--- a/scimap_phenotyping.py	Mon Aug 29 23:55:43 2022 +0000
+++ b/scimap_phenotyping.py	Mon Jun 10 18:44:35 2024 +0000
@@ -9,11 +9,12 @@
 def main(
     adata,
     output,
+    log,
     gating_workflow,
     gating_workflow_ext,
     manual_gates=None,
     manual_gates_ext=None,
-    rescale_plots=False
+    random_state=0
 ):
     """
     Parameter
@@ -22,6 +23,8 @@
         File path to the input AnnData.
     output : str
         File path to the output AnnData.
+    log: bool
+        Boolean whether to log the input data prior to rescaling
     gating_workflow : str
         File path to the gating workflow.
     gating_workflow_ext : str
@@ -30,8 +33,8 @@
         File path to the munual gating.
     manual_gates_ext : str
         Datatype for munual gate, either 'csv' or 'tabular'.
-    rescale_plots : boolean
-        Save plots from rescaling.
+    random_state: int
+        The seed used by the random number generator for GMM in sm.pp.rescale
     """
     warnings.simplefilter('ignore')
 
@@ -41,13 +44,22 @@
         sep = ',' if manual_gates_ext == 'csv' else '\t'
         manual_gates = pd.read_csv(manual_gates, sep=sep)
 
-    adata = sm.pp.rescale(adata, gate=manual_gates, save_fig=rescale_plots)
+    adata = sm.pp.rescale(
+        adata,
+        gate=manual_gates,
+        log=log,
+        random_state=random_state
+    )
 
     # Phenotype cells
     # Load the gating workflow
     sep = ',' if gating_workflow_ext == 'csv' else '\t'
     phenotype = pd.read_csv(gating_workflow, sep=sep)
-    adata = sm.tl.phenotype_cells(adata, phenotype=phenotype, label="phenotype")
+    adata = sm.tl.phenotype_cells(
+        adata,
+        phenotype=phenotype,
+        label="phenotype"
+    )
 
     # Summary of the phenotyping
     print(adata.obs['phenotype'].value_counts())
@@ -59,15 +71,50 @@
     aparser = argparse.ArgumentParser()
     aparser.add_argument("-a", "--adata", dest="adata", required=True)
     aparser.add_argument("-o", "--output", dest="output", required=True)
-    aparser.add_argument("-g", "--gating_workflow", dest="gating_workflow", required=True)
-    aparser.add_argument("-s", "--gating_workflow_ext", dest="gating_workflow_ext", required=True)
-    aparser.add_argument("-m", "--manual_gates", dest="manual_gates", required=False)
-    aparser.add_argument("-S", "--manual_gates_ext", dest="manual_gates_ext", required=False)
-    aparser.add_argument("-p", "--rescale_plots", dest="rescale_plots", action="store_true",
-                         default=False, required=False)
+    aparser.add_argument("-l", "--log", dest="log", action="store_true")
+    aparser.add_argument(
+        "-g",
+        "--gating_workflow",
+        dest="gating_workflow",
+        required=True
+    )
+    aparser.add_argument(
+        "-s",
+        "--gating_workflow_ext",
+        dest="gating_workflow_ext",
+        required=True
+    )
+    aparser.add_argument(
+        "-m",
+        "--manual_gates",
+        dest="manual_gates",
+        required=False
+    )
+    aparser.add_argument(
+        "-S",
+        "--manual_gates_ext",
+        dest="manual_gates_ext",
+        required=False
+    )
+    aparser.add_argument(
+        "--random_state",
+        dest="random_state",
+        type=int,
+        required=False
+    )
 
     args = aparser.parse_args()
 
-    main(args.adata, args.output, args.gating_workflow,
-         args.gating_workflow_ext, args.manual_gates,
-         args.manual_gates_ext, args.rescale_plots)
+    if args.log:
+        print("\n adata.raw.X will be log1p transformed \n")
+
+    main(
+        adata=args.adata,
+        output=args.output,
+        log=args.log,
+        gating_workflow=args.gating_workflow,
+        gating_workflow_ext=args.gating_workflow_ext,
+        manual_gates=args.manual_gates,
+        manual_gates_ext=args.manual_gates_ext,
+        random_state=args.random_state
+    )