rename ScaleFeature to ColumnSumNormalize

Author: xingzhongyu

README.md

@@ -414,3 +414,7 @@ pip install -e .
 | STdGCN       | 0.0058/0.0202/NA                              | 0.0145/0.0261/NA                                   | Test MSE          |
 
 **Note**: Stage 1, 2 and 3 (valid pseudo or dataset as metric for selection) for all methods.
+
+### A Note on Function Naming
+
+The function `ScaleFeature` has been renamed to `ColumnSumNormalize` in the code to resolve a naming ambiguity. However, historical WandB logs have not been modified and will still reference the old name (`ScaleFeature`). This is a naming change only and does not affect the program's execution.

dance/modules/single_modality/cell_type_annotation/scheteronet.py

@@ -36,7 +36,7 @@
 from dance.transforms.graph import HeteronetGraph
 from dance.transforms.interface import AnnDataTransform
 from dance.transforms.misc import Compose, SaveRaw, SetConfig
-from dance.transforms.normalize import Log1P, NormalizeTotal, ScaleFeature, UpdateSizeFactors
+from dance.transforms.normalize import ColumnSumNormalize, Log1P, NormalizeTotal, UpdateSizeFactors
 from dance.typing import Any, LogLevel, Mapping, Optional, Tuple, Union
 from dance.utils.metrics import resolve_score_func
 

dance/modules/spatial/cell_type_deconvo/dstg.py

@@ -22,11 +22,11 @@
 from dance.modules.base import BaseRegressionMethod
 from dance.transforms import (
     AnnDataTransform,
+    ColumnSumNormalize,
     Compose,
     FilterGenesCommon,
     PseudoMixture,
     RemoveSplit,
-    ScaleFeature,
     SetConfig,
 )
 from dance.transforms.graph import DSTGraph
@@ -181,7 +181,7 @@ def preprocessing_pipeline(
             AnnDataTransform(sc.pp.log1p),
             AnnDataTransform(sc.pp.highly_variable_genes, flavor=hvg_flavor, n_top_genes=n_top_genes, batch_key="batch",
                              subset=True),
-            ScaleFeature(split_names="ALL", mode="standardize"),
+            ColumnSumNormalize(split_names="ALL", mode="standardize"),
             DSTGraph(k_filter=k_filter, num_cc=num_cc, ref_split="pseudo", inf_split="test"),
             SetConfig({
                 "feature_channel": ["DSTGraph", None],

dance/transforms/__init__.py

@@ -40,11 +40,11 @@
 from dance.transforms.mask import CellwiseMaskData, MaskData
 from dance.transforms.misc import AlignMod, Compose, RemoveSplit, SaveRaw, SetConfig, UpdateRaw
 from dance.transforms.normalize import (
+    ColumnSumNormalize,
     Log1P,
     NormalizePlaceHolder,
     NormalizeTotal,
     NormalizeTotalLog1P,
-    ScaleFeature,
     ScTransform,
     ScTransformR,
     UpdateSizeFactors,
@@ -120,7 +120,7 @@
     "SaveRaw",
     "ScTransform",
     "ScTransformR",
-    "ScaleFeature",
+    "ColumnSumNormalize",
     "SetConfig",
     "SpatialIDEFeature",
     "TangramFeature",

dance/transforms/normalize.py

@@ -25,7 +25,7 @@
 
 @register_preprocessor("normalize")
 @add_mod_and_transform
-class ScaleFeature(BaseTransform):
+class ColumnSumNormalize(BaseTransform):
     """Scale the feature matrix in the AnnData object.
 
     This is an extension of :meth:`scanpy.pp.scale`, allowing split- or batch-wide scaling.

examples/atlas/config/atlas_template_yamls/cta_actinn/pipeline_params_tuning_config.yaml

@@ -18,7 +18,7 @@ pipeline:
         max_cells: 0.99
   - type: normalize
     include:
-      - ScaleFeature
+      - ColumnSumNormalize
       - ScTransform
       - Log1P
       - NormalizeTotal

examples/atlas/config/atlas_template_yamls/cta_celltypist/pipeline_params_tuning_config.yaml

@@ -18,7 +18,7 @@ pipeline:
         max_cells: 0.99
   - type: normalize
     include:
-      - ScaleFeature
+      - ColumnSumNormalize
       - ScTransform
       - Log1P
       - NormalizeTotal

examples/atlas/config/atlas_template_yamls/cta_scdeepsort/pipeline_params_tuning_config.yaml

@@ -18,7 +18,7 @@ pipeline:
         max_cells: 0.99
   - type: normalize
     include:
-      - ScaleFeature
+      - ColumnSumNormalize
       - ScTransform
       - Log1P
       - NormalizeTotal

examples/atlas/config/atlas_template_yamls/cta_singlecellnet/pipeline_params_tuning_config.yaml

@@ -18,7 +18,7 @@ pipeline:
         max_cells: 0.99
   - type: normalize
     include:
-      - ScaleFeature
+      - ColumnSumNormalize
       - ScTransform
       - Log1P
       - NormalizeTotal