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sim_net = {}
for inst_rc in which_sim:
sim_net[inst_rc] = deepcopy(Network())
sim_net[inst_rc].dat['mat'] = sim_dict[inst_rc]
sim_net[inst_rc].dat['nodes']['row'] = net.dat['nodes'][inst_rc]
sim_net[inst_rc].dat['nodes']['col'] = net.dat['nodes'][inst_rc]
sim_net[inst_rc].dat['node_info']['row'] = net.dat['node_info'][inst_rc]
sim_net[inst_rc].dat['node_info']['col'] = net.dat['node_info'][inst_rc]
calc_clust.cluster_row_and_col(sim_net[inst_rc])
all_views = []
df = sim_net[inst_rc].dat_to_df()
send_df = deepcopy(df)
sim_net[inst_rc].viz['views'] = all_views
return sim_net
keep_rows = rows_sorted[0:inst_keep]
tmp_df['mat'] = tmp_df['mat'].loc[keep_rows]
if 'mat_orig' in tmp_df:
tmp_df['mat_orig'] = tmp_df['mat_orig'].loc[keep_rows]
tmp_df = run_filter.df_filter_col_sum(tmp_df, 0.001)
tmp_net.df_to_dat(tmp_df)
else:
tmp_net.df_to_dat(tmp_df)
try:
try:
calc_clust.cluster_row_and_col(tmp_net, dist_type, run_clustering=True)
except:
calc_clust.cluster_row_and_col(tmp_net, dist_type, run_clustering=False)
# add view
inst_view = {}
inst_view['N_row_' + rank_type] = inst_keep
inst_view['dist'] = 'cos'
inst_view['nodes'] = {}
inst_view['nodes']['row_nodes'] = tmp_net.viz['row_nodes']
inst_view['nodes']['col_nodes'] = tmp_net.viz['col_nodes']
all_views.append(inst_view)
except:
# print('\t*** did not cluster N filtered view')
pass
run_enrichr=None, enrichrgram=None):
'''
This will perform hierarchical clustering
'''
# threshold = 0.0001
# df = run_filter.df_filter_row_sum(df, threshold)
# df = run_filter.df_filter_col_sum(df, threshold)
if run_enrichr is not None:
df = net.dat_to_df()
df = enr_fun.add_enrichr_cats(df, 'row', run_enrichr)
define_cat_colors = True
net.df_to_dat(df, define_cat_colors=True)
inst_dm = calc_clust.cluster_row_and_col(net, dist_type=dist_type,
linkage_type=linkage_type,
run_clustering=run_clustering,
dendro=dendro, ignore_cat=False,
calc_cat_pval=calc_cat_pval)
which_sim = []
if sim_mat == True:
which_sim = ['row', 'col']
elif sim_mat == 'row':
which_sim = ['row']
elif sim_mat == 'col':
which_sim = ['col']
if sim_mat is not False:
sim_net = make_sim_mat.main(net, inst_dm, which_sim, filter_sim, sim_mat_views)
cutoff = inst_filt * max_sum
copy_net = deepcopy(net)
inst_df = deepcopy(df)
inst_df = run_filter.df_filter_row_sum(inst_df, cutoff, take_abs=False)
tmp_net = deepcopy(Network())
tmp_net.df_to_dat(inst_df)
try:
try:
calc_clust.cluster_row_and_col(tmp_net, dist_type=dist_type,
run_clustering=True)
except:
calc_clust.cluster_row_and_col(tmp_net, dist_type=dist_type,
run_clustering=False)
inst_view = {}
inst_view['pct_row_' + rank_type] = inst_filt
inst_view['dist'] = 'cos'
inst_view['nodes'] = {}
inst_view['nodes']['row_nodes'] = tmp_net.viz['row_nodes']
inst_view['nodes']['col_nodes'] = tmp_net.viz['col_nodes']
all_views.append(inst_view)
except:
pass
return all_views