Mercurial > repos > goeckslab > scimap_plotting

comparison scimap_phenotyping.py @ 0:834ee9481948 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
author goeckslab
date Mon, 10 Jun 2024 18:45:07 +0000
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-1:000000000000 0:834ee9481948
1 import argparse
2 import warnings
3
4 import pandas as pd
5 import scimap as sm
6 from anndata import read_h5ad
7
8
9 def main(
10 adata,
11 output,
12 log,
13 gating_workflow,
14 gating_workflow_ext,
15 manual_gates=None,
16 manual_gates_ext=None,
17 random_state=0
18 ):
19 """
20 Parameter
21 ---------
22 adata : str
23 File path to the input AnnData.
24 output : str
25 File path to the output AnnData.
26 log: bool
27 Boolean whether to log the input data prior to rescaling
28 gating_workflow : str
29 File path to the gating workflow.
30 gating_workflow_ext : str
31 Datatype for gating workflow, either 'csv' or 'tabular'.
32 manual_gates : str
33 File path to the munual gating.
34 manual_gates_ext : str
35 Datatype for munual gate, either 'csv' or 'tabular'.
36 random_state: int
37 The seed used by the random number generator for GMM in sm.pp.rescale
38 """
39 warnings.simplefilter('ignore')
40
41 adata = read_h5ad(adata)
42 # Rescale data
43 if manual_gates:
44 sep = ',' if manual_gates_ext == 'csv' else '\t'
45 manual_gates = pd.read_csv(manual_gates, sep=sep)
46
47 adata = sm.pp.rescale(
48 adata,
49 gate=manual_gates,
50 log=log,
51 random_state=random_state
52 )
53
54 # Phenotype cells
55 # Load the gating workflow
56 sep = ',' if gating_workflow_ext == 'csv' else '\t'
57 phenotype = pd.read_csv(gating_workflow, sep=sep)
58 adata = sm.tl.phenotype_cells(
59 adata,
60 phenotype=phenotype,
61 label="phenotype"
62 )
63
64 # Summary of the phenotyping
65 print(adata.obs['phenotype'].value_counts())
66
67 adata.write(output)
68
69
70 if __name__ == '__main__':
71 aparser = argparse.ArgumentParser()
72 aparser.add_argument("-a", "--adata", dest="adata", required=True)
73 aparser.add_argument("-o", "--output", dest="output", required=True)
74 aparser.add_argument("-l", "--log", dest="log", action="store_true")
75 aparser.add_argument(
76 "-g",
77 "--gating_workflow",
78 dest="gating_workflow",
79 required=True
80 )
81 aparser.add_argument(
82 "-s",
83 "--gating_workflow_ext",
84 dest="gating_workflow_ext",
85 required=True
86 )
87 aparser.add_argument(
88 "-m",
89 "--manual_gates",
90 dest="manual_gates",
91 required=False
92 )
93 aparser.add_argument(
94 "-S",
95 "--manual_gates_ext",
96 dest="manual_gates_ext",
97 required=False
98 )
99 aparser.add_argument(
100 "--random_state",
101 dest="random_state",
102 type=int,
103 required=False
104 )
105
106 args = aparser.parse_args()
107
108 if args.log:
109 print("\n adata.raw.X will be log1p transformed \n")
110
111 main(
112 adata=args.adata,
113 output=args.output,
114 log=args.log,
115 gating_workflow=args.gating_workflow,
116 gating_workflow_ext=args.gating_workflow_ext,
117 manual_gates=args.manual_gates,
118 manual_gates_ext=args.manual_gates_ext,
119 random_state=args.random_state
120 )