def average_TPM(a,b):
log_a = np.log(1+a)
log_b = np.log(1+b)
if log_a > 0.1 and log_b > 0.1:
avg = np.mean([log_a,log_b])
else:
avg = np.nan
return avg
df.loc[:,'leaf'] = df.apply(lambda row: average_TPM(row['leaf1'],row['leaf2']),axis=1)
df.loc[:,'flag_leaf'] = df.apply(lambda row: average_TPM(row['flag_leaf1'],row['flag_leaf2']),axis=1)
df.loc[:,'anther'] = df.apply(lambda row: average_TPM(row['anther1'],row['anther2']),axis=1)
df.loc[:,'premeiotic'] = df.apply(lambda row: average_TPM(row['premeiotic1'],row['premeiotic2']),axis=1)
df.loc[:,'leptotene'] = df.apply(lambda row: average_TPM(row['leptotene1'],row['leptotene2']),axis=1)
df.loc[:,'zygotene'] = df.apply(lambda row: average_TPM(row['zygotene1'],row['zygotene2']),axis=1)
df.loc[:,'pachytene'] = df.apply(lambda row: average_TPM(row['pachytene1'],row['pachytene2']),axis=1)
df.loc[:,'diplotene'] = df.apply(lambda row: average_TPM(row['diplotene1'],row['diplotene2']),axis=1)
df.loc[:,'metaphase_I'] = df.apply(lambda row: average_TPM(row['metaphaseI_1'],row['metaphaseI_2']),axis=1)
df.loc[:,'metaphase_II'] = df.apply(lambda row: average_TPM(row['metaphaseII_1'],row['metaphaseII_2']),axis=1)
df.loc[:,'pollen'] = df.apply(lambda row: average_TPM(row['pollen1'],row['pollen2']),axis=1)
不确定为什么会出现内存错误,但是可以将问题向量化:
#dummy variable
np.random.seed = 2
df = pd.DataFrame(np.random.random(8*4).reshape(8,-1), columns=['a1','a2','b1','b2'])
print (df)
a1 a2 b1 b2
0 0.416493 0.964483 0.089547 0.218952
1 0.655331 0.468490 0.272494 0.652915
2 0.680433 0.461191 0.919223 0.552074
3 0.077158 0.138839 0.385818 0.462848
4 0.149198 0.912372 0.893708 0.081125
5 0.255422 0.143502 0.466123 0.524544
6 0.842095 0.486603 0.628405 0.686393
7 0.329461 0.714052 0.176126 0.566491
定义要创建的列的列表,然后一次对整个数据使用np.log1p
np.log1p
现在您可以使用col_create = ['a','b'] #what you need to redefine for your problem
col_get = [f'{col}{i}'for col in col_create for i in range(1,3)] #to ensure the order od columns
arr_log = np.log1p(df[col_get].to_numpy())
并将新列矢量化比较到np.where
:
assign