Python 使用形状的因子级别将pandas.DataFrame转换为numpy张量
我有完全析因实验的数据。例如,对于每个Python 使用形状的因子级别将pandas.DataFrame转换为numpy张量,python,pandas,numpy,tensor,numpy-ndarray,Python,Pandas,Numpy,Tensor,Numpy Ndarray,我有完全析因实验的数据。例如,对于每个N样本,我有J测量类型和K测量位点。例如,我以长格式接收这些数据 import numpy as np import pandas as pd import itertools from numpy.random import normal as rnorm # [[N], [J], [K]] levels = [[1,2,3,4], ['start', 'stop'], ['gene1', 'gene2', 'gene3']] # fully cros
N
样本,我有J
测量类型和K
测量位点。例如,我以长格式接收这些数据
import numpy as np
import pandas as pd
import itertools
from numpy.random import normal as rnorm
# [[N], [J], [K]]
levels = [[1,2,3,4], ['start', 'stop'], ['gene1', 'gene2', 'gene3']]
# fully crossed
exp_design = list(itertools.product(*levels))
df = pd.DataFrame(exp_design, columns=["sample", "mode", "gene"])
# some fake data
df['x'] = rnorm(size=len(exp_design))
这将产生24个观察结果(x
),其中三个因素各有一列
> df.head()
sample mode gene x
0 1 start gene1 -1.229370
1 1 start gene2 1.129773
2 1 start gene3 -1.155202
3 1 stop gene1 -0.757551
4 1 stop gene2 -0.166129
我想把这些观测值转换成相应的(N,J,K)
形张量(numpy数组)。我在考虑使用多索引旋转到宽格式,然后提取值将生成正确的张量,但它只是作为列向量:
> df.pivot_table(values='x', index=['sample', 'mode', 'gene']).values
array([[-1.22936989],
[ 1.12977346],
[-1.15520216],
...,
[-0.1031641 ],
[ 1.1296491 ],
[ 1.31113584]])
有没有一种快速的方法可以从长格式的pandas.DataFrame中获取张量格式的数据?试试
df.agg('nunique')
Out[69]:
sample 4
mode 2
gene 3
x 24
dtype: int64
s=df.agg('nunique')
df.x.values.reshape(s['sample'],s['mode'],s['gene'])
Out[71]:
array([[[-2.78133759e-01, -1.42234420e+00, 5.42439121e-01],
[ 2.15359867e+00, 6.55837886e-01, -1.01293568e+00]],
[[ 7.92306679e-01, -1.62539763e-01, -6.13120335e-01],
[-2.91567999e-01, -4.01257702e-01, 7.96422763e-01]],
[[ 1.05088264e-01, -7.23400925e-02, 2.78515041e-01],
[ 2.63088568e-01, 1.47477886e+00, -2.10735619e+00]],
[[-1.71756374e+00, 6.12224005e-04, -3.11562798e-02],
[ 5.26028807e-01, -1.18502045e+00, 1.88633760e+00]]])
我认为在这里需要注意的是,这假设数据帧首先排序为,
df.sort_值(按=['sample','mode','gene'])
@merv是的,您是对的