def calc_treatment_ratios(): from clustergrammer import Network net = Network() net.load_tsv_to_net('treated_cell_12_1_2015/treated_cl_phospho.tsv')
def calc_treatment_ratios(): from clustergrammer import Network net = Network() net.load_tsv_to_net('treated_cell_12_1_2015/treated_cl_phospho.tsv')
def main( buff, inst_filename, mongo_address, viz_id): import numpy as np import flask from bson.objectid import ObjectId from pymongo import MongoClient from flask import request from clustergrammer import Network import StringIO client = MongoClient(mongo_address) db = client.clustergrammer viz_id = ObjectId(viz_id) found_viz = db.networks.find_one({'_id':viz_id}) try: net = Network() net.load_tsv_to_net(buff) net.swap_nan_for_zero() views = ['N_row_sum', 'N_row_var'] net.make_clust(dist_type='cosine', dendro=True, views=views, \ linkage_type='average') export_dat = {} export_dat['name'] = inst_filename export_dat['dat'] = net.export_net_json('dat') export_dat['source'] = 'user_upload' dat_id = db.network_data.insert(export_dat) update_viz = net.viz update_dat = dat_id except: print('\n-----------------------') print('error in clustering') print('-----------------------\n') update_viz = 'error' update_dat = 'error' found_viz['viz'] = update_viz found_viz['dat'] = update_dat db.networks.update_one( {'_id':viz_id}, {'$set': found_viz} ) client.close()
def main(buff, inst_filename, mongo_address, viz_id): import numpy as np import flask from bson.objectid import ObjectId from pymongo import MongoClient from flask import request from clustergrammer import Network import StringIO client = MongoClient(mongo_address) db = client.clustergrammer viz_id = ObjectId(viz_id) found_viz = db.networks.find_one({'_id': viz_id}) try: net = Network() net.load_tsv_to_net(buff) net.swap_nan_for_zero() views = ['N_row_sum', 'N_row_var'] net.make_clust(dist_type='cosine', dendro=True, views=views, \ linkage_type='average') export_dat = {} export_dat['name'] = inst_filename export_dat['dat'] = net.export_net_json('dat') export_dat['source'] = 'user_upload' dat_id = db.network_data.insert(export_dat) update_viz = net.viz update_dat = dat_id except: print('\n-----------------------') print('error in clustering') print('-----------------------\n') update_viz = 'error' update_dat = 'error' found_viz['viz'] = update_viz found_viz['dat'] = update_dat db.networks.update_one({'_id': viz_id}, {'$set': found_viz}) client.close()
import time start_time = time.time() # import network class from Network.py from clustergrammer import Network net = Network() net.load_tsv_to_net('txt/example_tsv.txt') net.make_filtered_views(dist_type='cos',views=['N_row_sum','pct_row_sum']) net.write_json_to_file('viz', 'json/mult_view.json', 'indent') # your code elapsed_time = time.time() - start_time print('\n\n\nelapsed time') print(elapsed_time)