From f8e9be17d0eb57b732232e042b9180d75c952b84 Mon Sep 17 00:00:00 2001
From: beyondpie <panshi.pie@gmail.com>
Date: Wed, 24 Jan 2024 15:11:06 -0800
Subject: [PATCH 1/2] Add **kwargs in umap to allow other parameters in UMAP.

---
 snapatac2-python/snapatac2/tools/_embedding.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/snapatac2-python/snapatac2/tools/_embedding.py b/snapatac2-python/snapatac2/tools/_embedding.py
index dd71467f1..d6cb047e8 100644
--- a/snapatac2-python/snapatac2/tools/_embedding.py
+++ b/snapatac2-python/snapatac2/tools/_embedding.py
@@ -32,7 +32,7 @@ def umap2(
         Random seed.
     inplace
         Whether to store the result in the anndata object.
-
+    
     Returns
     -------
     np.ndarray | None
@@ -68,6 +68,7 @@ def umap(
     key_added: str = 'umap',
     random_state: int = 0,
     inplace: bool = True,
+    **kwargs
 ) -> np.ndarray | None:
     """
     Parameters
@@ -86,6 +87,8 @@ def umap(
         Random seed.
     inplace
         Whether to store the result in the anndata object.
+    **kwargs
+        Other parameters defined in umap.UMAP
 
     Returns
     -------
@@ -518,4 +521,4 @@ def multi_spectral(
         evals = evals[idx]
         evecs = evecs[:, idx] * np.sqrt(evals)
 
-    return (evals, evecs)
\ No newline at end of file
+    return (evals, evecs)

From 8b52bfc7cf9eb373209695f779aae3119f91772d Mon Sep 17 00:00:00 2001
From: beyondpie <panshi.pie@gmail.com>
Date: Wed, 24 Jan 2024 15:14:00 -0800
Subject: [PATCH 2/2] minor

---
 snapatac2-python/snapatac2/tools/_embedding.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/snapatac2-python/snapatac2/tools/_embedding.py b/snapatac2-python/snapatac2/tools/_embedding.py
index d6cb047e8..ca380dfb8 100644
--- a/snapatac2-python/snapatac2/tools/_embedding.py
+++ b/snapatac2-python/snapatac2/tools/_embedding.py
@@ -104,7 +104,9 @@ def umap(
     if use_dims is not None:
         data = data[:, :use_dims] if isinstance(use_dims, int) else data[:, use_dims]
 
-    umap = UMAP(random_state=random_state, n_components=n_comps).fit_transform(data)
+    umap = UMAP(random_state=random_state,
+                n_components=n_comps,
+                **kwargs).fit_transform(data)
     if inplace:
         adata.obsm["X_" + key_added] = umap
     else: