connectome plotting

gistfile1.txt

""" 
worm2nx.py
Simple script for turning connectome tables into NetworkX graphs.

Note that the tables were extracted manually from the connectivity spreadsheet
of the c. elegans and should accompany this script.

Author: Pedro Tabacof (tabacof at gmail dot com)
        Stephen Larson ([email protected])
License: Public Domain
"""

# -*- coding: utf-8 -*- 

import csv

import urllib2

import networkx as nx

worm = nx.DiGraph()

# Neuron table
csvfile = urllib2.urlopen('https://raw.github.com/openworm/data-viz/master/HivePlots/neurons.csv')

reader = csv.reader(csvfile, delimiter=';', quotechar='|')
for row in reader:
    neurontype = ""
    # Detects neuron function
    if "sensory" in row[1].lower():
        neurontype += "sensory"
    if "motor" in row[1].lower():
        neurontype += "motor"    
    if "interneuron" in row[1].lower():
        neurontype += "interneuron"
    if len(neurontype) == 0:
        neurontype = "unknown"
        
    if len(row[0]) > 0: # Only saves valid neuron names
        worm.add_node(row[0], ntype = neurontype)

# Connectome table
csvfile = urllib2.urlopen('https://raw.github.com/openworm/data-viz/master/HivePlots/connectome.csv')

reader = csv.reader(csvfile, delimiter=';', quotechar='|')
for row in reader:
    worm.add_edge(row[0], row[1], weight = row[3])
    worm[row[0]][row[1]]['synapse'] = row[2]
    worm[row[0]][row[1]]['neurotransmitter'] = row[4]

print "******DEGREES OF TOP FOUR INTERNEURONS*******"
print "Degree of AVAL: " + str(worm.degree('AVAL'))
print "Degree of AVAR: " + str(worm.degree('AVAR'))
print "Degree of AVBL: " + str(worm.degree('AVBL'))
print "Degree of AVBR: " + str(worm.degree('AVBR'))

print "******DEGREES OF NEXT FOUR INTERNEURONS*******"
print "Degree of PVCR: " + str(worm.degree('PVCR'))
print "Degree of PVCL: " + str(worm.degree('PVCL'))
print "Degree of AVDR: " + str(worm.degree('AVDR'))
print "Degree of AVER: " + str(worm.degree('AVER'))

print "******DEGREE OF TOP SENSORY NEURON*******"
print "Degree of ADEL: " + str(worm.degree('ADEL'))
print "******DEGREE OF TOP MOTOR NEURON*******"
print "Degree of RIMR: " + str(worm.degree('RIMR'))

def GJ_degree(node):
    count = 0
    for item in worm.in_edges_iter(node,data=True):
        if 'GapJunction' in item[2]['synapse']:
            count = count + 1
    for item in worm.out_edges_iter(node,data=True):
        if 'GapJunction' in item[2]['synapse']:
            count = count + 1
    return count

def Syn_degree(node):
    count = 0
    for item in worm.in_edges_iter(node,data=True):
        if 'Send' in item[2]['synapse']:
            count = count + 1
    for item in worm.out_edges_iter(node,data=True):
        if 'Send' in item[2]['synapse']:
            count = count + 1
    return count

ids = {}
ids_GJ = {}
ids_Syn = {}
for item in worm.nodes_iter(data=True):
    if item[0] in ['AVAL', 'AVAR', 'AVBL', 'AVBR', 'PVCR', 'PVCL', 'AVDR', 'AVER']:
        if 'interneuron' in item[1]['ntype']:
            ids[item[0]] = worm.degree(item[0])
            ids_GJ[item[0]] = GJ_degree(item[0])
            ids_Syn[item[0]] = Syn_degree(item[0])

import operator

ids = sorted(ids.iteritems(), key=operator.itemgetter(1))
ids_GJ = sorted(ids_GJ.iteritems(), key=operator.itemgetter(1))
ids_Syn = sorted(ids_Syn.iteritems(), key=operator.itemgetter(1))

from pylab import *

pos = arange(len(ids))+1    # the bar centers on the y axis

#fig = figure(figsize=(20,20))
fig = figure(figsize=(10,10))
ax = fig.add_subplot(111)

p1 = bar(pos,[x[1] for x in ids], align='center', color='r')

p2 = bar(pos,[x[1] for x in ids_Syn], align='center')

p3 = bar(pos,[x[1] for x in ids_GJ], align='center', color='y')

xlabel('Interneurons')
ylabel('Degree')
xticks( pos, [x[0] for x in ids])
title('Interneurons by node degree')
legend( (p1[0], p2[0], p3[0]), ('All edges', 'Synapses only', 'Gap junctions only'), loc=2)
setp(ax.get_xticklabels(), fontsize=12, rotation='vertical')

show()