Python Network.load_tsv_to_net Beispiele

Beispiel #1

Datei: load_latest_cst.py Projekt: Amal-Alnouri/CST_Lung_Cancer_Viz

def calc_treatment_ratios():

    from clustergrammer import Network

    net = Network()

    net.load_tsv_to_net('treated_cell_12_1_2015/treated_cl_phospho.tsv')

Beispiel #2

Datei: load_latest_cst.py Projekt: MaayanLab/cst_drug_treatment

def calc_treatment_ratios():

  from clustergrammer import Network

  net = Network()

  net.load_tsv_to_net('treated_cell_12_1_2015/treated_cl_phospho.tsv')

Beispiel #3

Datei: load_tsv_file.py Projekt: abdohlman/clustergrammer

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()


  

Beispiel #4

Datei: load_tsv_file.py Projekt: jjdblast/clustergrammer

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()

Beispiel #5

Datei: make_clustergram.py Projekt: msyinmei/clustergrammer.js

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)