feat: default to tie_correct=True in v2 (#4504)

Author: flying-sheep

docs/release-notes/4504.feat.md

@@ -0,0 +1 @@
+Add preset support to the `tie_correct` parameter of {func}`scanpy.tl.rank_genes_groups`: {attr}`~scanpy.Preset.ScanpyV2Preview` enables tie correction for `wilcoxon`, which changes its scores, p-values, and gene ranking on sparse data {smaller}`P Angerer`

src/scanpy/_settings/presets.py

@@ -97,6 +97,7 @@ class BasicEmbeddingPreset(NamedTuple):
 class RankGenesGroupsPreset(NamedTuple):
     method: DETest
     mean_in_log_space: bool
+    tie_correct: bool
 
 
 class ScalePreset(NamedTuple):
@@ -221,16 +222,16 @@ def pca() -> Mapping[Preset, PcaPreset]:
     def umap() -> Mapping[Preset, UmapPreset]:
         """Settings for :func:`~scanpy.tl.umap`."""  # noqa: D401
         return {
-            Preset.ScanpyV1: DiffmapPreset(key_added=None),
-            Preset.ScanpyV2Preview: DiffmapPreset(key_added="umap"),
+            Preset.ScanpyV1: UmapPreset(key_added=None),
+            Preset.ScanpyV2Preview: UmapPreset(key_added="umap"),
         }
 
     @preset_property
     def tsne() -> Mapping[Preset, UmapPreset]:
         """Settings for :func:`~scanpy.tl.tsne`."""  # noqa: D401
         return {
-            Preset.ScanpyV1: DiffmapPreset(key_added=None),
-            Preset.ScanpyV2Preview: DiffmapPreset(key_added="tsne"),
+            Preset.ScanpyV1: TsnePreset(key_added=None),
+            Preset.ScanpyV2Preview: TsnePreset(key_added="tsne"),
         }
 
     @preset_property
@@ -258,10 +259,10 @@ def rank_genes_groups() -> Mapping[Preset, RankGenesGroupsPreset]:
         """
         return {
             Preset.ScanpyV1: RankGenesGroupsPreset(
-                method="t-test", mean_in_log_space=True
+                method="t-test", mean_in_log_space=True, tie_correct=False
             ),
             Preset.ScanpyV2Preview: RankGenesGroupsPreset(
-                method="wilcoxon", mean_in_log_space=False
+                method="wilcoxon", mean_in_log_space=False, tie_correct=True
             ),
         }
 

src/scanpy/tools/_rank_genes_groups.py

@@ -801,7 +801,7 @@ def rank_genes_groups(  # noqa: PLR0912, PLR0913, PLR0915
     pts: bool = False,
     method: DETest | Default = Default(preset=("rank_genes_groups", "method")),
     corr_method: _CorrMethod = "benjamini-hochberg",
-    tie_correct: bool = False,
+    tie_correct: bool | Default = Default(preset=("rank_genes_groups", "tie_correct")),
     use: LayerAcc | str | None = None,
     mean_in_log_space: bool | Default = Default(
         preset=("rank_genes_groups", "mean_in_log_space")
@@ -939,6 +939,8 @@ def rank_genes_groups(  # noqa: PLR0912, PLR0913, PLR0915
     mask = _mask_arg(mask, mask_var, dim="var")
     if isinstance(mean_in_log_space, Default):
         mean_in_log_space = settings.preset.rank_genes_groups.mean_in_log_space
+    if isinstance(tie_correct, Default):
+        tie_correct = settings.preset.rank_genes_groups.tie_correct
     # If scanpy presets are used for v2, use illico - prevents the presets from showing the `wilcoxon_illico` method and allows us to silently replace `wilcoxon`'s implementation.
     if method is None or isinstance(method, Default):
         method = settings.preset.rank_genes_groups.method