lotsofcells 0.3.0__tar.gz → 0.4.1__tar.gz

{lotsofcells-0.3.0 → lotsofcells-0.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lotsofcells
-Version: 0.3.0
+Version: 0.4.1
 Summary: Python port of lotsOfCells: proportion-test statistics and visualization on single-cell metadata. Compatible with scanpy/AnnData and spatial transcriptomics.
 Author: Oscar Gonzalez-Velasco
 License: MIT

{lotsofcells-0.3.0 → lotsofcells-0.4.1}/lotsofcells/_utils.py

@@ -6,12 +6,14 @@ from typing import Optional, Sequence, Union
 import numpy as np
 import pandas as pd
 
-# Default palette mirrors the R version (alpha 0.95 + slight desaturation).
+# Default categorical palette — scanpy `default_20` (Vega-20 with
+# yellow/green hues swapped for higher contrast). The de facto standard in
+# the single-cell community, so colours feel native to scanpy figures.
 _DEFAULT_PALETTE = [
-    "#8DA0CB", "#926F99", "#9FBE8F", "#E8D161", "#DD8080",
-    "#613269", "#B9E8F5", "#CBB8D0", "#F9BE8D", "#B25356",
-    "#519B84", "#B79C76", "#C1D63C", "#F28D35", "#CA4133",
-    "#F0DA88", "#7EAB6F", "#666666", "#3C7DA6", "#4AA147",
+    "#1F77B4", "#FF7F0E", "#279E68", "#D62728", "#AA40FC",
+    "#8C564B", "#E377C2", "#B5BD61", "#17BECF", "#AEC7E8",
+    "#FFBB78", "#98DF8A", "#FF9896", "#C5B0D5", "#C49C94",
+    "#F7B6D2", "#DBDB8D", "#9EDAE5", "#AD494A", "#8C6D31",
 ]
 
 

{lotsofcells-0.3.0 → lotsofcells-0.4.1}/lotsofcells/lotsofcells.py

@@ -83,6 +83,34 @@ def lots_of_cells(
     metadata = get_metadata(sc_object, table=table)
 
     main_vals = metadata[main_variable].astype(str).to_numpy()
+
+    if isinstance(label_order[0], list) or isinstance(label_order[1], list):
+        if verbose:
+            print(f"Multiple sub-groups detected.")
+        # If several levels, process:
+        flat_order = np.array([a for b in label_order for a in b]).astype(str)
+        group_1 = np.array(label_order[0]).astype(str)
+        group_2 = np.array(label_order[1]).astype(str)
+        # Clean data with unwanted levels:
+        mask = np.isin(main_vals, flat_order)
+        metadata = metadata.loc[mask].copy()
+
+        # Obtain group labels:
+        mask_g1 = np.isin(main_vals, group_1)
+        mask_g2 = np.isin(main_vals, group_2)
+        # Define new labels:
+        label_1 = "loc_group_one [" + " ".join(group_1)+"]"
+        label_2 = "loc_group_two [" + " ".join(group_2)+"]"
+        # Create synthetic labels:
+        metadata.loc[mask_g1,"loc_tmp_group"] = label_1
+        metadata.loc[mask_g2,"loc_tmp_group"] = label_2
+        # relevel and recompute
+        main_variable = "loc_tmp_group"
+        main_vals = metadata[main_variable].astype(str).to_numpy()
+        # Copy original and push new:
+        label_order_original = label_order
+        label_order = [label_1, label_2]
+
     if not all(l in np.unique(main_vals) for l in label_order):
         missing = [l for l in label_order if l not in np.unique(main_vals)]
         raise ValueError(f"Some groups in label_order not found in data: {missing}")

{lotsofcells-0.3.0 → lotsofcells-0.4.1}/lotsofcells.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lotsofcells
-Version: 0.3.0
+Version: 0.4.1
 Summary: Python port of lotsOfCells: proportion-test statistics and visualization on single-cell metadata. Compatible with scanpy/AnnData and spatial transcriptomics.
 Author: Oscar Gonzalez-Velasco
 License: MIT

{lotsofcells-0.3.0 → lotsofcells-0.4.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "lotsofcells"
-version = "0.3.0"
+version = "0.4.1"
 description = "Python port of lotsOfCells: proportion-test statistics and visualization on single-cell metadata. Compatible with scanpy/AnnData and spatial transcriptomics."
 readme = "README.md"
 authors = [