From 7bc9c4f004855fc0d1b080011ca6179c74d2600a Mon Sep 17 00:00:00 2001
From: dburkhardt <dburkhardt@cellarity.com>
Date: Tue, 28 Nov 2023 15:46:19 +0000
Subject: [PATCH 01/14] Generalize dendrogram to multiple axes, fix #1549

---
 ...rogram_key_added.py => test_dendrogram.py} |   5 +
 scanpy/tools/_dendrogram.py                   | 124 ++++++++++++------
 2 files changed, 88 insertions(+), 41 deletions(-)
 rename scanpy/tests/{test_dendrogram_key_added.py => test_dendrogram.py} (77%)

diff --git a/scanpy/tests/test_dendrogram_key_added.py b/scanpy/tests/test_dendrogram.py
similarity index 77%
rename from scanpy/tests/test_dendrogram_key_added.py
rename to scanpy/tests/test_dendrogram.py
index 586612962a..23fbd69867 100644
--- a/scanpy/tests/test_dendrogram_key_added.py
+++ b/scanpy/tests/test_dendrogram.py
@@ -22,3 +22,8 @@ def test_dendrogram_key_added(groupby, key_added):
     if key_added is None:
         key_added = dendrogram_key
     assert key_added in adata.uns
+
+def test_dendrogram_var_names():
+    adata = pbmc68k_reduced()
+    sc.tl.dendrogram(adata, var_names=adata.var_names[:10], axis=1)
+    assert len(adata.uns["dendrogram_var"]["categories_ordered"]) == 10
diff --git a/scanpy/tools/_dendrogram.py b/scanpy/tools/_dendrogram.py
index ccae494748..de0f9092fd 100644
--- a/scanpy/tools/_dendrogram.py
+++ b/scanpy/tools/_dendrogram.py
@@ -9,11 +9,14 @@
 import pandas as pd
 from pandas.api.types import CategoricalDtype
 
+from anndata._core.merge import _resolve_dim
+
 from .. import logging as logg
 from .._utils import _doc_params
 from ..neighbors._doc import doc_n_pcs, doc_use_rep
 from ._utils import _choose_representation
 
+
 if TYPE_CHECKING:
     from collections.abc import Sequence
 
@@ -23,7 +26,9 @@
 @_doc_params(n_pcs=doc_n_pcs, use_rep=doc_use_rep)
 def dendrogram(
     adata: AnnData,
-    groupby: str | Sequence[str],
+    groupby: str | Sequence[str] | None = None,
+    dim: Literal["obs", "var"] | None = None,
+    axis: Literal[0, 1] | None = None,
     n_pcs: int | None = None,
     use_rep: str | None = None,
     var_names: Sequence[str] | None = None,
@@ -60,6 +65,12 @@ def dendrogram(
     ----------
     adata
         Annotated data matrix
+    groupby
+        Optional, the obs column(s) to use to group observations. Default is None.
+    dim
+        Dimension (obs or var) along which to calculate the dedrogram. Pass either `dim` or `axis` but not both.
+    axis
+        Axis (0 or 1) along which to calculate the dendrogram. Pass either `dim` or `axis` but not both.
     {n_pcs}
     {use_rep}
     var_names
@@ -103,49 +114,77 @@ def dendrogram(
     >>> markers = ['C1QA', 'PSAP', 'CD79A', 'CD79B', 'CST3', 'LYZ']
     >>> sc.pl.dotplot(adata, markers, groupby='bulk_labels', dendrogram=True)
     """
-    if isinstance(groupby, str):
-        # if not a list, turn into a list
-        groupby = [groupby]
-    for group in groupby:
-        if group not in adata.obs_keys():
-            raise ValueError(
-                "groupby has to be a valid observation. "
-                f"Given value: {group}, valid observations: {adata.obs_keys()}"
-            )
-        if not isinstance(adata.obs[group].dtype, CategoricalDtype):
-            raise ValueError(
-                "groupby has to be a categorical observation. "
-                f"Given value: {group}, Column type: {adata.obs[group].dtype}"
+    if dim is None and axis is None:
+        dim = "obs"
+    axis, dim = _resolve_dim(axis=axis, dim=dim)
+    alt_axis, alt_dim = _resolve_dim(axis=1-axis)
+    
+    if dim == "obs":
+        dim_names = adata.obs_names
+        metadata = adata.obs
+        metadata_keys = adata.obs_keys()
+    else:
+        metadata = adata.var
+        metadata_keys = adata.var_keys()
+    
+    if groupby is not None:
+        if isinstance(groupby, str):
+            # if not a list, turn into a list
+            groupby = [groupby]
+        for group in groupby:
+            if group not in adata.obs_keys():
+                raise ValueError(
+                    "groupby has to be a valid observation. "
+                    f"Given value: {group}, valid observations: {adata.obs_keys()}"
+                )
+            if not isinstance(adata.obs[group].dtype, CategoricalDtype):
+                raise ValueError(
+                    "groupby has to be a categorical observation. "
+                    f"Given value: {group}, Column type: {adata.obs[group].dtype}"
+                )
+    
+        if var_names is None:
+            rep_df = pd.DataFrame(
+                _choose_representation(adata, use_rep=use_rep, n_pcs=n_pcs)
             )
-
-    if var_names is None:
-        rep_df = pd.DataFrame(
-            _choose_representation(adata, use_rep=use_rep, n_pcs=n_pcs)
-        )
-        categorical = adata.obs[groupby[0]]
-        if len(groupby) > 1:
-            for group in groupby[1:]:
-                # create new category by merging the given groupby categories
-                categorical = (
-                    categorical.astype(str) + "_" + adata.obs[group].astype(str)
-                ).astype("category")
-        categorical.name = "_".join(groupby)
-
-        rep_df.set_index(categorical, inplace=True)
-        categories = rep_df.index.categories
+            categorical = adata.obs[groupby[0]]
+            if len(groupby) > 1:
+                for group in groupby[1:]:
+                    # create new category by merging the given groupby categories
+                    categorical = (
+                        categorical.astype(str) + "_" + adata.obs[group].astype(str)
+                    ).astype("category")
+            categorical.name = "_".join(groupby)
+    
+            rep_df.set_index(categorical, inplace=True)
+            categories = rep_df.index.categories
+        else:
+            from scanpy.plotting._anndata import _prepare_dataframe
+    
+            categories, rep_df = _prepare_dataframe(adata, var_names, groupby, use_raw)
+    
+        # aggregate values within categories using 'mean'
+        rep_df = rep_df.groupby(level=0).mean()
     else:
-        gene_names = adata.raw.var_names if use_raw else adata.var_names
-        from ..plotting._anndata import _prepare_dataframe
-
-        categories, rep_df = _prepare_dataframe(adata, gene_names, groupby, use_raw)
-
-    # aggregate values within categories using 'mean'
-    mean_df = rep_df.groupby(level=0).mean()
-
+        if var_names is None:
+            rep_df = pd.DataFrame(
+                _choose_representation(adata, use_rep=use_rep, n_pcs=n_pcs)
+            )
+            
+        else:
+            rep_df = pd.DataFrame(
+                _choose_representation(adata[:, var_names], use_rep=use_rep, n_pcs=n_pcs)
+            )
+        categories = rep_df.axes[axis]
+        
     import scipy.cluster.hierarchy as sch
     from scipy.spatial import distance
 
-    corr_matrix = mean_df.T.corr(method=cor_method)
+
+    if axis == 0:
+        corr_matrix = rep_df.T.corr(method=cor_method)
+    else:
+        corr_matrix = rep_df.corr(method=cor_method)
     corr_condensed = distance.squareform(1 - corr_matrix)
     z_var = sch.linkage(
         corr_condensed, method=linkage_method, optimal_ordering=optimal_ordering
@@ -166,8 +205,11 @@ def dendrogram(
 
     if inplace:
         if key_added is None:
-            key_added = f'dendrogram_{"_".join(groupby)}'
+            if groupby is None:
+                key_added = f"dendrogram_{dim}"
+            else:
+                key_added = f'dendrogram_{"_".join(groupby)}'
         logg.info(f"Storing dendrogram info using `.uns[{key_added!r}]`")
         adata.uns[key_added] = dat
     else:
-        return dat
+        return dat
\ No newline at end of file

From d0f189479ee082622045b6921e6b8ecd39940028 Mon Sep 17 00:00:00 2001
From: dburkhardt <dburkhardt@cellarity.com>
Date: Tue, 28 Nov 2023 15:47:23 +0000
Subject: [PATCH 02/14] Add dendrogram test for no groupby on obs

---
 scanpy/tests/test_dendrogram.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/scanpy/tests/test_dendrogram.py b/scanpy/tests/test_dendrogram.py
index 23fbd69867..437afcbbc3 100644
--- a/scanpy/tests/test_dendrogram.py
+++ b/scanpy/tests/test_dendrogram.py
@@ -9,13 +9,15 @@
 key = "test"
 
 
-@pytest.mark.parametrize("groupby", ["bulk_labels", ["bulk_labels", "phase"]])
+@pytest.mark.parametrize("groupby", [None, "bulk_labels", ["bulk_labels", "phase"]])
 @pytest.mark.parametrize("key_added", [None, "custom_key"])
 def test_dendrogram_key_added(groupby, key_added):
     adata = pbmc68k_reduced()
     sc.tl.dendrogram(adata, groupby=groupby, key_added=key_added, use_rep="X_pca")
     if isinstance(groupby, list):
         dendrogram_key = f'dendrogram_{"_".join(groupby)}'
+    elif groupby is None:
+        dendrogram_key = "dendrogram_obs"
     else:
         dendrogram_key = f"dendrogram_{groupby}"
 

From 6b446032fc6343e9c474c86ccef2337b557fd541 Mon Sep 17 00:00:00 2001
From: dburkhardt <dburkhardt@cellarity.com>
Date: Tue, 28 Nov 2023 16:36:47 +0000
Subject: [PATCH 03/14] add release notes

---
 scanpy/tools/_dendrogram.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/scanpy/tools/_dendrogram.py b/scanpy/tools/_dendrogram.py
index de0f9092fd..95eed74aa4 100644
--- a/scanpy/tools/_dendrogram.py
+++ b/scanpy/tools/_dendrogram.py
@@ -16,7 +16,6 @@
 from ..neighbors._doc import doc_n_pcs, doc_use_rep
 from ._utils import _choose_representation
 
-
 if TYPE_CHECKING:
     from collections.abc import Sequence
 

From 660853d9e5b7635fbdb503640a9716564106cf8c Mon Sep 17 00:00:00 2001
From: dburkhardt <dburkhardt@cellarity.com>
Date: Tue, 28 Nov 2023 16:46:57 +0000
Subject: [PATCH 04/14] lint

---
 docs/release-notes/1.10.0.md    |  2 ++
 scanpy/tests/test_dendrogram.py |  1 +
 scanpy/tools/_dendrogram.py     | 36 +++++++++++++--------------------
 3 files changed, 17 insertions(+), 22 deletions(-)

diff --git a/docs/release-notes/1.10.0.md b/docs/release-notes/1.10.0.md
index 856a66b233..46e2d36e7f 100644
--- a/docs/release-notes/1.10.0.md
+++ b/docs/release-notes/1.10.0.md
@@ -13,6 +13,7 @@
 * Enhanced dask support for some internal utilities, paving the way for more extensive dask support {pr}`2696` {smaller}`P Angerer`
 * {func}`scanpy.pp.pca`, {func}`scanpy.pp.scale`, {func}`scanpy.pl.embedding`, and {func}`scanpy.experimental.pp.normalize_pearson_residuals_pca`
   now support a `mask` parameter {pr}`2272` {smaller}`C Bright, T Marcella, & P Angerer`
+* {func}`scanpy.tl.dendrogram` now accepts and axis or dim argument to enable dendrograms on obs or var {pr}`2770` {smaller}`D Burkhardt`
 
 ```{rubric} Docs
 ```
@@ -26,6 +27,7 @@
 * Fix {func}`~scanpy.pp.normalize_total` {pr}`2466` {smaller}`P Angerer`
 * Fix testing package build {pr}`2468` {smaller}`P Angerer`
 * Fix setting `sc.settings.verbosity` in some cases {pr}`2605` {smaller}`P Angerer`
+* Fix `sc.tl.dendrogram` ignoring passed var_names
 
 ```{rubric} Ecosystem
 ```
diff --git a/scanpy/tests/test_dendrogram.py b/scanpy/tests/test_dendrogram.py
index 437afcbbc3..c06d63aabc 100644
--- a/scanpy/tests/test_dendrogram.py
+++ b/scanpy/tests/test_dendrogram.py
@@ -25,6 +25,7 @@ def test_dendrogram_key_added(groupby, key_added):
         key_added = dendrogram_key
     assert key_added in adata.uns
 
+
 def test_dendrogram_var_names():
     adata = pbmc68k_reduced()
     sc.tl.dendrogram(adata, var_names=adata.var_names[:10], axis=1)
diff --git a/scanpy/tools/_dendrogram.py b/scanpy/tools/_dendrogram.py
index 95eed74aa4..6c4cb81b47 100644
--- a/scanpy/tools/_dendrogram.py
+++ b/scanpy/tools/_dendrogram.py
@@ -4,12 +4,11 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING, Any, Literal
 
 import pandas as pd
-from pandas.api.types import CategoricalDtype
-
 from anndata._core.merge import _resolve_dim
+from pandas.api.types import CategoricalDtype
 
 from .. import logging as logg
 from .._utils import _doc_params
@@ -116,16 +115,8 @@ def dendrogram(
     if dim is None and axis is None:
         dim = "obs"
     axis, dim = _resolve_dim(axis=axis, dim=dim)
-    alt_axis, alt_dim = _resolve_dim(axis=1-axis)
-    
-    if dim == "obs":
-        dim_names = adata.obs_names
-        metadata = adata.obs
-        metadata_keys = adata.obs_keys()
-    else:
-        metadata = adata.var
-        metadata_keys = adata.var_keys()
-    
+    alt_axis, alt_dim = _resolve_dim(axis=1 - axis)
+
     if groupby is not None:
         if isinstance(groupby, str):
             # if not a list, turn into a list
@@ -141,7 +132,7 @@ def dendrogram(
                     "groupby has to be a categorical observation. "
                     f"Given value: {group}, Column type: {adata.obs[group].dtype}"
                 )
-    
+
         if var_names is None:
             rep_df = pd.DataFrame(
                 _choose_representation(adata, use_rep=use_rep, n_pcs=n_pcs)
@@ -154,14 +145,14 @@ def dendrogram(
                         categorical.astype(str) + "_" + adata.obs[group].astype(str)
                     ).astype("category")
             categorical.name = "_".join(groupby)
-    
+
             rep_df.set_index(categorical, inplace=True)
             categories = rep_df.index.categories
         else:
             from scanpy.plotting._anndata import _prepare_dataframe
-    
+
             categories, rep_df = _prepare_dataframe(adata, var_names, groupby, use_raw)
-    
+
         # aggregate values within categories using 'mean'
         rep_df = rep_df.groupby(level=0).mean()
     else:
@@ -169,17 +160,18 @@ def dendrogram(
             rep_df = pd.DataFrame(
                 _choose_representation(adata, use_rep=use_rep, n_pcs=n_pcs)
             )
-            
+
         else:
             rep_df = pd.DataFrame(
-                _choose_representation(adata[:, var_names], use_rep=use_rep, n_pcs=n_pcs)
+                _choose_representation(
+                    adata[:, var_names], use_rep=use_rep, n_pcs=n_pcs
+                )
             )
         categories = rep_df.axes[axis]
-        
+
     import scipy.cluster.hierarchy as sch
     from scipy.spatial import distance
 
-
     if axis == 0:
         corr_matrix = rep_df.T.corr(method=cor_method)
     else:
@@ -211,4 +203,4 @@ def dendrogram(
         logg.info(f"Storing dendrogram info using `.uns[{key_added!r}]`")
         adata.uns[key_added] = dat
     else:
-        return dat
\ No newline at end of file
+        return dat

From 042d13555759c9c0b4d4df9d53985a527fe124c9 Mon Sep 17 00:00:00 2001
From: dburkhardt <dburkhardt@cellarity.com>
Date: Tue, 28 Nov 2023 16:50:04 +0000
Subject: [PATCH 05/14] update release notes

---
 docs/release-notes/1.10.0.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/release-notes/1.10.0.md b/docs/release-notes/1.10.0.md
index 46e2d36e7f..572a6b943a 100644
--- a/docs/release-notes/1.10.0.md
+++ b/docs/release-notes/1.10.0.md
@@ -13,7 +13,7 @@
 * Enhanced dask support for some internal utilities, paving the way for more extensive dask support {pr}`2696` {smaller}`P Angerer`
 * {func}`scanpy.pp.pca`, {func}`scanpy.pp.scale`, {func}`scanpy.pl.embedding`, and {func}`scanpy.experimental.pp.normalize_pearson_residuals_pca`
   now support a `mask` parameter {pr}`2272` {smaller}`C Bright, T Marcella, & P Angerer`
-* {func}`scanpy.tl.dendrogram` now accepts and axis or dim argument to enable dendrograms on obs or var {pr}`2770` {smaller}`D Burkhardt`
+* {func}`scanpy.tl.dendrogram` now accepts and axis or dim argument to enable dendrograms on obs or var {pr}`2771` {smaller}`D Burkhardt`
 
 ```{rubric} Docs
 ```

From e36ee273adccb97023baf1089527f88caeb8381f Mon Sep 17 00:00:00 2001
From: Philipp A <flying-sheep@web.de>
Date: Mon, 15 Jan 2024 12:24:47 +0100
Subject: [PATCH 06/14] Update scanpy/tools/_dendrogram.py

Co-authored-by: Ilan Gold <ilanbassgold@gmail.com>
---
 scanpy/tools/_dendrogram.py | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/scanpy/tools/_dendrogram.py b/scanpy/tools/_dendrogram.py
index 6c4cb81b47..ef48934347 100644
--- a/scanpy/tools/_dendrogram.py
+++ b/scanpy/tools/_dendrogram.py
@@ -137,13 +137,10 @@ def dendrogram(
             rep_df = pd.DataFrame(
                 _choose_representation(adata, use_rep=use_rep, n_pcs=n_pcs)
             )
-            categorical = adata.obs[groupby[0]]
-            if len(groupby) > 1:
-                for group in groupby[1:]:
-                    # create new category by merging the given groupby categories
-                    categorical = (
-                        categorical.astype(str) + "_" + adata.obs[group].astype(str)
-                    ).astype("category")
+            if len(groupby) == 1:
+                categorical = adata.obs[groupby[0]]
+            else:
+                categorical = adata.obs[groupby].apply("_".join, axis=1).astype("category")
             categorical.name = "_".join(groupby)
 
             rep_df.set_index(categorical, inplace=True)

From d797d43f23b0dcb1824f7e5afc0cf71a0bb72bb3 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 15 Jan 2024 11:30:32 +0000
Subject: [PATCH 07/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 scanpy/tools/_dendrogram.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/scanpy/tools/_dendrogram.py b/scanpy/tools/_dendrogram.py
index c941217fbe..78d3dcc923 100644
--- a/scanpy/tools/_dendrogram.py
+++ b/scanpy/tools/_dendrogram.py
@@ -153,7 +153,9 @@ def dendrogram(
             if len(groupby) == 1:
                 categorical = adata.obs[groupby[0]]
             else:
-                categorical = adata.obs[groupby].apply("_".join, axis=1).astype("category")
+                categorical = (
+                    adata.obs[groupby].apply("_".join, axis=1).astype("category")
+                )
             categorical.name = "_".join(groupby)
 
             rep_df.set_index(categorical, inplace=True)

From fc88b9fb029996b1b0d94670b2b02629131c2682 Mon Sep 17 00:00:00 2001
From: Philipp A <flying-sheep@web.de>
Date: Mon, 15 Jan 2024 12:31:43 +0100
Subject: [PATCH 08/14] remove unused var

---
 scanpy/tools/_dendrogram.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/scanpy/tools/_dendrogram.py b/scanpy/tools/_dendrogram.py
index 78d3dcc923..dcd5a1c15b 100644
--- a/scanpy/tools/_dendrogram.py
+++ b/scanpy/tools/_dendrogram.py
@@ -128,7 +128,6 @@ def dendrogram(
     if dim is None and axis is None:
         dim = "obs"
     axis, dim = _resolve_dim(axis=axis, dim=dim)
-    alt_axis, alt_dim = _resolve_dim(axis=1 - axis)
 
     if groupby is not None:
         if isinstance(groupby, str):

From c34fd3a9186de990ca2c624cb162cec12354d362 Mon Sep 17 00:00:00 2001
From: Philipp A <flying-sheep@web.de>
Date: Thu, 18 Jan 2024 15:21:07 +0100
Subject: [PATCH 09/14] adapt to #1244

---
 scanpy/tools/_dendrogram.py | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/scanpy/tools/_dendrogram.py b/scanpy/tools/_dendrogram.py
index dcd5a1c15b..b843bec048 100644
--- a/scanpy/tools/_dendrogram.py
+++ b/scanpy/tools/_dendrogram.py
@@ -7,7 +7,7 @@
 from typing import TYPE_CHECKING, Any, Literal
 
 import pandas as pd
-from anndata._core.merge import _resolve_dim
+from anndata._core.merge import _resolve_axis
 from pandas.api.types import CategoricalDtype
 
 from .. import logging as logg
@@ -38,8 +38,7 @@ def dendrogram(
     adata: AnnData,
     groupby: str | Sequence[str] | None = None,
     *,
-    dim: Literal["obs", "var"] | None = None,
-    axis: Literal[0, 1] | None = None,
+    axis: Literal["obs", 0, "var", 1] = "obs",
     n_pcs: int | None = None,
     use_rep: str | None = None,
     var_names: Sequence[str] | None = None,
@@ -78,10 +77,8 @@ def dendrogram(
         Annotated data matrix
     groupby
         Optional, the obs column(s) to use to group observations. Default is None.
-    dim
-        Dimension (obs or var) along which to calculate the dedrogram. Pass either `dim` or `axis` but not both.
     axis
-        Axis (0 or 1) along which to calculate the dendrogram. Pass either `dim` or `axis` but not both.
+        Axis along which to calculate the dendrogram.
     {n_pcs}
     {use_rep}
     var_names
@@ -125,9 +122,7 @@ def dendrogram(
     >>> markers = ['C1QA', 'PSAP', 'CD79A', 'CD79B', 'CST3', 'LYZ']
     >>> sc.pl.dotplot(adata, markers, groupby='bulk_labels', dendrogram=True)
     """
-    if dim is None and axis is None:
-        dim = "obs"
-    axis, dim = _resolve_dim(axis=axis, dim=dim)
+    axis, axis_name = _resolve_axis(axis)
 
     if groupby is not None:
         if isinstance(groupby, str):
@@ -208,7 +203,7 @@ def dendrogram(
     if inplace:
         if key_added is None:
             if groupby is None:
-                key_added = f"dendrogram_{dim}"
+                key_added = f"dendrogram_{axis_name}"
             else:
                 key_added = f'dendrogram_{"_".join(groupby)}'
         logg.info(f"Storing dendrogram info using `.uns[{key_added!r}]`")

From 24acb72f28c429b703ae192443d5b93083319528 Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Tue, 23 Jan 2024 15:15:14 +0100
Subject: [PATCH 10/14] add util

---
 scanpy/tests/test_dendrogram.py | 25 ++++++++++++++++---------
 scanpy/tools/_dendrogram.py     |  3 +--
 scanpy/tools/_utils.py          | 12 +++++++++++-
 3 files changed, 28 insertions(+), 12 deletions(-)

diff --git a/scanpy/tests/test_dendrogram.py b/scanpy/tests/test_dendrogram.py
index c06d63aabc..073ee4988b 100644
--- a/scanpy/tests/test_dendrogram.py
+++ b/scanpy/tests/test_dendrogram.py
@@ -9,17 +9,24 @@
 key = "test"
 
 
-@pytest.mark.parametrize("groupby", [None, "bulk_labels", ["bulk_labels", "phase"]])
-@pytest.mark.parametrize("key_added", [None, "custom_key"])
-def test_dendrogram_key_added(groupby, key_added):
+@pytest.mark.parametrize(
+    ("groupby", "dendrogram_key"),
+    [
+        pytest.param(None, "dendrogram_obs", id="obs"),
+        pytest.param("bulk_labels", "dendrogram_bulk_labels", id="bulk_labels"),
+        pytest.param(
+            ["bulk_labels", "phase"],
+            "dendrogram_bulk_labels_phase",
+            id="bulk_labels+phase",
+        ),
+    ],
+)
+@pytest.mark.parametrize(
+    "key_added", [None, "custom_key"], ids=["derived", "custom_key"]
+)
+def test_dendrogram_key_added(groupby, dendrogram_key, key_added):
     adata = pbmc68k_reduced()
     sc.tl.dendrogram(adata, groupby=groupby, key_added=key_added, use_rep="X_pca")
-    if isinstance(groupby, list):
-        dendrogram_key = f'dendrogram_{"_".join(groupby)}'
-    elif groupby is None:
-        dendrogram_key = "dendrogram_obs"
-    else:
-        dendrogram_key = f"dendrogram_{groupby}"
 
     if key_added is None:
         key_added = dendrogram_key
diff --git a/scanpy/tools/_dendrogram.py b/scanpy/tools/_dendrogram.py
index b843bec048..f9107202af 100644
--- a/scanpy/tools/_dendrogram.py
+++ b/scanpy/tools/_dendrogram.py
@@ -7,14 +7,13 @@
 from typing import TYPE_CHECKING, Any, Literal
 
 import pandas as pd
-from anndata._core.merge import _resolve_axis
 from pandas.api.types import CategoricalDtype
 
 from .. import logging as logg
 from .._compat import old_positionals
 from .._utils import _doc_params
 from ..neighbors._doc import doc_n_pcs, doc_use_rep
-from ._utils import _choose_representation
+from ._utils import _choose_representation, _resolve_axis
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
diff --git a/scanpy/tools/_utils.py b/scanpy/tools/_utils.py
index 317948caf6..0c3e932d93 100644
--- a/scanpy/tools/_utils.py
+++ b/scanpy/tools/_utils.py
@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Literal
 
 import numpy as np
 
@@ -129,3 +129,13 @@ def get_init_pos_from_paga(
     else:
         raise ValueError("Plot PAGA first, so that adata.uns['paga']" "with key 'pos'.")
     return init_pos
+
+
+def _resolve_axis(
+    axis: Literal["obs", 0, "var", 1],
+) -> tuple[Literal[0], Literal["obs"]] | tuple[Literal[1], Literal["var"]]:
+    if axis in {0, "obs"}:
+        return (0, "obs")
+    if axis in {1, "var"}:
+        return (1, "var")
+    raise ValueError(f"`axis` must be either 0, 1, 'obs', or 'var', was {axis}")

From 4c9c2774ef04afbf36c993742b035ab3ad05071a Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Tue, 23 Jan 2024 15:22:55 +0100
Subject: [PATCH 11/14] Fix relnotes

---
 docs/release-notes/1.10.0.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/release-notes/1.10.0.md b/docs/release-notes/1.10.0.md
index 4fa716f399..2430d5f3d6 100644
--- a/docs/release-notes/1.10.0.md
+++ b/docs/release-notes/1.10.0.md
@@ -11,7 +11,7 @@
   now uses numba for variance computation {pr}`2612` {smaller}`S Dicks & P Angerer`
 * {func}`scanpy.external.pp.harmony_integrate` now runs with 64 bit floats improving reproducibility {pr}`2655` {smaller}`S Dicks`
 * Enhanced dask support for some internal utilities, paving the way for more extensive dask support {pr}`2696` {smaller}`P Angerer`
-* {func}`scanpy.tl.dendrogram` now accepts and axis or dim argument to enable dendrograms on obs or var {pr}`2771` {smaller}`D Burkhardt`
+* {func}`scanpy.tl.dendrogram` now accepts `axis` argument to enable dendrograms on `obs` or `var` {pr}`2771` {smaller}`D Burkhardt`
 * {func}`scanpy.pp.pca`, {func}`scanpy.pp.scale`, {func}`scanpy.pl.embedding`, and {func}`scanpy.experimental.pp.normalize_pearson_residuals_pca`
   now support a `mask` parameter {pr}`2272` {smaller}`C Bright, T Marcella, & P Angerer`
 * {func}`scanpy.tl.rank_genes_groups` no longer warns that it's default was changed from t-test_overestim_var to t-test {pr}`2798` {smaller}`L Heumos`
@@ -29,7 +29,7 @@
 * Fix {func}`~scanpy.pp.normalize_total` {pr}`2466` {smaller}`P Angerer`
 * Fix testing package build {pr}`2468` {smaller}`P Angerer`
 * Fix setting `sc.settings.verbosity` in some cases {pr}`2605` {smaller}`P Angerer`
-* Fix `sc.tl.dendrogram` ignoring passed var_names {pr}`2771` {smaller}`D Burkhardt`
+* Fix `sc.tl.dendrogram` ignoring passed `var_names` {pr}`2771` {smaller}`D Burkhardt`
 * Fix all remaining pandas warnings {pr}`2789` {smaller}`P Angerer`
 
 ```{rubric} Ecosystem

From fa2a7815c9b2fd8644df023391fc2da907c7a7da Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Tue, 23 Jan 2024 15:32:54 +0100
Subject: [PATCH 12/14] extract

---
 scanpy/tools/_dendrogram.py | 127 ++++++++++++++++++++----------------
 1 file changed, 70 insertions(+), 57 deletions(-)

diff --git a/scanpy/tools/_dendrogram.py b/scanpy/tools/_dendrogram.py
index f9107202af..bc810f68f4 100644
--- a/scanpy/tools/_dendrogram.py
+++ b/scanpy/tools/_dendrogram.py
@@ -75,7 +75,7 @@ def dendrogram(
     adata
         Annotated data matrix
     groupby
-        Optional, the obs column(s) to use to group observations. Default is None.
+        The obs column(s) to use to group observations. Default is None.
     axis
         Axis along which to calculate the dendrogram.
     {n_pcs}
@@ -127,60 +127,28 @@ def dendrogram(
         if isinstance(groupby, str):
             # if not a list, turn into a list
             groupby = [groupby]
-        for group in groupby:
-            if group not in adata.obs_keys():
-                raise ValueError(
-                    "groupby has to be a valid observation. "
-                    f"Given value: {group}, valid observations: {adata.obs_keys()}"
-                )
-            if not isinstance(adata.obs[group].dtype, CategoricalDtype):
-                raise ValueError(
-                    "groupby has to be a categorical observation. "
-                    f"Given value: {group}, Column type: {adata.obs[group].dtype}"
-                )
-
-        if var_names is None:
-            rep_df = pd.DataFrame(
-                _choose_representation(adata, use_rep=use_rep, n_pcs=n_pcs)
-            )
-            if len(groupby) == 1:
-                categorical = adata.obs[groupby[0]]
-            else:
-                categorical = (
-                    adata.obs[groupby].apply("_".join, axis=1).astype("category")
-                )
-            categorical.name = "_".join(groupby)
-
-            rep_df.set_index(categorical, inplace=True)
-            categories = rep_df.index.categories
-        else:
-            from scanpy.plotting._anndata import _prepare_dataframe
-
-            categories, rep_df = _prepare_dataframe(adata, var_names, groupby, use_raw)
-
-        # aggregate values within categories using 'mean'
-        rep_df = rep_df.groupby(level=0, observed=True).mean()
+        rep_df, categories = _dendrogram_grouped(
+            adata,
+            groupby,
+            n_pcs=n_pcs,
+            use_rep=use_rep,
+            var_names=var_names,
+            use_raw=use_raw,
+        )
     else:
-        if var_names is None:
-            rep_df = pd.DataFrame(
-                _choose_representation(adata, use_rep=use_rep, n_pcs=n_pcs)
-            )
-
-        else:
-            rep_df = pd.DataFrame(
-                _choose_representation(
-                    adata[:, var_names], use_rep=use_rep, n_pcs=n_pcs
-                )
+        rep_df = pd.DataFrame(
+            _choose_representation(
+                adata if var_names is None else adata[:, var_names],
+                use_rep=use_rep,
+                n_pcs=n_pcs,
             )
+        )
         categories = rep_df.axes[axis]
 
     import scipy.cluster.hierarchy as sch
     from scipy.spatial import distance
 
-    if axis == 0:
-        corr_matrix = rep_df.T.corr(method=cor_method)
-    else:
-        corr_matrix = rep_df.corr(method=cor_method)
+    corr_matrix = (rep_df.T if axis == 0 else rep_df).corr(method=cor_method)
     corr_condensed = distance.squareform(1 - corr_matrix)
     z_var = sch.linkage(
         corr_condensed, method=linkage_method, optimal_ordering=optimal_ordering
@@ -199,13 +167,58 @@ def dendrogram(
         correlation_matrix=corr_matrix.values,
     )
 
-    if inplace:
-        if key_added is None:
-            if groupby is None:
-                key_added = f"dendrogram_{axis_name}"
-            else:
-                key_added = f'dendrogram_{"_".join(groupby)}'
-        logg.info(f"Storing dendrogram info using `.uns[{key_added!r}]`")
-        adata.uns[key_added] = dat
-    else:
+    if not inplace:
         return dat
+    if key_added is None:
+        if groupby is None:
+            key_added = f"dendrogram_{axis_name}"
+        else:
+            key_added = f'dendrogram_{"_".join(groupby)}'
+    logg.info(f"Storing dendrogram info using `.uns[{key_added!r}]`")
+    adata.uns[key_added] = dat
+    return None
+
+
+def _dendrogram_grouped(
+    adata: AnnData,
+    groupby: Sequence[str],
+    *,
+    n_pcs: int | None,
+    use_rep: str | None,
+    var_names: Sequence[str] | None,
+    use_raw: bool | None,
+) -> tuple[pd.DataFrame, pd.Index[str]]:
+    for group in groupby:
+        if group not in adata.obs_keys():
+            raise ValueError(
+                "groupby has to be a valid observation. "
+                f"Given value: {group}, valid observations: {adata.obs_keys()}"
+            )
+        if not isinstance(adata.obs[group].dtype, CategoricalDtype):
+            raise ValueError(
+                "groupby has to be a categorical observation. "
+                f"Given value: {group}, Column type: {adata.obs[group].dtype}"
+            )
+
+    if var_names is None:
+        rep_df = pd.DataFrame(
+            _choose_representation(adata, use_rep=use_rep, n_pcs=n_pcs)
+        )
+        if len(groupby) == 1:
+            categorical = adata.obs[groupby[0]]
+        else:
+            categorical = adata.obs[groupby].apply("_".join, axis=1).astype("category")
+        categorical.name = "_".join(groupby)
+
+        rep_df.set_index(categorical, inplace=True)
+        categories = rep_df.index.categories
+    else:
+        from scanpy.plotting._anndata import _prepare_dataframe
+
+        categories, rep_df = _prepare_dataframe(
+            adata, var_names, groupby, use_raw=use_raw
+        )
+
+        # aggregate values within categories using 'mean'
+    rep_df = rep_df.groupby(level=0, observed=True).mean()
+    return rep_df, categories

From 01561a9effa2eefdc816687371359c30324ea689 Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Tue, 6 Feb 2024 12:07:26 +0100
Subject: [PATCH 13/14] Use helper everywhere

---
 scanpy/plotting/_anndata.py        | 60 ++++++++++++------------------
 scanpy/plotting/_baseplot_class.py |  8 ++--
 scanpy/tools/_dendrogram.py        | 49 ++++++++++++++++++++----
 3 files changed, 70 insertions(+), 47 deletions(-)

diff --git a/scanpy/plotting/_anndata.py b/scanpy/plotting/_anndata.py
index c54ee5cc3b..0d5a63f2c7 100755
--- a/scanpy/plotting/_anndata.py
+++ b/scanpy/plotting/_anndata.py
@@ -21,6 +21,8 @@
 from .._compat import old_positionals
 from .._settings import settings
 from .._utils import _check_use_raw, _doc_params, sanitize_anndata
+from ..tools._dendrogram import _get_dendrogram_key
+from ..tools._utils import _resolve_axis
 from . import _utils
 from ._docs import (
     doc_common_plot_args,
@@ -1737,8 +1739,9 @@ def tracksplot(
 @_doc_params(show_save_ax=doc_show_save_ax)
 def dendrogram(
     adata: AnnData,
-    groupby: str,
+    groupby: str | Sequence[str] | None = None,
     *,
+    axis: Literal["obs", 0, "var", 1] = "obs",
     dendrogram_key: str | None = None,
     orientation: Literal["top", "bottom", "left", "right"] = "top",
     remove_labels: bool = False,
@@ -1757,6 +1760,8 @@ def dendrogram(
         Annotated data matrix.
     groupby
         Categorical data column used to create the dendrogram
+    axis
+        Axis for which to plot the dendrogram.
     dendrogram_key
         Key under with the dendrogram information was stored.
         By default the dendrogram information is stored under
@@ -1787,10 +1792,12 @@ def dendrogram(
     """
     if ax is None:
         _, ax = plt.subplots()
+    axis, axis_name = _resolve_axis(axis)
     _plot_dendrogram(
         ax,
         adata,
         groupby,
+        axis_name=axis_name,
         dendrogram_key=dendrogram_key,
         remove_labels=remove_labels,
         orientation=orientation,
@@ -1866,7 +1873,9 @@ def correlation_matrix(
     >>> sc.pl.correlation_matrix(adata, 'bulk_labels')
     """
 
-    dendrogram_key = _get_dendrogram_key(adata, dendrogram, groupby)
+    dendrogram_key = _get_dendrogram_key(
+        dendrogram, groupby, axis_name="obs", adata=adata
+    )
 
     index = adata.uns[dendrogram_key]["categories_idx_ordered"]
     corr_matrix = adata.uns[dendrogram_key]["correlation_matrix"]
@@ -2243,8 +2252,8 @@ def _plot_gene_groups_brackets(
 
 def _reorder_categories_after_dendrogram(
     adata: AnnData,
-    groupby,
-    dendrogram,
+    groupby: str | Sequence[str],
+    dendrogram: bool | str | None,
     *,
     var_names=None,
     var_group_labels=None,
@@ -2269,12 +2278,14 @@ def _reorder_categories_after_dendrogram(
     'var_group_labels', and 'var_group_positions'
     """
 
-    key = _get_dendrogram_key(adata, dendrogram, groupby)
+    dendrogram_key = _get_dendrogram_key(
+        dendrogram, groupby, axis_name="obs", adata=adata
+    )
 
     if isinstance(groupby, str):
         groupby = [groupby]
 
-    dendro_info = adata.uns[key]
+    dendro_info = adata.uns[dendrogram_key]
     if groupby != dendro_info["groupby"]:
         raise ValueError(
             "Incompatible observations. The precomputed dendrogram contains "
@@ -2354,50 +2365,25 @@ def _format_first_three_categories(categories):
     return ", ".join(categories)
 
 
-def _get_dendrogram_key(adata, dendrogram_key, groupby):
-    # the `dendrogram_key` can be a bool an NoneType or the name of the
-    # dendrogram key. By default the name of the dendrogram key is 'dendrogram'
-    if not isinstance(dendrogram_key, str):
-        if isinstance(groupby, str):
-            dendrogram_key = f"dendrogram_{groupby}"
-        elif isinstance(groupby, list):
-            dendrogram_key = f'dendrogram_{"_".join(groupby)}'
-
-    if dendrogram_key not in adata.uns:
-        from ..tools._dendrogram import dendrogram
-
-        logg.warning(
-            f"dendrogram data not found (using key={dendrogram_key}). "
-            "Running `sc.tl.dendrogram` with default parameters. For fine "
-            "tuning it is recommended to run `sc.tl.dendrogram` independently."
-        )
-        dendrogram(adata, groupby, key_added=dendrogram_key)
-
-    if "dendrogram_info" not in adata.uns[dendrogram_key]:
-        raise ValueError(
-            f"The given dendrogram key ({dendrogram_key!r}) does not contain "
-            "valid dendrogram information."
-        )
-
-    return dendrogram_key
-
-
 def _plot_dendrogram(
     dendro_ax: Axes,
     adata: AnnData,
-    groupby: str,
+    groupby: str | Sequence[str] | None,
     *,
+    axis_name: Literal["obs", "var"] = "obs",
     dendrogram_key: str | None = None,
     orientation: Literal["top", "bottom", "left", "right"] = "right",
     remove_labels: bool = True,
     ticks: Collection[float] | None = None,
-):
+) -> None:
     """\
     Plots a dendrogram on the given ax using the precomputed dendrogram
     information stored in `.uns[dendrogram_key]`
     """
 
-    dendrogram_key = _get_dendrogram_key(adata, dendrogram_key, groupby)
+    dendrogram_key = _get_dendrogram_key(
+        dendrogram_key, groupby, axis_name=axis_name, adata=adata
+    )
 
     def translate_pos(pos_list, new_ticks, old_ticks):
         """\
diff --git a/scanpy/plotting/_baseplot_class.py b/scanpy/plotting/_baseplot_class.py
index 22ff04913e..c204b46a8b 100644
--- a/scanpy/plotting/_baseplot_class.py
+++ b/scanpy/plotting/_baseplot_class.py
@@ -857,7 +857,7 @@ def savefig(self, filename: str, bbox_inches: str | None = "tight", **kwargs):
         self.make_figure()
         plt.savefig(filename, bbox_inches=bbox_inches, **kwargs)
 
-    def _reorder_categories_after_dendrogram(self, dendrogram) -> None:
+    def _reorder_categories_after_dendrogram(self, dendrogram_key: str | None) -> None:
         """\
         Function used by plotting functions that need to reorder the the groupby
         observations based on the dendrogram results.
@@ -883,9 +883,11 @@ def _format_first_three_categories(_categories):
                 _categories = _categories[:3] + ["etc."]
             return ", ".join(_categories)
 
-        key = _get_dendrogram_key(self.adata, dendrogram, self.groupby)
+        dendrogram_key = _get_dendrogram_key(
+            dendrogram_key, self.groupby, axis_name="obs", adata=self.adata
+        )
 
-        dendro_info = self.adata.uns[key]
+        dendro_info = self.adata.uns[dendrogram_key]
         if self.groupby != dendro_info["groupby"]:
             raise ValueError(
                 "Incompatible observations. The precomputed dendrogram contains "
diff --git a/scanpy/tools/_dendrogram.py b/scanpy/tools/_dendrogram.py
index bc810f68f4..c2066e2065 100644
--- a/scanpy/tools/_dendrogram.py
+++ b/scanpy/tools/_dendrogram.py
@@ -4,6 +4,7 @@
 
 from __future__ import annotations
 
+from collections.abc import Sequence
 from typing import TYPE_CHECKING, Any, Literal
 
 import pandas as pd
@@ -16,8 +17,6 @@
 from ._utils import _choose_representation, _resolve_axis
 
 if TYPE_CHECKING:
-    from collections.abc import Sequence
-
     from anndata import AnnData
 
 
@@ -169,11 +168,7 @@ def dendrogram(
 
     if not inplace:
         return dat
-    if key_added is None:
-        if groupby is None:
-            key_added = f"dendrogram_{axis_name}"
-        else:
-            key_added = f'dendrogram_{"_".join(groupby)}'
+    key_added = _get_dendrogram_key(key_added, groupby, axis_name=axis_name)
     logg.info(f"Storing dendrogram info using `.uns[{key_added!r}]`")
     adata.uns[key_added] = dat
     return None
@@ -222,3 +217,43 @@ def _dendrogram_grouped(
         # aggregate values within categories using 'mean'
     rep_df = rep_df.groupby(level=0, observed=True).mean()
     return rep_df, categories
+
+
+def _get_dendrogram_key(
+    dendrogram_key: bool | str | None,
+    groupby: str | Sequence[str] | None,
+    *,
+    axis_name: Literal["obs", "var"],
+    adata: AnnData | None = None,
+) -> str:
+    # the `dendrogram_key` can be a bool an NoneType or the name of the
+    # dendrogram key. By default the name of the dendrogram key is 'dendrogram'
+    if not isinstance(dendrogram_key, str):
+        if groupby is None:
+            dendrogram_key = f"dendrogram_{axis_name}"
+        elif isinstance(groupby, str):
+            dendrogram_key = f"dendrogram_{groupby}"
+        elif isinstance(groupby, Sequence):
+            dendrogram_key = f'dendrogram_{"_".join(groupby)}'
+        else:
+            msg = "Either `groupby` or `dendrogram_key` must be specified."
+            raise TypeError(msg)
+
+    if adata is None:
+        return dendrogram_key
+
+    if dendrogram_key not in adata.uns:
+        logg.warning(
+            f"dendrogram data not found (using key={dendrogram_key}). "
+            "Running `sc.tl.dendrogram` with default parameters. For fine "
+            "tuning it is recommended to run `sc.tl.dendrogram` independently."
+        )
+        dendrogram(adata, groupby, key_added=dendrogram_key)
+
+    if "dendrogram_info" not in adata.uns[dendrogram_key]:
+        raise ValueError(
+            f"The given dendrogram key ({dendrogram_key!r}) does not contain "
+            "valid dendrogram information."
+        )
+
+    return dendrogram_key

From 521a590df85459a24987994bd36ee0ff13f2c3d4 Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Tue, 20 Feb 2024 09:01:49 +0100
Subject: [PATCH 14/14] error msg

---
 scanpy/tools/_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scanpy/tools/_utils.py b/scanpy/tools/_utils.py
index 0c3e932d93..ffc2fca3cb 100644
--- a/scanpy/tools/_utils.py
+++ b/scanpy/tools/_utils.py
@@ -138,4 +138,4 @@ def _resolve_axis(
         return (0, "obs")
     if axis in {1, "var"}:
         return (1, "var")
-    raise ValueError(f"`axis` must be either 0, 1, 'obs', or 'var', was {axis}")
+    raise ValueError(f"`axis` must be either 0, 1, 'obs', or 'var', was {axis!r}")