In [1]:

from profile_binr import ProfileBin

In [2]:

import pandas as pd

In [3]:

!curl -fOL https://github.com/pinellolab/STREAM/raw/master/stream/tests/datasets/Nestorowa_2016/data_Nestorowa.tsv.gz

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   183  100   183    0     0    516      0 --:--:-- --:--:-- --:--:--   515
100 29.7M  100 29.7M    0     0  11.2M      0  0:00:02  0:00:02 --:--:-- 27.4M0:24  0:00:02  0:00:22 5475k

Important columns should be genes, rows should be cells

In [4]:

data = pd.read_csv("data_Nestorowa.tsv.gz", compression="gzip", sep="\t", index_col=0).T
data.head()

Out[4]:

	Kdm3a	Coro2b	Phf6	Usp14	Tmem167b	Kbtbd7	Rag2	...	Zfp438	Rab18	Mzb1	B4galt6	Rnf125	Impact	Taf4b	Zfp521	Psma8
HSPC_025	4.891604	1.426148	2.599758	2.954035	6.357369	2.129140	1.426148	...	1.426148	9.660368	1.426148	1.426148	2.12914	8.177546	1.426148	1.426148	7.869409
HSPC_031	6.877725	0.000000	2.423483	1.804914	0.000000	0.000000	0.000000	...	0.000000	0.699126	0.000000	6.562672	0.00000	5.439604	0.699126	0.000000	0.000000
HSPC_037	0.000000	6.913384	2.051659	8.265465	0.000000	1.363402	0.000000	...	1.363402	8.885311	0.000000	1.363402	0.00000	8.068215	0.000000	2.051659	1.363402
LT-HSC_001	0.000000	8.178374	6.419817	3.453502	2.579528	2.579528	0.000000	...	2.579528	6.501342	4.947883	0.000000	0.00000	0.000000	2.579528	8.178374	2.579528
HSPC_001	0.000000	9.475577	7.733370	1.478900	0.000000	10.045601	0.532906	...	0.000000	1.693409	7.975432	8.561045	0.00000	6.539920	0.532906	0.000000	0.532906

5 rows × 4768 columns

In [5]:

probin = ProfileBin(data)

In [6]:

%time probin.fit()

CPU times: user 24.3 s, sys: 182 ms, total: 24.5 s
Wall time: 58.4 s

In [7]:

probin.criteria.head()

Out[7]:

	Dip	BI	Kurtosis	DropOutRate	MeanNZ	DenPeak	Amplitude	Category
Clec1b	0.358107	1.635698	54.017736	0.876208	1.520978	-0.007249	8.852181	ZeroInf
Kbtbd7	0.000000	2.137107	3.577214	0.571256	2.928988	-0.000556	10.910051	ZeroInf
Mns1	0.000000	2.066577	-1.260230	0.100242	4.743786	1.884848	10.862714	Bimodal
Nek1	0.000000	2.292238	-0.196326	0.304348	3.339581	0.218894	10.153184	Bimodal
Zfp758	0.000000	2.656696	0.424673	0.410024	3.392367	0.032378	10.114596	Bimodal

In [8]:

%time bindata = probin.binarize()

CPU times: user 35.8 s, sys: 89.8 ms, total: 35.9 s
Wall time: 35.9 s

In [9]:

bindata.head()

Out[9]:

	Clec1b	Kdm3a	Coro2b	8430408G22Rik	Clec9a	Phf6	Usp14	Tmem167b	Kbtbd7	Rag2	...	Zfp438	Rab18	Mzb1	B4galt6	Impact	Taf4b	Zfp521	Hrh4	Psma8
HSPC_025	NaN	1.0	NaN	NaN	NaN	0.0	0.0	1.0	NaN	NaN	...	1.0	1.0	1.0	0.0	1.0	NaN	NaN	NaN	1.0
HSPC_031	NaN	1.0	NaN	NaN	NaN	0.0	0.0	0.0	NaN	NaN	...	NaN	0.0	NaN	1.0	NaN	NaN	NaN	NaN	NaN
HSPC_037	NaN	0.0	1.0	NaN	NaN	0.0	1.0	0.0	NaN	NaN	...	1.0	1.0	NaN	0.0	1.0	NaN	NaN	NaN	NaN
LT-HSC_001	NaN	0.0	1.0	NaN	NaN	1.0	0.0	0.0	NaN	NaN	...	1.0	1.0	1.0	0.0	0.0	NaN	1.0	NaN	NaN
HSPC_001	NaN	0.0	1.0	NaN	NaN	1.0	0.0	0.0	1.0	NaN	...	NaN	0.0	1.0	1.0	1.0	NaN	NaN	NaN	NaN

5 rows × 4768 columns

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