💄 add auxiliary files around autologicle normalization

docs/tutorials/quickstart.ipynb

@@ -157,6 +157,16 @@
     "adata_logicle = pm.tl.normalize_logicle(adata, inplace=False)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f528f69a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "adata_autologicle = pm.tl.normalize_autologicle(adata, inplace=False)"
+   ]
+  },
   {
    "attachments": {},
    "cell_type": "markdown",
@@ -193,7 +203,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.9.18"
   },
   "vscode": {
    "interpreter": {

pyproject.toml

@@ -23,6 +23,7 @@ dependencies = [
     "seaborn",
     "matplotlib",
     "readfcs >=1.1.0",
+    "flowutils",
     "datashader",
     "consensusclustering",
     "minisom"

pytometry/__init__.py

@@ -37,6 +37,7 @@
    tools.normalize_arcsinh
    tools.normalize_logicle
    tools.normalize_biExp
+   tools.normalize_autologicle
 
 Plotting (`pl`)
 ===============
@@ -50,7 +51,7 @@
 
 """
 
-__version__ = "0.1.4"  # denote a pre-release for 0.1.0 with 0.1a1
+__version__ = "0.1.5"  # denote a pre-release for 0.1.0 with 0.1a1
 
 from . import plotting as pl
 from . import preprocessing as pp

pytometry/tools/__init__.py

@@ -1,2 +1,7 @@
-from ._normalization import normalize_arcsinh, normalize_biExp, normalize_logicle
+from ._normalization import (
+    normalize_arcsinh,
+    normalize_autologicle,
+    normalize_biExp,
+    normalize_logicle,
+)
 from .clustering._flowsom import flowsom_clustering, meta_clustering, som_clustering

pytometry/tools/_normalization.py

@@ -1,5 +1,6 @@
 import numpy as np
 from anndata import AnnData
+from flowutils import transforms
 from scipy import interpolate
 from flowutils import transforms
 
@@ -556,6 +557,7 @@ def _log_root(b: float, w: float) -> float:
 
     return d
 
+
 def normalize_autologicle(adata, channels=None, m=4.5, q=0.05, inplace=True):
     """Autologicle transformation.