From 93ca2758e1bb2eeb0a1c1d46c4c922cc029d3015 Mon Sep 17 00:00:00 2001
From: const-ae <artjom31415@googlemail.com>
Date: Mon, 27 May 2024 13:35:42 +0200
Subject: [PATCH] Fix

---
 docs/api.md                |  1 -
 src/pylemur/pp/__init__.py |  2 +-
 src/pylemur/pp/basic.py    | 27 ---------------------------
 3 files changed, 1 insertion(+), 29 deletions(-)

diff --git a/docs/api.md b/docs/api.md
index 3bc5d98..4ce3700 100644
--- a/docs/api.md
+++ b/docs/api.md
@@ -15,5 +15,4 @@ To create the LEMUR object that provides functionality to fit, align, predict, a
 
     tl.LEMUR
     pp.shifted_log_transform
-    pp.get_top_hvgs
 ```
diff --git a/src/pylemur/pp/__init__.py b/src/pylemur/pp/__init__.py
index dea9400..ce6d507 100644
--- a/src/pylemur/pp/__init__.py
+++ b/src/pylemur/pp/__init__.py
@@ -1 +1 @@
-from .basic import get_top_hvgs, shifted_log_transform
+from .basic import shifted_log_transform
diff --git a/src/pylemur/pp/basic.py b/src/pylemur/pp/basic.py
index 02bbae3..9b968cf 100644
--- a/src/pylemur/pp/basic.py
+++ b/src/pylemur/pp/basic.py
@@ -1,5 +1,4 @@
 import numpy as np
-import scanpy.preprocessing._simple
 import scipy
 
 
@@ -50,29 +49,3 @@ def shifted_log_transform(counts, overdispersion=0.05, pseudo_count=None, minimu
     if scipy.sparse.issparse(counts):
         res = scipy.sparse.csr_matrix(res)
     return res
-
-
-def get_top_hvgs(adata, n=1000, layer=None):
-    """
-    Get the indices of the most variable genes
-
-    Parameters
-    ----------
-    adata
-        The `AnnData` object.
-    n
-        The number of highly variable genes
-    layer
-        The layer with the variance-stabilized values from `adata`. If
-        `layer=None`, the function uses `adata.X`.
-
-    Returns
-    -------
-    A list with the indices of the most highly variable genes from `adata`.
-    """
-    if layer is None:
-        mat = adata.X
-    else:
-        mat = adata.layers[layer]
-    var = scanpy.preprocessing._simple._get_mean_var(mat)[1]
-    return var.argsort()[: -(n + 1) : -1]