[pre-commit.ci] auto fixes from pre-commit.com hooks

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src/scirpy/pl/__init__.py

@@ -5,8 +5,8 @@
 from ._clonotypes import COLORMAP_EDGES, clonotype_network
 from ._diversity import alpha_diversity
 from ._group_abundance import group_abundance
+from ._logoplots import logoplot_cdr3_motif
 from ._repertoire_overlap import repertoire_overlap
 from ._spectratype import spectratype
 from ._vdj_usage import vdj_usage
-from ._logoplots import logoplot_cdr3_motif
 from .base import embedding

src/scirpy/pl/_logoplots.py

@@ -1,21 +1,20 @@
-from scirpy.util import DataHandler
-from typing import Callable, Literal, Union
 from collections.abc import Sequence
-from scirpy.get import obs_context
-from scirpy.get import airr as get_airr
-
-import numpy as np
-import pandas as pd
+from typing import Literal, Union
 
 import palmotif as palm
+import pandas as pd
 from IPython.display import SVG
 
+from scirpy.get import airr as get_airr
+from scirpy.util import DataHandler
+
+
 @DataHandler.inject_param_docs()
 def logoplot_cdr3_motif(
     adata: DataHandler.TYPE,
     chains: Union[
-    Literal["VJ_1", "VDJ_1", "VJ_2", "VDJ_2"],
-    Sequence[Literal["VJ_1", "VDJ_1", "VJ_2", "VDJ_2"]],
+        Literal["VJ_1", "VDJ_1", "VJ_2", "VDJ_2"],
+        Sequence[Literal["VJ_1", "VDJ_1", "VJ_2", "VDJ_2"]],
     ] = "VDJ_1",
     airr_mod="airr",
     airr_key="airr",
@@ -29,8 +28,9 @@ def logoplot_cdr3_motif(
     clonotype_key: Union[None, str] = None,
     cdr_len: int,
     plot: bool = True,
-    color_scheme: Sequence[Literal["nucleotide", "base_pairing", "hydrophobicity", "chemistry", "charge", "taylor",
-                      "logojs", "shapely"]] = "taylor"
+    color_scheme: Sequence[
+        Literal["nucleotide", "base_pairing", "hydrophobicity", "chemistry", "charge", "taylor", "logojs", "shapely"]
+    ] = "taylor",
 ):
     """
     A user friendly wrapper function for the palmotif python package.
@@ -68,38 +68,42 @@ def logoplot_cdr3_motif(
         set to false to retrieve the raw sequence motif for customised use
     color_scheme
         different color schemes used by palmotif. see https://github.com/agartland/palmotif/blob/master/palmotif/aacolors.py for more details
-    
+
     Returns
-    ----------
+    -------
     Depending on `plot` either returns a SVG object or the calculated sequence motif as a pd.DataFrame
     """
     params = DataHandler(adata, airr_mod, airr_key, chain_idx_key)
 
-    if by is "length":
-
+    if by == "length":
         airr_df = get_airr(params, [cdr3_col], chains)
         if type(chains) is list:
             if len(chains) > 2:
                 raise Exception("Only two different chains are allowed e.g. VDJ_1 and VDJ_2")
 
             else:
-                cdr3_list = airr_df[airr_df[chains[0] + "_" + cdr3_col].str.len() == cdr_len][chains[0] + "_" + cdr3_col].to_list()
-                cdr3_list += airr_df[airr_df[chains[1] + "_" + cdr3_col].str.len() == cdr_len][chains[1] + "_" + cdr3_col].to_list()
+                cdr3_list = airr_df[airr_df[chains[0] + "_" + cdr3_col].str.len() == cdr_len][
+                    chains[0] + "_" + cdr3_col
+                ].to_list()
+                cdr3_list += airr_df[airr_df[chains[1] + "_" + cdr3_col].str.len() == cdr_len][
+                    chains[1] + "_" + cdr3_col
+                ].to_list()
                 motif = palm.compute_motif(cdr3_list)
         else:
             motif = palm.compute_motif(
                 airr_df[airr_df[chains + "_" + cdr3_col].str.len() == cdr_len][chains + "_" + cdr3_col].to_list()
-                )
-            
+            )
+
         if plot:
-            return SVG(palm.svg_logo(motif, return_str = False, color_scheme=color_scheme))
+            return SVG(palm.svg_logo(motif, return_str=False, color_scheme=color_scheme))
         else:
             return motif
 
-
-    if by is "gene_segment":
+    if by == "gene_segment":
         if target_col is None or gene_annotation is None:
-            raise Exception("Please specify where the gene information is stored (`target_col`) and which genes to include (`gene_annotation`) as a list")
+            raise Exception(
+                "Please specify where the gene information is stored (`target_col`) and which genes to include (`gene_annotation`) as a list"
+            )
         if type(gene_annotation) is not list:
             gene_annotation = list(gene_annotation.split(" "))
 
@@ -108,27 +112,35 @@ def logoplot_cdr3_motif(
             if len(chains) > 2:
                 raise Exception("Only two different chains are allowed e.g. VDJ_1 and VDJ_2")
 
-            cdr3_list = airr_df[(airr_df[chains[0] + "_" + target_col].isin(gene_annotation)) &
-            (airr_df[chains[0] + "_" + cdr3_col].str.len() == cdr_len)][chains[0] + "_" + cdr3_col].to_list()
-            cdr3_list += airr_df[(airr_df[chains[1] + "_" + target_col].isin(gene_annotation)) &
-            (airr_df[chains[1] + "_" + cdr3_col].str.len() == cdr_len)][chains[1] + "_" + cdr3_col].to_list()
+            cdr3_list = airr_df[
+                (airr_df[chains[0] + "_" + target_col].isin(gene_annotation))
+                & (airr_df[chains[0] + "_" + cdr3_col].str.len() == cdr_len)
+            ][chains[0] + "_" + cdr3_col].to_list()
+            cdr3_list += airr_df[
+                (airr_df[chains[1] + "_" + target_col].isin(gene_annotation))
+                & (airr_df[chains[1] + "_" + cdr3_col].str.len() == cdr_len)
+            ][chains[1] + "_" + cdr3_col].to_list()
             motif = palm.compute_motif(cdr3_list)
-            
+
         else:
             motif = palm.compute_motif(
-            airr_df[(airr_df[chains + "_" + target_col].isin(gene_annotation)) &
-            (airr_df[chains + "_" + cdr3_col].str.len() == cdr_len)][chains + "_" + cdr3_col].to_list()
-        )
+                airr_df[
+                    (airr_df[chains + "_" + target_col].isin(gene_annotation))
+                    & (airr_df[chains + "_" + cdr3_col].str.len() == cdr_len)
+                ][chains + "_" + cdr3_col].to_list()
+            )
 
         if plot:
-            return SVG(palm.svg_logo(motif, return_str = False, color_scheme=color_scheme))
+            return SVG(palm.svg_logo(motif, return_str=False, color_scheme=color_scheme))
         else:
             return motif
-    
-    if by is "clonotype":
+
+    if by == "clonotype":
         if clonotype_id is None or clonotype_key is None:
-            raise Exception("Please select desired clonotype cluster and the name of the column where this information is stored!")
-
+            raise Exception(
+                "Please select desired clonotype cluster and the name of the column where this information is stored!"
+            )
+
         if type(clonotype_id) is not list:
             clonotype_id = list(clonotype_id.split(" "))
 
@@ -139,25 +151,27 @@ def logoplot_cdr3_motif(
         airr_df = pd.concat([airr_df, params.get_obs(clonotype_key)])
         airr_df = airr_df.loc[params.get_obs(clonotype_key).isin(clonotype_id)]
 
-
-
         if type(chains) is list:
             if len(chains) > 2:
                 raise Exception("Only two different chains are allowed e.g. VDJ_1 and VDJ_2")
 
             else:
-                cdr3_list = airr_df[airr_df[chains[0] + "_" + cdr3_col].str.len() == cdr_len][chains[0] + "_" + cdr3_col].to_list()
-                cdr3_list += airr_df[airr_df[chains[1] + "_" + cdr3_col].str.len() == cdr_len][chains[1] + "_" + cdr3_col].to_list()
+                cdr3_list = airr_df[airr_df[chains[0] + "_" + cdr3_col].str.len() == cdr_len][
+                    chains[0] + "_" + cdr3_col
+                ].to_list()
+                cdr3_list += airr_df[airr_df[chains[1] + "_" + cdr3_col].str.len() == cdr_len][
+                    chains[1] + "_" + cdr3_col
+                ].to_list()
                 motif = palm.compute_motif(cdr3_list)
         else:
             motif = palm.compute_motif(
                 airr_df[airr_df[chains + "_" + cdr3_col].str.len() == cdr_len][chains + "_" + cdr3_col].to_list()
-                )
-            
+            )
+
         if plot:
-            return SVG(palm.svg_logo(motif, return_str = False, color_scheme=color_scheme))
+            return SVG(palm.svg_logo(motif, return_str=False, color_scheme=color_scheme))
         else:
             return motif
 
     else:
-        raise Exception("Invalid input for parameter `by`!")
+        raise Exception("Invalid input for parameter `by`!")