Mercurial > repos > goeckslab > scimap_spatial

comparison scimap_phenotyping.py @ 2:d19c068c2490 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 18:44:35 +0000
parents 42e6c251bfd0
children
comparison
equal deleted inserted replaced
1:fd38e533a54b 2:d19c068c2490
7 7
8 8
9 def main( 9 def main(
10 adata, 10 adata,
11 output, 11 output,
12 log,
12 gating_workflow, 13 gating_workflow,
13 gating_workflow_ext, 14 gating_workflow_ext,
14 manual_gates=None, 15 manual_gates=None,
15 manual_gates_ext=None, 16 manual_gates_ext=None,
16 rescale_plots=False 17 random_state=0
17 ): 18 ):
18 """ 19 """
19 Parameter 20 Parameter
20 --------- 21 ---------
21 adata : str 22 adata : str
22 File path to the input AnnData. 23 File path to the input AnnData.
23 output : str 24 output : str
24 File path to the output AnnData. 25 File path to the output AnnData.
26 log: bool
27 Boolean whether to log the input data prior to rescaling
25 gating_workflow : str 28 gating_workflow : str
26 File path to the gating workflow. 29 File path to the gating workflow.
27 gating_workflow_ext : str 30 gating_workflow_ext : str
28 Datatype for gating workflow, either 'csv' or 'tabular'. 31 Datatype for gating workflow, either 'csv' or 'tabular'.
29 manual_gates : str 32 manual_gates : str
30 File path to the munual gating. 33 File path to the munual gating.
31 manual_gates_ext : str 34 manual_gates_ext : str
32 Datatype for munual gate, either 'csv' or 'tabular'. 35 Datatype for munual gate, either 'csv' or 'tabular'.
33 rescale_plots : boolean 36 random_state: int
34 Save plots from rescaling. 37 The seed used by the random number generator for GMM in sm.pp.rescale
35 """ 38 """
36 warnings.simplefilter('ignore') 39 warnings.simplefilter('ignore')
37 40
38 adata = read_h5ad(adata) 41 adata = read_h5ad(adata)
39 # Rescale data 42 # Rescale data
40 if manual_gates: 43 if manual_gates:
41 sep = ',' if manual_gates_ext == 'csv' else '\t' 44 sep = ',' if manual_gates_ext == 'csv' else '\t'
42 manual_gates = pd.read_csv(manual_gates, sep=sep) 45 manual_gates = pd.read_csv(manual_gates, sep=sep)
43 46
44 adata = sm.pp.rescale(adata, gate=manual_gates, save_fig=rescale_plots) 47 adata = sm.pp.rescale(
48 adata,
49 gate=manual_gates,
50 log=log,
51 random_state=random_state
52 )
45 53
46 # Phenotype cells 54 # Phenotype cells
47 # Load the gating workflow 55 # Load the gating workflow
48 sep = ',' if gating_workflow_ext == 'csv' else '\t' 56 sep = ',' if gating_workflow_ext == 'csv' else '\t'
49 phenotype = pd.read_csv(gating_workflow, sep=sep) 57 phenotype = pd.read_csv(gating_workflow, sep=sep)
50 adata = sm.tl.phenotype_cells(adata, phenotype=phenotype, label="phenotype") 58 adata = sm.tl.phenotype_cells(
59 adata,
60 phenotype=phenotype,
61 label="phenotype"
62 )
51 63
52 # Summary of the phenotyping 64 # Summary of the phenotyping
53 print(adata.obs['phenotype'].value_counts()) 65 print(adata.obs['phenotype'].value_counts())
54 66
55 adata.write(output) 67 adata.write(output)
57 69
58 if __name__ == '__main__': 70 if __name__ == '__main__':
59 aparser = argparse.ArgumentParser() 71 aparser = argparse.ArgumentParser()
60 aparser.add_argument("-a", "--adata", dest="adata", required=True) 72 aparser.add_argument("-a", "--adata", dest="adata", required=True)
61 aparser.add_argument("-o", "--output", dest="output", required=True) 73 aparser.add_argument("-o", "--output", dest="output", required=True)
62 aparser.add_argument("-g", "--gating_workflow", dest="gating_workflow", required=True) 74 aparser.add_argument("-l", "--log", dest="log", action="store_true")
63 aparser.add_argument("-s", "--gating_workflow_ext", dest="gating_workflow_ext", required=True) 75 aparser.add_argument(
64 aparser.add_argument("-m", "--manual_gates", dest="manual_gates", required=False) 76 "-g",
65 aparser.add_argument("-S", "--manual_gates_ext", dest="manual_gates_ext", required=False) 77 "--gating_workflow",
66 aparser.add_argument("-p", "--rescale_plots", dest="rescale_plots", action="store_true", 78 dest="gating_workflow",
67 default=False, required=False) 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 )
68 105
69 args = aparser.parse_args() 106 args = aparser.parse_args()
70 107
71 main(args.adata, args.output, args.gating_workflow, 108 if args.log:
72 args.gating_workflow_ext, args.manual_gates, 109 print("\n adata.raw.X will be log1p transformed \n")
73 args.manual_gates_ext, args.rescale_plots) 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 )