diff --git a/docs/tutorials/quickstart.ipynb b/docs/tutorials/quickstart.ipynb index 3f0e933..183f797 100644 --- a/docs/tutorials/quickstart.ipynb +++ b/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": { diff --git a/pyproject.toml b/pyproject.toml index 1c2d992..8620d21 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,6 +23,7 @@ dependencies = [ "seaborn", "matplotlib", "readfcs >=1.1.0", + "flowutils", "datashader", "consensusclustering", "minisom" diff --git a/pytometry/__init__.py b/pytometry/__init__.py index 6cf1ad3..66d423d 100644 --- a/pytometry/__init__.py +++ b/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 diff --git a/pytometry/tools/__init__.py b/pytometry/tools/__init__.py index 630e66f..0f5c455 100644 --- a/pytometry/tools/__init__.py +++ b/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 diff --git a/pytometry/tools/_normalization.py b/pytometry/tools/_normalization.py index 177810d..488107f 100644 --- a/pytometry/tools/_normalization.py +++ b/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.