sciv 0.0.102__py3-none-any.whl → 0.0.103__py3-none-any.whl

sciv/model/_core_.py

@@ -76,8 +76,8 @@ def core(
     early_stopping_patience: int = 50,
     batch_key: Optional[str] = None,
     resolution: float = 0.5,
-    k: int = 30,
-    or_k: int = 1,
+    k: int = 50,
+    or_k: int = 25,
     weight: float = 0.1,
     kernel: Literal["laplacian", "gaussian"] = "gaussian",
     local_k: int = 10,

sciv/plot/_scatter_.py

@@ -174,6 +174,8 @@ def scatter_3d(
     edge_color: str = None,
     size: Union[float, collection] = 0.1,
     legend_name: str = None,
+    is_add_max_label: bool = False,
+    text_left_offset: float = 0.5,
     output: path = None,
     show: bool = True,
     close: bool = False,
@@ -186,13 +188,14 @@ def scatter_3d(
     fig = plt.figure(figsize=(width, height))
     ax = fig.add_subplot(projection='3d')
 
-    hue_cat = pd.Categorical(df[hue])
+    if hue is not None:
+        hue_cat = pd.Categorical(df[hue])
 
     scatter = ax.scatter(
         df[x],
         df[y],
         df[z],
-        c=hue_cat.codes,
+        c=hue_cat.codes if hue is not None else None,
         cmap=cmap,
         s=size,
         edgecolors=edge_color,
@@ -214,7 +217,7 @@ def scatter_3d(
     if title is not None:
         ax.set_title(title, fontsize=font_size)
 
-    if is_add_legend:
+    if is_add_legend and hue is not None:
         unique_types = hue_cat.categories
         legend_elements = [
             plt.Line2D(
@@ -226,6 +229,24 @@ def scatter_3d(
 
         ax.legend(handles=legend_elements, title=legend_name, loc='upper left')
 
+    if is_add_max_label:
+
+        max_idx = df[z].idxmax()
+        max_x = df.loc[max_idx, x]
+        max_y = df.loc[max_idx, y]
+        max_value = df.loc[max_idx, z]
+
+        # 在最大值点的位置添加文本标签
+        ax.text(
+            max_x - text_left_offset,
+            max_y,
+            max_value,
+            f'({max_x}, {max_y}): {max_value:.3f}',
+            fontsize=font_size - 2,
+            color='red',
+            ha='left'
+        )
+
     plot_end(fig, None, None, None, output, show, close)
 
 

sciv/preprocessing/_scvi_.py

@@ -137,7 +137,7 @@ def poisson_vi(
                 ul.log(__name__).warning(f"GPU failed to run, try to switch to CPU running.\n {ome}")
 
                 try:
-                    model = scvi.external.POISSONVI.load(model_dir, adata=adata, accelerator="cpu", device="cpu")
+                    model = scvi.external.POISSONVI.load(model_dir, adata=adata, accelerator="cpu")
                 except Exception as e:
                     ul.log(__name__).error(f"File `model.pt` failed to load, you can execute `Poisson VI` again by deleting file `model.pt` ({model_dir}/model.pt).\n {e}")
                     raise ValueError(f"File `model.pt` failed to load, you can execute `Poisson VI` again by deleting file `model.pt` ({model_dir}/model.pt).")

sciv/tool/__init__.py

@@ -36,7 +36,7 @@ from ._algorithm_ import (
     calculate_init_score_weight,
     obtain_cell_cell_network,
     perturb_data,
-    add_noise
+    add_bernoulli_fluctuation_noise
 )
 
 from ._random_walk_ import (
@@ -98,7 +98,7 @@ __all__ = [
     "calculate_init_score_weight",
     "obtain_cell_cell_network",
     "perturb_data",
-    "add_noise",
+    "add_bernoulli_fluctuation_noise",
     "split_matrix",
     "merge_matrix",
     "down_sampling_data",

sciv/tool/_algorithm_.py

@@ -8,7 +8,6 @@ from scipy import sparse
 from scipy.stats import norm
 from tqdm import tqdm
 from joblib import Parallel, delayed
-import multiprocessing
 
 import numpy as np
 from anndata import AnnData
@@ -1005,15 +1004,15 @@ def overlap_sum(regions: AnnData, variants: dict, trait_info: DataFrame, n_jobs:
     total = sum(len(ld) for ld, _, _ in results)
     row_indices = np.empty(total, dtype=np.int32)
     col_indices = np.empty(total, dtype=np.int32)
-    data_vals  = np.empty(total, dtype=np.float32)
+    data_vals = np.empty(total, dtype=np.float32)
 
     ptr = 0
 
     for local_data, local_rows, local_cols in results:
         n = len(local_data)
-        row_indices[ptr:ptr+n] = local_rows
-        col_indices[ptr:ptr+n] = local_cols
-        data_vals[ptr:ptr+n] = local_data
+        row_indices[ptr:ptr + n] = local_rows
+        col_indices[ptr:ptr + n] = local_cols
+        data_vals[ptr:ptr + n] = local_data
         ptr += n
 
     # Build sparse matrix, then convert to csr format
@@ -1404,39 +1403,36 @@ def perturb_data(data: collection, percentage: float) -> collection:
     return new_data
 
 
-def add_noise(data: matrix_data, rate: float) -> matrix_data:
-    """
-    Add peak percentage noise to each cell
+def add_bernoulli_fluctuation_noise(
+    counts_matrix: matrix_data,
+    noise_level: float = 0.1
+) -> matrix_data:
     """
+    Add Bernoulli fluctuation noise to the counts matrix (add 1 with probability noise_level)
 
-    if rate <= 0 or rate >= 1:
-        raise ValueError("The value of the `rate` parameter must be greater than 0 and less than 1.")
+    Parameters
+    ----------
+    counts_matrix : matrix_data
+        Input counts matrix
+    noise_level : float, default 0.1
+        Noise level, i.e., the probability of randomly adding 1 (range: 0.0 - 1.0)
 
-    shape = data.shape
-    noise = to_dense(data.copy())
-
-    for i in tqdm(range(shape[0])):
-        count_i = np.array(noise[i, :]).flatten()
-        # Add noise to the accessibility of unopened chromatin
-        count0_i = count_i[count_i == 0]
-        max_i = np.max(count_i)
-        count0 = int(count0_i.size * rate)
-        noise0_i = np.random.randint(low=1, high=2 if max_i < 2 else max_i, size=count0)
-        random_index0 = np.random.choice(np.arange(0, count0_i.size), size=count0, replace=False)
-        count0_i[random_index0] = noise0_i
-        count_i_value = count_i.copy()
-        count_i_value[count_i_value == 0] = count0_i
-        noise[i, :] = count_i_value
+    Returns
+    -------
+    matrix_data
+        Matrix after adding noise
+    """
+    if noise_level < 0 or noise_level > 1:
+        ul.log(__name__).error("The value of the `noise_level` parameter must be greater than 0 and less than 1.")
+        raise ValueError("The value of the `noise_level` parameter must be greater than 0 and less than 1.")
 
-        # Close open chromatin accessibility
-        count1_i = count_i[count_i == 1]
-        count1 = int(count1_i.size * rate)
-        random_index1 = np.random.choice(np.arange(0, count1_i.size), size=count1, replace=False)
-        count1_i[random_index1] = 0
-        count_i[count_i == 1] = count1_i
-        noise[i, :] = count_i
+    if noise_level == 0:
+        return counts_matrix.copy()
 
-        # disturbance
-        noise[i, :] = perturb_data(noise[i, :], rate)
+    noise = np.random.binomial(
+        n=1,
+        p=noise_level,
+        size=counts_matrix.shape
+    ).astype(counts_matrix.dtype)
 
-    return noise
+    return counts_matrix + noise

{sciv-0.0.102.dist-info → sciv-0.0.103.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sciv
-Version: 0.0.102
+Version: 0.0.103
 Summary: Unveiling the pivotal cell types involved in variant function regulation at a single-cell resolution
 Project-URL: github, https://github.com/YuZhengM/sciv
 Author-email: Zheng-Min Yu <yuzmbio@163.com>

{sciv-0.0.102.dist-info → sciv-0.0.103.dist-info}/RECORD

@@ -3,7 +3,7 @@ sciv/file/__init__.py,sha256=8cYLG0S0nilblmyX46CWFrbLr-rmLbO1EEO477pZ-gk,520
 sciv/file/_read_.py,sha256=UZJpN3_5hBiTjzEYO6YXORcE_dqA8HmLpV80nqTLNSo,30554
 sciv/file/_write_.py,sha256=W3M9CmPi7BuKAffz1fdi-vA5DzAFZ7wmcggp33N9Xtg,7848
 sciv/model/__init__.py,sha256=k8SO9FpJaGn2ANqJyaz3HXMas7jH9toPVtpw703kOqg,149
-sciv/model/_core_.py,sha256=UHJW6r5j54v_0-AJuqw-o_mumElvFMVUFfcrxNMjllU,33722
+sciv/model/_core_.py,sha256=ELOhkkKYTPEx4mJ5bJ47Si53afJpJ4weSzW6EPAmvvQ,33723
 sciv/plot/__init__.py,sha256=2tRNT6TZNz9r38lnna712RGsH7OJ2QkGa37XKgzejHQ,1865
 sciv/plot/_bar_.py,sha256=iQoFsFFbPbFj3JX2BgG45dqG-hjOka90LDw0WfdYNY8,14823
 sciv/plot/_barcode_.py,sha256=RDOedQ8ZtXWFyJ2c772RDfqO4TMIpHMvcMZMAVqky90,5073
@@ -16,7 +16,7 @@ sciv/plot/_kde_.py,sha256=A7_NFoSD0ih9h0Hh_1Y8ZOOz06AyANfi3M6sdkz61ZE,2399
 sciv/plot/_line_.py,sha256=qOSf4MJSXCTh8WCcd_dFlTsqMp-MeR2fGqR9lzEVPwo,3834
 sciv/plot/_pie_.py,sha256=GDoHES4AfOtnFeK99gh0a1KdUXIs7ZCCs6YHzoBLpbk,6451
 sciv/plot/_radar_.py,sha256=g_abzmzibJIR6it59TendUI236inbzYl0IzzdoA3Uuc,6304
-sciv/plot/_scatter_.py,sha256=HPy1eFqDk4vksAiKjn_Qk00fYO4GyqRs1O3ZZh44Ezw,16998
+sciv/plot/_scatter_.py,sha256=XoRl4I9L1bmTTnH-ByAXEf4q2P0VABCjvk4FoBw1sfU,17632
 sciv/plot/_venn_.py,sha256=TfNTuxog2pT7sicKBEEMtleoHXwnenbl3CMWJu9c2vs,2675
 sciv/plot/_violin_.py,sha256=IoeAv-ipGkBO0LouI2Y2huPP44u_-6O9CfBkgrPsK6s,6486
 sciv/preprocessing/__init__.py,sha256=56RgDai5I3sZ4hl3aaV80ogOeUscYsU3nJUWE80jZ-k,742
@@ -24,16 +24,16 @@ sciv/preprocessing/_anndata_.py,sha256=3d1cHFs1YA9UZkIPE089nZHFi-DjK-c1fRyi2shfS
 sciv/preprocessing/_gencode_.py,sha256=HKhRgK76khGepdv4FaKiOvTys1uJTbvIyrKUta5W0K8,2108
 sciv/preprocessing/_gsea_.py,sha256=AH_PpUNfMN7WkF0pqAuUhEC6qZwKrtQm6VaaYu6JLfI,3803
 sciv/preprocessing/_scanpy_.py,sha256=95kt6ylfqKmjLr8GZ1XH1khP9Q3uBYy4vqc4_2Zf1J4,11629
-sciv/preprocessing/_scvi_.py,sha256=MdiR0OWe1tc4HprK2RfwmHetsjRL1oQPjHYLqVm3MIA,10796
+sciv/preprocessing/_scvi_.py,sha256=vtMzaAuy3LZXPmg92MNJfFw5jIZv71_tZdpeEyl3JHc,10782
 sciv/preprocessing/_snapatac_.py,sha256=Dq8CHF7Psl3CQszaEokQYO56Oe2uzyWOy_cGlaOywfc,27798
-sciv/tool/__init__.py,sha256=WXzHkWt6RgBC3qqD-98nR5wQmt6oC850ox_VpMrapSU,2468
-sciv/tool/_algorithm_.py,sha256=55G9fuMdH-QDxw8ngIHhYn9gFWGqKelILUfnHUxVioE,54060
+sciv/tool/__init__.py,sha256=WgyiWuCvBadTZfNEB70VurbN1YfpNodnVCIcAABTYEA,2512
+sciv/tool/_algorithm_.py,sha256=5H_LHGyRfx0ng9wm8pux0_dEXuJJJVdnGLM9MjD12Fo,53682
 sciv/tool/_matrix_.py,sha256=SnC3sXic_ufuEXStcD_HncvYH6apBdNK6nhG6jFLmjA,24324
 sciv/tool/_random_walk_.py,sha256=2DPBRtd4A2MadfYDhkTw33WOATriiCULozNsUPE6lsY,48912
 sciv/util/__init__.py,sha256=nER-hRRaBGl3CGgl2rLZAUOQ3uY6-m9wQ9VNrjO5EFE,2014
 sciv/util/_constant_.py,sha256=w0wKQd8guLd1ZTW24_5aECrWsIWDiNQmEpLsWlHar1A,3000
 sciv/util/_core_.py,sha256=3Z5r_ssFEYGc0ZHSaRPLz6Ur4LKKMyOBA76qX_Kmemw,16982
-sciv-0.0.102.dist-info/METADATA,sha256=N5KQ3-MTOHaQDFhMRtvFGJXCOrXA79EIRRWEQwG3aXQ,3495
-sciv-0.0.102.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-sciv-0.0.102.dist-info/licenses/LICENSE,sha256=4UvHVf3qCOZjHLs4LkYz8u96XRpXnZrpTKrkUQPs5_A,1075
-sciv-0.0.102.dist-info/RECORD,,
+sciv-0.0.103.dist-info/METADATA,sha256=sUdT4krE1mTLee_PvzQXg0syisUxPtNf-1DHXVGVFyE,3495
+sciv-0.0.103.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+sciv-0.0.103.dist-info/licenses/LICENSE,sha256=4UvHVf3qCOZjHLs4LkYz8u96XRpXnZrpTKrkUQPs5_A,1075
+sciv-0.0.103.dist-info/RECORD,,