Merge pull request #157 from BayraktarLab/revise_pymc_tutorial

Removing old code (pymc-based) and updating the tutorial
BayraktarLab · May 17, 2022 · 7b72e41 · 7b72e41
2 parents 18d874c + 1811beb
commit 7b72e41
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Showing 30 changed files with 1,063 additions and 7,379 deletions.
diff --git a/cell2location/__init__.py b/cell2location/__init__.py
@@ -2,13 +2,11 @@
 from pyro.distributions.transforms import SoftplusTransform
 from torch.distributions import biject_to, transform_to
 
-from .run_c2l import run_cell2location
+from . import models
 from .run_colocation import run_colocation
-from .run_regression import run_regression
 
 __all__ = [
-    "run_cell2location",
-    "run_regression",
+    "models",
     "run_colocation",
 ]
 

diff --git a/cell2location/distributions/Gamma.py b/cell2location/distributions/Gamma.py
diff --git a/cell2location/models/__init__.py b/cell2location/models/__init__.py
@@ -3,17 +3,11 @@
     LocationModelLinearDependentWMultiExperimentLocationBackgroundNormLevelGeneAlphaPyroModel,
 )
 from .downstream import CoLocatedGroupsSklearnNMF
-from .pymc3.LocationModelLinearDependentWMultiExperimentLocationBackgroundNormGeneAlpha import (
-    LocationModelLinearDependentWMultiExperimentLocationBackgroundNormGeneAlpha,
-)
-from .pymc3.LocationModelWTA import LocationModelWTA
 from .reference import RegressionModel
 
 __all__ = [
     "Cell2location",
     "RegressionModel",
-    "LocationModelLinearDependentWMultiExperimentLocationBackgroundNormGeneAlpha",
     "LocationModelLinearDependentWMultiExperimentLocationBackgroundNormLevelGeneAlphaPyroModel",
-    "LocationModelWTA",
     "CoLocatedGroupsSklearnNMF",
 ]
diff --git a/cell2location/models/_cell2location_module.py b/cell2location/models/_cell2location_module.py
@@ -81,7 +81,7 @@ def __init__(
         cell_state_mat,
         n_groups: int = 50,
         detection_mean=1 / 2,
-        detection_alpha=200.0,
+        detection_alpha=20.0,
         m_g_gene_level_prior={"mean": 1, "mean_var_ratio": 1.0, "alpha_mean": 3.0},
         N_cells_per_location=8.0,
         A_factors_per_location=7.0,

diff --git a/cell2location/models/base/__init__.py b/cell2location/models/base/__init__.py
@@ -1,6 +0,0 @@
-from . import pymc3_loc_model, pymc3_model
-
-__all__ = [
-    "pymc3_loc_model",
-    "pymc3_model",
-]

diff --git a/cell2location/models/base/pymc3_loc_model.py b/cell2location/models/base/pymc3_loc_model.py