random.rand(50) * 3).astype('int')
g2 = (random.rand(50) * 3).astype('int')
group = [g2, g1]
lgn.circle(connections, group=group)
from lightning import Lightning
from numpy import random
lgn = Lightning()
connections = random.rand(50, 50)
connections[connections < 0.98] = 0
g1 = (random.rand(50) * 3).astype('int')
g2 = (random.rand(50) * 3).astype('int')
group = [g2, g1]
lgn.circle(connections, group=group)
import numpy as np
from lightning import Lightning
lgn = Lightning(local=True)
connections = np.matrix("0 0 0 1;0 0 0 0;0 0 0 0;0 0 0 0")
lgn.circle(connections)