Updated docs for gene_graph and adjacency_matrix

docs/source/conf.py

@@ -68,10 +68,10 @@
 # html_theme = "scanpydoc"
 html_theme = "sphinx_rtd_theme"
 html_static_path = ["_static"]
-html_theme_options = {
-    "repository_url": repository_url,
-    "use_repository_button": True,
-}
+# html_theme_options = { # Meeds sphinx-book-theme or scanpydoc
+#     "repository_url": repository_url,
+#     "use_repository_button": True,
+# }
 html_show_sphinx = False
 # html_logo = "_static/img/Scanpy_Logo_BrightFG.svg"
 html_title = "scdemon"

notebooks/example.py

@@ -1,9 +1,6 @@
 #!/usr/bin/env python3
 """Example code for using scdemon part of the library."""
-# ---------------------------------------------------------------------
 # Example - compute co-expression modules using a scanpy anndata object
-# Updated: 04/08/24
-# ---------------------------------------------------------------------
 import os
 import logging
 import numpy as np

pyproject.toml

@@ -24,9 +24,7 @@ dependencies = [
     # Added from original modules, can prune:
     "scanpy", "anndata",
     "seaborn", "matplotlib",
-    "gprofiler-official",
-    "igraph", "adjustText",
-    "numba"
+    "igraph", "numba"
 ]
 
 [project.urls]
@@ -35,7 +33,7 @@ Source = "https://github.com/kellislab/scdemon"
 Home-page = "https://github.com/kellislab/scdemon"
 
 [project.optional-dependencies]
-test = ["pytest", "pytest-cov", "statsmodels", "anndata"]
+test = ["adjustText", "gprofiler-official"]
 
 [tool.scikit-build]
 wheel.expand-macos-universal-tags = true
@@ -45,9 +43,6 @@ packages = ["scdemon",
          "scdemon.utils", "scdemon.plotting",
          "scdemon.graph", "scdemon.data"]
 
-[tool.pytest.ini_options]
-python_files = "test_*.py"
-
 [tool.coverage.run]
 branch = true
 

scdemon/graph/adjacency_matrix.py

@@ -17,12 +17,9 @@
 
 
 class adjacency_matrix(object):
+    """\
+        Process given correlation matrix into the adjacency matrix.
     """
-    Turn a correlation matrix into an adjacency matrix.
-
-    Process given correlation matrix into the adjacency matrix.
-    """
-
     def __init__(
         self,
         corr,
@@ -40,7 +37,46 @@ def __init__(
         scale=None,
         degree_cutoff=0
     ):
-        """Initialize adjacency matrix class."""
+        """\
+            Initialize adjacency matrix class.
+
+
+            Parameters
+            ----------
+            corr : np.array | sparse.csr_matrix
+                Gene-gene correlation matrix
+            adjacency : np.array
+                Adjacency matrix
+            method : str
+                Thresholding method for graph:
+
+                ``'bivariate'``
+                    default, threshold based on bivariate spline fit to gene-gene sparsity
+                ``'cutoff'``
+                    single cutoff across full matrix
+                ``'sd'``
+                    based on estimated sd, expensive
+            corr_sd : np.array
+                Estimated standard deviation of correlations. Only used for ``sd`` method
+            labels : np.array
+                Labels for nodes (genes)
+            margin : np.array
+                Fraction non-zero values for each of the variables in the original dataset (gene sparsity)
+            cutoff : float
+                Raw correlation threshold
+            z : float
+                Z-score threshold
+            zero_outliers : bool
+                Whether to set outliers to 0 when calculating splines
+            keep_all_z : bool
+                Whether to keep z-score matrix dense by removing all values below threshold
+            knn_k : int
+                Pruning: keep only the top k edges per node
+            scale : float
+                Pruning: remove edges below a certain fraction (in (0.0, 1.0]) of the top edge for the node
+            degree_cutoff : int
+                Pruning: remove graph nodes with degree below this cutoff
+        """
         self.corr = corr
         self.adjacency = adjacency
         self.method = method