def changeIndex():
if not os.path.exists(args.index_path):
printT("don't find index file, fail to change index.")
return
# change index
with open(args.index_path, 'r') as f:
lines = f.readlines()
index = [line.strip() for line in lines]
for i in range(data.type_num):
data.trainDatas_df[i].index = index
def del_non_value():
remainIndexs = None
for i in range(data.type_num):
nanIndex = data.edges_df_all[i][data.edges_df_all[i].isnull().all()].index
remainIndexs = nanIndex if remainIndexs is None else remainIndexs & nanIndex
for i in range(data.type_num):
data.edges_df_all[i] = data.edges_df_all[i].drop(index=remainIndexs, columns=remainIndexs)
printT(" output file", args.result_dir + str(i) + '_cor_new.csv')
data.edges_df_all[i].to_csv(args.result_dir + str(i) + '_cor_new.csv')
printT(" remain shape", data.edges_df_all[0].shape)
def cutOffByMin(minNum):
remainIndexs = None
for i in range(data.type_num):
meanFt = data.trainDatas_df[i].mean(1) # get mean
remainIndex = meanFt[meanFt > minNum].index
if remainIndexs is None:
remainIndexs = remainIndex
else:
remainIndexs = remainIndexs & remainIndex
for i in range(data.type_num):
data.trainDatas_df[i] = data.trainDatas_df[i].loc[remainIndexs]
printT(' remain features count:', data.trainDatas_df[0].shape[0])
return
def run(cor_cut, limit_up, limit_down, model_4trend, path_model_cor, name_list,
model_edges_count):
dir_int_str = {}
trends_pos_int_list = []
trends_neg_int_list = []
trends81_int_list = []
for a in range(3):
a_ = a - 1
for b in range(3):
b_ = b - 1
for c in range(3):
c_ = c - 1
for d in range(3):
d_ = d - 1
pre = a_ * 1000 + b_ * 100 + c_ * 10 + d_
pre_str = "%2d%2d%2d%2d" % (a_, b_, c_, d_)
trends81_int_list.append(pre)
dir_int_str[pre] = pre_str
sum_ = a_ + b_ + c_ + d_
if (sum_ > 2) & (a_ == 1):
trends_pos_int_list.append(pre)
elif (sum_ < -2) & (a_ == -1):
trends_neg_int_list.append(pre)
printT(dir_int_str)
printT(trends81_int_list)
pl = multiprocessing.Pool(processes=5)
resultBuffer = []
for name in name_list:
resultBuffer.append(
pl.apply_async(each_data,
(name, cor_cut, limit_up, limit_down, model_4trend,
path_model_cor, dir_int_str, trends_pos_int_list,
trends_neg_int_list, model_edges_count)))
pl.close()
pl.join()
def draw_boxplot(
name,
f_list,
data_path_model,
data_path_p_model,
out_path_pic_model,
):
data_f = []
for f in f_list:
data_f_pre = []
for i in range(5):
printT("read data ", data_path_model % (name, name, i, f))
with open(data_path_model % (name, name, i, f), 'rb') as fr:
data_pre = pickle.load(fr)[0]
with open(data_path_p_model % (name, name, i, f), 'rb') as fr:
p_pre = pickle.load(fr)[0]
data_pre[p_pre > 0.01] = 0
data_pre[data_pre < 0] = -data_pre
data_pre_np = data_pre.values
data_list = data_pre_np.ravel()[np.flatnonzero(data_pre_np)]
data_f_pre.append(data_list)
data_f.append(data_f_pre)
plt.figure(figsize=(20, 10))
p_list = ["Normal", "S1", "S2", "S3", "S4"]
y = np.linspace(0, 1, 6)
printT("draw ", name)
plt.subplot(1, 2, 1)
plt.boxplot(data_f[0], labels=p_list)
plt.yticks(y)
plt.title(f_list[0])
plt.subplot(1, 2, 2)
plt.boxplot(data_f[1], labels=p_list)
plt.yticks(y)
plt.title(f_list[1])
plt.suptitle(name)
printT("save ", name)
plt.savefig(out_path_pic_model % name)
printT("finish ", name, f)
def cal_out_subgraph(connect_graph, data_name, index, trend_data_pre,
subgraphs_model, trend_pre, subgraph_nodelist_model_new,
subgraphs_max_edges_model,
subgraphs_max_model_edges_v_new):
connect_graph_pd = pd.DataFrame(connect_graph, index=index, columns=index)
remainIndex = connect_graph_pd.index
subgraphs = []
added_index = []
for pre in remainIndex:
if pre in added_index:
continue
pre_index = connect_graph_pd.loc[connect_graph_pd[pre] >= 1].index
subgraphs.append(pre_index.tolist())
added_index.extend(pre_index)
printT(data_name, trend_pre, "subgraph count:", len(subgraphs))
subgraphs.sort(key=functools.cmp_to_key(cmp))
output = open(subgraphs_model % (trend_pre, data_name), 'w')
for row in subgraphs:
row_str = str(row).replace("[", "").replace("]", "")
output.write(row_str + '\n')
submax_pd = pd.DataFrame(subgraphs[0])
submax_pd.to_csv(subgraph_nodelist_model_new % (data_name, trend_pre),
header=None,
index=False)
subnet = trend_data_pre[trend_data_pre['Node_A'].isin(subgraphs[0])
& trend_data_pre['Node_B'].isin(subgraphs[0])]
printT(data_name, trend_pre, "subnet nodes count", len(subgraphs[0]))
printT(data_name, trend_pre, "subnet edges count", subnet.shape[0])
subnet[['Node_A', 'Node_B'
]].to_csv(subgraphs_max_edges_model % (trend_pre, data_name),
index=False,
sep="\t")
subnet.to_csv(subgraphs_max_model_edges_v_new % (trend_pre, data_name),
index=False)
def draw_heatmap(
name,
f_list,
data_path_model,
out_path_pic_model,
):
sort_by = ["4", "0"]
for i, f in enumerate(f_list):
printT("read data ", data_path_model % (f, name))
edges_pre = pd.read_csv(data_path_model % (f, name))
edges_pre.sort_values(sort_by)
printT("draw ", name)
plt.figure()
plt.suptitle(name + f)
sns.clustermap(edges_pre[["0", "1", "2", "3", "4"]],
col_cluster=False,
cmap=sns.diverging_palette(270, 5, as_cmap=True))
plt.savefig(out_path_pic_model % (name, f))
printT("finish ", name)
def runAll():
initFile(args)
initCode()
# start
printT("1.0 read data")
initData.createDataSet()
printT("1.1 initData min by", args.cut_value)
initData.cutOffByMin(minNum=args.cut_value)
printT("1.2 change data to log")
initData.toLog()
printT("2 calculate the similarity matrix")
calculate.getSprearmon(need_output=True)
printT("3 delete pvalue larger than", args.remain_p_value)
calculate.del_non_value()
# # if want to compare co-expression with expression value
# printT("cal wilcox")
# cal_wilconxon.get_wilcox()
printT("over.")
def run(namelist, path_model, sub_model, stat_model):
df_stat = pd.DataFrame(None, columns=namelist)
trendlist = ['pos', 'neg']
df_result = pd.DataFrame(None, columns=['C1', 'C2', 'C3', 'C4'])
for name in namelist:
index_maxsub_s = []
index_secsub_s = []
printT()
printT(name)
for trend in trendlist:
subgraph_path = sub_model % (trend, name)
printT(subgraph_path, end=" ")
with open(subgraph_path, 'r') as f:
lines = f.readlines()
points_list = lines[0].split(', ')
points_list2 = lines[1].split(', ')
points_list = [pre.replace("'", "").strip() for pre in points_list]
points_list2 = [
pre.replace("'", "").strip() for pre in points_list2
]
printT(len(points_list))
index_maxsub_s.append(points_list)
index_secsub_s.append(points_list2)
df_stat.at['sub_' + trend + '_points',
name] = len(list(set(points_list)))
df_stat.at['sec_' + trend + '_points',
name] = len(list(set(points_list2)))
node_count_s = []
for i, trend in enumerate(trendlist):
data_path = path_model % (trend, name)
data = pd.read_csv(data_path)
df_stat.at['all_' + trend + '_edges', name] = data.shape[0]
df_stat.at['all_' + trend + '_points', name] = len(
list(set(data['Node_A'].tolist() + data['Node_B'].tolist())))
printT(data.shape, end="->")
data_sec = data[data['Node_A'].isin(index_secsub_s[i])]
data_sec = data_sec[data_sec['Node_B'].isin(index_secsub_s[i])]
printT(data_sec.shape)
df_stat.at['sec_' + trend + '_edges', name] = data_sec.shape[0]
data = data[data['Node_A'].isin(index_maxsub_s[i])]
data = data[data['Node_B'].isin(index_maxsub_s[i])]
printT(data.shape, data_path)
df_stat.at['sub_' + trend + '_edges', name] = data.shape[0]
index = data['Node_A'].tolist() + data['Node_B'].tolist()
df_stat.at['sub_' + trend + '_points',
name] = len(list(set(index)))
result = Counter(index)
node_count_pre = pd.DataFrame(list(result.most_common()),
columns=['Node', trend + '_num'])
node_count_pre.set_index(["Node"], inplace=True)
printT(i, "node count", node_count_pre.shape)
node_count_s.append(node_count_pre)
node_count_df = node_count_s[0].join(node_count_s[1], how='outer')
printT("all node count", node_count_df.shape)
node_count_df = node_count_df.fillna(0)
c1 = node_count_df[(node_count_df[trendlist[0] + '_num'] != 0)
& (node_count_df[trendlist[1] + '_num'] != 0)]
c2 = node_count_df[(node_count_df[trendlist[0] + '_num'] > 5)
& (node_count_df[trendlist[1] + '_num'] > 5)]
c3_pos = node_count_df[(node_count_df[trendlist[0] + '_num'] >= 1)
& (node_count_df[trendlist[1] + '_num'] == 0)]
c3_neg = node_count_df[(node_count_df[trendlist[0] + '_num'] == 0)
& (node_count_df[trendlist[1] + '_num'] >= 1)]
df_result.loc[name] = [
c1.shape[0], c2.shape[0], c3_pos.shape[0], c3_neg.shape[0]
]
df_stat = df_stat.sort_index()
print(df_stat)
df_stat.to_csv(stat_model)
def each_data(data_name, cor_cut, limit_up, limit_down, model_4trend,
path_model_cor, dir_int_str, trends_pos_int_list,
trends_neg_int_list, model_edges_count):
adj_sum = None
na_num_list = []
cors_ori_pd = []
cors_sign_np = []
cal_sign_np = None
for i in range(5):
# init
printT(path_model_cor % (data_name, i))
cor_pre_pd = pd.read_csv(path_model_cor % (data_name, i), index_col=0)
cor_pre_np = np.triu(cor_pre_pd.values, 1)
cor_pre_pd[np.abs(cor_pre_pd) < cor_cut] = 0
cor_pre_pd = pd.DataFrame(cor_pre_np,
index=cor_pre_pd.index,
columns=cor_pre_pd.columns)
cor_pre_pd = cor_pre_pd.fillna(0)
if adj_sum is None:
adj_sum = cor_pre_pd
else:
adj_sum = adj_sum + abs(cor_pre_pd)
na_num_list.append((cor_pre_pd != 0).sum().sum())
# cal signal
cors_ori_pd.append(cor_pre_pd)
cors_sign_pre_np = np.where(cor_pre_pd > 0, 1, cor_pre_pd)
cors_sign_pre_np = np.where(cors_sign_pre_np < 0, 10, cor_pre_pd)
cors_sign_np.append(cors_sign_pre_np)
if cal_sign_np is None:
cal_sign_np = cors_sign_pre_np
else:
cal_sign_np = cal_sign_np + cors_sign_pre_np
na_num_list.append((adj_sum != 0).sum().sum())
pd.DataFrame(na_num_list).to_csv(model_edges_count % data_name)
# set abs or ori
cal_sign_np = np.where((cal_sign_np % 10 == 0) & (cal_sign_np != 0), -1,
1) # all<0 | all=0
cors_abs = []
printT("calculate sign", data_name)
for i in range(5):
cors_abs.append(cal_sign_np * cors_ori_pd[i])
# cal trend up
printT("calculate trend", data_name)
trends = None
trends_add = None
for i in range(4):
pre_distance = cors_abs[i + 1] - cors_abs[i]
if i == 0:
pre_distance[pre_distance >= limit_up] = 1
pre_distance[pre_distance <= -limit_up] = -1
pre_distance[(pre_distance < limit_up)
& (pre_distance > -limit_up)] = 0
else:
"""
add>0 (-d,u)
add=0 (-u,u)
add<0 (-u,d)
"""
pre_distance[(pre_distance >= limit_up) & (trends_add >= 0)] = 1
pre_distance[(pre_distance >= limit_down) & (trends_add < 0)] = 1
pre_distance[(pre_distance <= -limit_down) & (trends_add > 0)] = -1
pre_distance[(pre_distance <= -limit_up) & (trends_add <= 0)] = -1
pre_distance[(pre_distance < limit_up)
& (pre_distance > -limit_down) & (trends_add > 0)] = 0
pre_distance[(pre_distance < limit_up) & (pre_distance > -limit_up)
& (trends_add == 0)] = 0
pre_distance[(pre_distance < limit_down)
& (pre_distance > -limit_up) & (trends_add < 0)] = 0
if trends is None:
trends = pre_distance
trends_add = pre_distance
else:
trends = trends * 10 + pre_distance
trends_add = trends_add + pre_distance
# output
index = trends.index
columns = trends.columns
for trend_pre, trends_int_list in zip(
["pos", "neg"], [trends_pos_int_list, trends_neg_int_list]):
trends4_pre = pd.DataFrame(
None,
columns=["trend", "Node_A", "Node_B", "0", "1", "2", "3", "4"])
printT("collect", data_name, trend_pre)
for pre_trend in trends_int_list:
locs = np.where(trends == pre_trend)
index_pre_name = [index[i] for i in locs[0]]
columns_pre_name = [columns[i] for i in locs[1]]
pd_pre = pd.DataFrame(None, columns=trends4_pre.columns)
pd_pre["Node_A"] = index_pre_name
pd_pre["Node_B"] = columns_pre_name
for i in range(5):
pd_pre[str(i)] = [
cors_ori_pd[i].at[a, b]
for a, b in zip(index_pre_name, columns_pre_name)
]
pd_pre["trend"] = dir_int_str[pre_trend]
trends4_pre = pd.concat([trends4_pre, pd_pre], axis=0)
printT(data_name, trend_pre, trends4_pre.shape, "output",
model_4trend % ("pos", data_name))
trends4_pre.to_csv(model_4trend % (trend_pre, data_name))
def readFile(path):
dataSet = pd.read_csv(path, sep='\t')
printT(' ' + path, dataSet.shape)
data.trainDatas_df.append(dataSet)
return
def each_process_fold(sample_num, i, trainDataFrame, need_output): # non-multi
import pickle
printT(" calculate spearmon %d, " % i, trainDataFrame.shape)
# # doesn't use fold
# scc_unfold, p_unfold = getSimilarAndPvalue(trainDataFrame)
# cDF_unfold = pd.DataFrame(scc_unfold, index=trainDataFrame.index, columns=trainDataFrame.index)
# pDF_unfold = pd.DataFrame(p_unfold, index=trainDataFrame.index, columns=trainDataFrame.index)
# printT(" output file", args.result_dir + args.data_name + '_' + str(i) + '_cor_unfold.pkl')
# with open(args.result_dir + args.data_name + '_' + str(i) + '_cor_unfold.pkl', 'wb') as fw:
# pickle.dump([cDF_unfold], fw, 0)
# printT(" output file", args.result_dir + args.data_name + '_' + str(i) + '_p_unfold.pkl')
# with open(args.result_dir + args.data_name + '_' + str(i) + '_p_unfold.pkl', 'wb') as fw:
# pickle.dump([pDF_unfold], fw, 0)
np.random.seed(66)
fold_num = 10
sccDF = 0
pDF = 1
need_g = 1 + int((sample_num * fold_num) / data.trainDatas_df[i].shape[1])
list_all = []
for nee in range(need_g):
list_pre = [j for j in range(data.trainDatas_df[i].shape[1])]
shuffle(list_pre)
list_all.extend(list_pre)
for j in range(fold_num): # 10-fold
train_index = list_all[j * sample_num:(j + 1) * sample_num]
printT(" spearmon %d by fold=%d/%d %d sample=%s" % (i, j, fold_num, len(train_index), train_index))
trainDataFrame_pre = trainDataFrame.iloc[:, train_index]
scc, p = getSimilarAndPvalue(trainDataFrame_pre)
sccDF_pre = pd.DataFrame(scc, index=trainDataFrame_pre.index, columns=trainDataFrame_pre.index)
pDF_pre = pd.DataFrame(p, index=trainDataFrame_pre.index, columns=trainDataFrame_pre.index)
sccDF = sccDF + sccDF_pre
pDF = pDF * pDF_pre
printT(" spearmon %d finish" % i)
cDF_result = sccDF / fold_num
pDF_result = pDF ** (1 / fold_num)
if need_output:
printT(" output file", args.result_dir + args.data_name + '_' + str(i) + '_cor_fold.pkl')
with open(args.result_dir + args.data_name + '_' + str(i) + '_cor_fold.pkl', 'wb') as fw:
pickle.dump([cDF_result], fw, 0)
printT(" output file", args.result_dir + args.data_name + '_' + str(i) + '_p_fold.pkl')
with open(args.result_dir + args.data_name + '_' + str(i) + '_p_fold.pkl', 'wb') as fw:
pickle.dump([pDF_result], fw, 0)
printT(" delete spearmon %d by p>%f" % (i, args.remain_p_value))
cDF_result[pDF_result > args.remain_p_value] = np.nan
printT(" calculate spearmon %d finish" % i)
return cDF_result
