Merge pull request #118 from PixelgenTechnologies/feature/exe-1132-im…

…plement-permuted-polarity-scores

Reimplementation of Moran's I and MPX graph preserving permuted polarity scores

CHANGELOG.md

@@ -41,7 +41,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * The term `edges` in `metrics` and `adata` is now replaced with `molecules`.
 * Renaming of variables in per-stage JSON reports.
 * Changed name of TCRb to TCRVb5 antibody in human-immunology-panel file and bumped to version 0.5.0.
-* Renaming of component metrics in adata and
+* Renaming of component metrics in adata
+* Use MPX graph compatible permutation strategy when calculating Moran's I.
 
 ### Fixed
 

pyproject.toml

@@ -36,8 +36,6 @@ yappi = "*"
 pandas = "^2.0.0"
 numpy = "<1.24.0"
 annoy = "<=1.17.0"
-esda = "*"
-libpysal = ">=4.9.2"
 xopen = "*"
 anndata = ">=0.8.0"
 numba = ">=0.56.4"

src/pixelator/analysis/__init__.py

@@ -104,7 +104,7 @@ def analyse_pixels(
             edgelist=edgelist,
             use_full_bipartite=use_full_bipartite,
             normalization=polarization_normalization,
-            permutations=polarization_n_permutations,
+            n_permutations=polarization_n_permutations,
         )
         dataset.polarization = scores
 
@@ -137,7 +137,9 @@ def analyse_pixels(
         )
     }
     # save dataset
-    dataset.save(Path(output) / f"{output_prefix}.analysis.dataset.pxl")
+    dataset.save(
+        Path(output) / f"{output_prefix}.analysis.dataset.pxl", force_overwrite=True
+    )
 
     polarization_report = PolarizationReport()
     colocalization_report = ColocalizationReport()

src/pixelator/analysis/colocalization/__init__.py

@@ -16,7 +16,6 @@
     estimate_observation_statistics,
     permutation_analysis_results,
 )
-from pixelator.analysis.colocalization.permute import permutations
 from pixelator.analysis.colocalization.prepare import (
     filter_by_region_counts,
     filter_by_unique_values,
@@ -31,6 +30,7 @@
     MarkerColocalizationResults,
     TransformationTypes,
 )
+from pixelator.analysis.permute import permutations
 from pixelator.graph.utils import Graph
 from pixelator.statistics import correct_pvalues, log1p_transformation
 

src/pixelator/analysis/colocalization/estimate.py

@@ -12,8 +12,8 @@
 
 from pixelator.analysis.colocalization.types import (
     CoLocalizationFunction,
-    RegionByCountsDataFrame,
 )
+from pixelator.analysis.types import RegionByCountsDataFrame
 
 logger = logging.getLogger(__name__)
 

src/pixelator/analysis/colocalization/prepare.py

@@ -7,7 +7,7 @@
 
 import pandas as pd
 
-from pixelator.analysis.colocalization.types import RegionByCountsDataFrame
+from pixelator.analysis.types import RegionByCountsDataFrame
 from pixelator.graph.utils import Graph, create_node_markers_counts
 
 

src/pixelator/analysis/colocalization/statistics.py

@@ -12,8 +12,8 @@
 from pixelator.analysis.colocalization.types import (
     CoLocalizationFunction,
     MarkerColocalizationResults,
-    RegionByCountsDataFrame,
 )
+from pixelator.analysis.types import RegionByCountsDataFrame
 
 
 def _wide_correlation_matrix_to_long_correlation_results(

src/pixelator/analysis/colocalization/types.py

@@ -8,7 +8,8 @@
 
 import pandas as pd
 
-RegionByCountsDataFrame = pd.DataFrame
+from pixelator.analysis.types import RegionByCountsDataFrame
+
 MarkerColocalizationResults = pd.DataFrame
 
 TransformationTypes = Literal["raw", "log1p"]

src/pixelator/analysis/colocalization/permute.py → src/pixelator/analysis/permute.py

@@ -10,7 +10,7 @@
 from numpy.random import Generator as RandomNumberGenerator
 from numpy.random import default_rng
 
-from pixelator.analysis.colocalization.types import (
+from pixelator.analysis.types import (
     RegionByCountsDataFrame,
 )