X.ix[X.ix[:,'Inhib_GSK690693_GSK1120212']>0,'Inhib_GSK690693_GSK1120212'] = 1 X.ix[X.ix[:,'Inhib_GSK690693']<0,'Inhib_GSK690693'] = 0 X.ix[X.ix[:,'Inhib_GSK690693_GSK1120212']<0,'Inhib_GSK690693_GSK1120212'] = 0 n_estimators = 100 max_depth = 3 regGBR[stim] = do_gbr(X, Y, n_estimators=n_estimators, max_depth=max_depth) adj = build_adj_matrix(regGBR, node_list, stims) A_true_bt20 = prior for stim in adj: path = 'results/sakev-BT20-{0}-Network'.format(stim) for row in A_true_bt20.index: for col in A_true_bt20.columns: if A_true_bt20.ix[row,col] == 1: adj[stim].ix[row,col] = 1 utilities.write_SIF_EDA(adj[stim], path) ## BT549 ############################################## print '----------- ' + 'BT549' + ' ------------' inhibs = set(bt549['Inhibitor']) stims = set(bt549['Stimulus']) node_list = bt549.columns[4:] inhib_targets = {'GSK690693' : ['AKT_pT308','AKT_pS473'], 'GSK690693_GSK1120212' : ['AKT_pT308','AKT_pS473','MEK1_pS217_S221']} regGBR= {} scalar = {} td_bt549 = utilities.prepare_markov_data(utilities.introduce_inhibs(bt549, inhib_targets=inhib_targets, perfect=True), 'level', group_stimuli=False) for stim in td_bt549: X, Y = td_bt549[stim] scalar[stim] = preprocessing.StandardScaler()
# load in the insilico data insilico_data = pd.read_csv('data/insilico.csv', header=0) inhibs = set(insilico_data['Inhibitor']) stims = set(insilico_data['Stimulus']) node_list = ['AB{0}'.format(i) for i in range(1, 21)] inhib_targets = {'INH1' : 'AB12', 'INH2' : 'AB5', 'INH3' : 'AB8'} regGBR= {} scalar = {} td = utilities.prepare_markov_data(utilities.introduce_inhibs(insilico_data, inhib_targets=inhib_targets, perfect=True), 'level', group_stimuli=True) X, Y = td['all_stimuli'] scalar['all_stimuli'] = preprocessing.StandardScaler() scalar['all_stimuli'].fit_transform(X) X.ix[X.ix[:,'Inhib_INH1']>0,'Inhib_INH1'] = 1 X.ix[X.ix[:,'Inhib_INH2']>0,'Inhib_INH2'] = 1 X.ix[X.ix[:,'Inhib_INH3']>0,'Inhib_INH3'] = 1 X.ix[X.ix[:,'Inhib_INH1']<0,'Inhib_INH1'] = 0 X.ix[X.ix[:,'Inhib_INH2']<0,'Inhib_INH2'] = 0 X.ix[X.ix[:,'Inhib_INH3']<0,'Inhib_INH3'] = 0 # Step 2 : Fit n_estimators = 100 max_depth = 3 regGBR['all_stimuli'] = do_gbr(X, Y, n_estimators=n_estimators, max_depth=max_depth) # Step 3 : build and write adjacency matrix adj = build_adj_matrix(regGBR, node_list, ['all_stimuli']) utilities.write_SIF_EDA(adj['all_stimuli'], 'results/sakev-Network-Insilico')