sciv 0.0.91__py3-none-any.whl → 0.0.93__py3-none-any.whl

sciv/plot/__init__.py

@@ -7,6 +7,7 @@ from ._heat_map_ import heatmap, heatmap_annotation
 
 from ._scatter_ import (
     scatter_base,
+    scatter_3d,
     scatter_atac,
     scatter_trait,
     volcano_base,

sciv/plot/_bar_.py

@@ -32,10 +32,11 @@ def bar(
     direction: Literal['vertical', 'horizontal'] = "vertical",
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ) -> None:
 
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     ax_x = np.array(ax_x).astype(str)
 
@@ -59,7 +60,7 @@ def bar(
             color=text_color
         )
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)
 
 
 def two_bar(
@@ -78,10 +79,11 @@ def two_bar(
     title: str = None,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ):
 
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     ax_x = np.array(ax_x).astype(str)
     ax.bar(ax_x, ax_y[0], label=legend[0], color=color[0], **kwargs)
@@ -101,7 +103,7 @@ def two_bar(
             color=text_color
         )
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)
 
 
 def class_bar(
@@ -123,6 +125,7 @@ def class_bar(
     text_left_move: float = 0.15,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ):
 
@@ -159,6 +162,7 @@ def class_bar(
         title=title,
         output=output,
         show=show,
+        close=close,
         **kwargs
     )
 
@@ -183,6 +187,7 @@ def bar_trait(
     text_left_move: float = 0.15,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ):
     def trait_plot(trait_: str, cell_df_: DataFrame) -> None:
@@ -214,6 +219,7 @@ def bar_trait(
             text_color=text_color,
             output=os.path.join(output, f"cell_{trait_}_enrichment_bar.pdf") if output is not None else None,
             show=show,
+            close=close,
             **kwargs
         )
 
@@ -272,6 +278,7 @@ def bar_significance(
     title: str = None,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ) -> None:
     """
@@ -311,10 +318,11 @@ def bar_significance(
     :param title: Plot title
     :param output: Path to save figure (optional)
     :param show: Whether to display the plot
+    :param close:
     :return: None
     """
 
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     if legend_list is not None:
         new_data: DataFrame = df[df[hue].isin(legend_list)].copy()
@@ -432,4 +440,4 @@ def bar_significance(
 
     plt.legend(loc='upper left', bbox_to_anchor=(0.0, legend_gap), ncol=2)
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)

sciv/plot/_barcode_.py

@@ -29,7 +29,8 @@ def barcode_base(
     colors: list = None,
     ground_true: list = None,
     output: path = None,
-    show: bool = True
+    show: bool = True,
+    close: bool = False
 ):
     # sort
     df_sort = df.sort_values([trait_column_name, sort_column], ascending=False)
@@ -58,9 +59,6 @@ def barcode_base(
 
     plt.axis("off")
 
-    if title is not None:
-        plt.title(title)
-
     gs = GridSpec(20, 20)
     ax1 = fig.add_subplot(gs[:17, 11:14] if is_ticks else gs[:18, 11:14])
     ax2 = fig.add_subplot(gs[:17, :8] if is_ticks else gs[:18, :8])
@@ -91,7 +89,7 @@ def barcode_base(
     ticks = np.linspace(round(df_sort[sort_column].min(), 2), round(df_sort[sort_column].max() - 0.05, 2), 3)
     color_bar.set_ticks(ticks if is_ticks else [])
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, output=output, show=show, close=close)
 
 
 def barcode_trait(
@@ -107,8 +105,10 @@ def barcode_trait(
     colors: list = None,
     ground_true: list = None,
     title: str = None,
+    suffix: str = "pdf",
     output: path = None,
-    show: bool = True
+    show: bool = True,
+    close: bool = False
 ):
     data: DataFrame = trait_df.copy()
     cluster_list = list(set(trait_df[clusters]))
@@ -137,8 +137,9 @@ def barcode_trait(
             cmap=cmap,
             ground_true=ground_true,
             title=f"{title} {trait_}" if title is not None else title,
-            output=os.path.join(output, f"cell_{trait_}_score_rank.pdf") if output is not None else None,
-            show=show
+            output=os.path.join(output, f"cell_{trait_}_score_rank.{suffix}") if output is not None else None,
+            show=show,
+            close=close
         )
 
     # noinspection DuplicatedCode

sciv/plot/_box_.py

@@ -33,6 +33,7 @@ def box_base(
     order_names: list = None,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ) -> None:
 
@@ -43,7 +44,7 @@ def box_base(
         ul.log(__name__).error(f"The `value` ({value}) parameter must be in the `df` parameter data column name ({df_columns})")
         raise ValueError(f"The `value` ({value}) parameter must be in the `df` parameter data column name ({df_columns})")
 
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     group_columns = [clusters]
 
@@ -78,7 +79,7 @@ def box_base(
                 colors = new_df["color"]
 
     # scatter
-    ax1 = sns.boxplot(
+    sns.boxplot(
         data=df,
         x=clusters,
         y=value,
@@ -87,6 +88,7 @@ def box_base(
         fliersize=marker_size,
         orient=orient,
         whis=whis,
+        ax=ax,
         flierprops={'marker': 'o', 'markersize': marker_size},
         boxprops={'linestyle': '-', 'linewidth': line_width},
         whiskerprops={'linestyle': '-', 'linewidth': line_width},
@@ -95,7 +97,7 @@ def box_base(
         **kwargs
     )
 
-    lines = ax1.lines
+    lines = ax.lines
 
     for line in lines:
         line.set_linewidth(line_width)
@@ -107,7 +109,9 @@ def box_base(
     ax.spines['left'].set_linewidth(line_width)
     ax.spines['right'].set_linewidth(line_width)
 
-    plot_end(fig, output, show)
+    ax.yaxis.grid(True, linestyle='-', linewidth=line_width)
+
+    plot_end(fig, title, x_name, y_name, output, show, close)
 
 
 def box_trait(
@@ -133,6 +137,7 @@ def box_trait(
     title: str = None,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ) -> None:
 
@@ -170,6 +175,7 @@ def box_trait(
             title=f"{title} {trait_}" if title is not None else title,
             output=os.path.join(output, f"cell_{trait_}_score_box.pdf") if output is not None else None,
             show=show,
+            close=close,
             **kwargs
         )
 

sciv/plot/_bubble_.py

@@ -25,10 +25,11 @@ def bubble(
     bottom: float = 0,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ):
 
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     if size is not None:
         _size_ = df[size].values
@@ -49,4 +50,4 @@ def bubble(
         **kwargs
     )
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)

sciv/plot/_core_.py

@@ -315,7 +315,8 @@ def rate_bar_plot(
     title: str = None,
     text_left_move: float = 0.15,
     plot_output: path = None,
-    show: bool = True
+    show: bool = True,
+    close: bool = False
 ) -> None:
 
     if dir_name is not None:
@@ -349,7 +350,8 @@ def rate_bar_plot(
         rotation=rotation,
         text_left_move=text_left_move,
         output=new_path if plot_output is not None else None,
-        show=show
+        show=show,
+        close=close
     )
 
 
@@ -373,7 +375,8 @@ def rate_circular_bar_plot(
     y_limit: Tuple = (-0.5, 1),
     y_axis_scale: Tuple = (0, 1),
     plot_output: path = None,
-    show: bool = True
+    show: bool = True,
+    close: bool = False
 ) -> None:
 
     if dir_name is not None:
@@ -412,7 +415,8 @@ def rate_circular_bar_plot(
         y_limit=y_limit,
         y_axis_scale=y_axis_scale,
         output=new_path if plot_output is not None else None,
-        show=show
+        show=show,
+        close=close
     )
 
 

sciv/plot/_graph_.py

@@ -41,15 +41,16 @@ def graph(
     bottom: float = 0,
     is_font: bool = False,
     output: path = None,
-    show: bool = True
+    show: bool = True,
+    close: bool = False
 ) -> None:
     if output is None and not show:
         ul.log(__name__).error(f"At least one of the `output` and `show` parameters is required")
         raise ValueError(f"At least one of the `output` and `show` parameters is required")
 
-    plt.figure(figsize=(width, height), dpi=150)
+    plt.figure(figsize=(width, height), dpi=300)
 
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     # Determine whether it is a square array
     if data.shape[0] != data.shape[1]:
@@ -94,7 +95,7 @@ def graph(
     else:
         nx.draw(gr, pos=pos, labels={}, **options)
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)
 
 
 def communities_graph(
@@ -113,7 +114,8 @@ def communities_graph(
     start_color_index: int = 0,
     color_step_size: int = 0,
     output: path = None,
-    show: bool = True
+    show: bool = True,
+    close: bool = False
 ):
     if output is None and not show:
         ul.log(__name__).error(f"At least one of the `output` and `show` parameters is required")
@@ -133,7 +135,7 @@ def communities_graph(
 
     type_colors = type_20_colors if len(__hue_order__) <= 20 else type_50_colors
 
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     ul.log(__name__).info("Get position")
     color_index = 0
@@ -170,7 +172,7 @@ def communities_graph(
         width=line_widths
     )
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)
 
 
 def network_two_types(
@@ -197,7 +199,8 @@ def network_two_types(
     is_fluctuate: bool = True,
     layout_type: str = 'spring',
     output: path = None,
-    show: bool = True
+    show: bool = True,
+    close: bool = False
 ):
     if output is None and not show:
         ul.log(__name__).error(f"At least one of the `output` and `show` parameters is required")
@@ -375,4 +378,4 @@ def network_two_types(
 
     plt.axis('off')
 
-    plot_end(fig, output, show)
+    plot_end(fig, output=output, show=show, close=close)

sciv/plot/_heat_map_.py

@@ -68,6 +68,7 @@ def heatmap_annotation(
     cmap: str = "Oranges",
     is_sort: bool = True,
     show: bool = True,
+    close: bool = False,
     output: path = None,
     **kwargs
 ) -> None:
@@ -130,12 +131,13 @@ def heatmap_annotation(
     :param cmap: Display color themes for heat maps;
     :param is_sort: If set to true, when displaying the heatmap, the row and column names are sorted and displayed;
     :param show: If true, display the image;
+    :param close: If true, close the image;
     :param output: Output file for image saving;
     :return: Display of image or saved file.
     """
 
     ul.log(__name__).info("Start plotting the heatmap")
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     data = adata.copy()
 
@@ -287,7 +289,7 @@ def heatmap_annotation(
         **kwargs
     )
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)
 
 
 def heatmap(
@@ -308,9 +310,10 @@ def heatmap(
     y_name: str = None,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ) -> None:
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     data = adata.copy()
 
@@ -337,4 +340,4 @@ def heatmap(
         # noinspection PyUnresolvedReferences
         plt.setp(heat_map.ax_heatmap.get_xticklabels(), rotation=rotation)
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)

sciv/plot/_kde_.py

@@ -28,11 +28,12 @@ def kde(
     is_legend: bool = True,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ) -> None:
     ul.log(__name__).info("Start plotting the Kernel density estimation chart")
 
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     data = check_adata_get(adata, layer=layer, is_dense=True, is_matrix=False)
 
@@ -72,4 +73,4 @@ def kde(
         if is_legend:
             ax.legend(list(adata.obs.index))
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)

sciv/plot/_line_.py

@@ -40,10 +40,11 @@ def stability_line(
     output: Optional[path] = None,
     is_str: bool = True,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ) -> None:
 
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     new_data = data.copy()
 
@@ -122,4 +123,4 @@ def stability_line(
     else:
         plt.xticks(x_ticks, rotation=x_name_rotation)
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)

sciv/plot/_pie_.py

@@ -27,9 +27,10 @@ def base_pie(
     autopct: str = '%1.2f%%',
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ) -> None:
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     size = len(values)
 
@@ -54,7 +55,7 @@ def base_pie(
 
     ax.axis('off')
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)
 
 
 def pie_label(
@@ -75,9 +76,10 @@ def pie_label(
     colors: list = None,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ) -> None:
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     # judge
     df_columns = list(df.columns)
@@ -128,7 +130,7 @@ def pie_label(
 
     ax.axis('off')
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)
 
 
 def pie_trait(
@@ -150,6 +152,7 @@ def pie_trait(
     colors: list = None,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ) -> None:
     trait_cluster_map_key_list = list(trait_cluster_map.keys())
@@ -191,6 +194,7 @@ def pie_trait(
             title=f"{title} {trait_}" if title is not None else title,
             output=os.path.join(output, f"cell_{trait_}_score_pie.pdf") if output is not None else None,
             show=show,
+            close=close,
             **kwargs
         )
 

sciv/plot/_radar_.py

@@ -35,10 +35,11 @@ def radar(
     y_axis_scale: Tuple = (0, 1),
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ):
 
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     ax_x = list(ax_x)
     ax_y = list(ax_y)
@@ -96,7 +97,7 @@ def radar(
     # Adjust the layout to prevent label overlap
     plt.tight_layout()
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)
 
 
 def radar_trait(
@@ -119,6 +120,7 @@ def radar_trait(
     y_axis_scale: Tuple = (0, 1),
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ):
 
@@ -166,6 +168,7 @@ def radar_trait(
             center_text=trait_,
             output=os.path.join(output, f"{trait_}_enrichment_radar.pdf") if output is not None else None,
             show=show,
+            close=close,
             **kwargs
         )
 

sciv/plot/_scatter_.py

@@ -5,6 +5,7 @@ from typing import Union, Tuple, Optional, Any
 
 import matplotlib
 import numpy as np
+import pandas as pd
 from anndata import AnnData
 from matplotlib import pyplot as plt
 from pandas import DataFrame
@@ -45,9 +46,10 @@ def scatter_base(
     is_text: bool = False,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ) -> None:
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     # scatter
     if number:
@@ -82,7 +84,8 @@ def scatter_base(
             if legend is not None:
                 df.loc[df[df["__hue__"] == elem].index, "__hue__"] = legend[elem]
                 colors.update(
-                    {legend[elem]: type_colors[start_color_index + i * color_step_size + __hue_order__.index(elem)]})
+                    {legend[elem]: type_colors[start_color_index + i * color_step_size + __hue_order__.index(elem)]}
+                )
             else:
                 colors.update(
                     {
@@ -147,7 +150,76 @@ def scatter_base(
     ax.spines['bottom'].set_visible(False)
     ax.spines['left'].set_visible(False)
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)
+
+
+def scatter_3d(
+    df: DataFrame,
+    x: str,
+    y: str,
+    z: str,
+    hue: str = None,
+    x_name: str = None,
+    y_name: str = None,
+    z_name: str = None,
+    title: str = None,
+    width: float = 2,
+    height: float = 2,
+    bottom: float = 0,
+    edge_color: str = None,
+    size: Union[float, collection] = 1.0,
+    legend_name: str = None,
+    output: path = None,
+    show: bool = True,
+    close: bool = False,
+    **kwargs: Any
+):
+    if output is None and not show:
+        ul.log(__name__).error(f"At least one of the `output` and `show` parameters is required")
+        raise ValueError(f"At least one of the `output` and `show` parameters is required")
+
+    fig, ax = plt.subplots(figsize=(width, height))
+    fig.subplots_adjust(bottom=bottom, projection='3d')
+
+    hue_cat = pd.Categorical(df[hue])
+
+    scatter = ax.scatter(
+        df[x],
+        df[y],
+        df[z],
+        c=hue_cat.codes,
+        cmap='tab20',
+        s=size,
+        edgecolors=edge_color,
+        **kwargs
+    )
+
+    # 设置坐标轴标签和标题
+
+    if x_name is not None:
+        ax.set_xlabel(x_name)
+
+    if y_name is not None:
+        ax.set_ylabel(y_name)
+
+    if z_name is not None:
+        ax.set_zlabel(z_name)
+
+    if title is not None:
+        ax.set_title(title)
+
+    unique_types = hue_cat.categories
+    legend_elements = [
+        plt.Line2D(
+            [0], [0], marker='o', color='w', label=type_,
+            markerfacecolor=scatter.cmap(scatter.norm(i))
+        )
+        for i, type_ in enumerate(unique_types)
+    ]
+
+    ax.legend(handles=legend_elements, title=legend_name, bbox_to_anchor=(1.05, 1), loc='upper left')
+
+    plot_end(fig, None, None, None, output, show, close)
 
 
 def scatter_atac(
@@ -169,6 +241,7 @@ def scatter_atac(
     is_text: bool = False,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ) -> None:
     # DataFrame
@@ -195,6 +268,7 @@ def scatter_atac(
         legend_fontsize=legend_fontsize,
         output=output,
         show=show,
+        close=close,
         right=0.75,
         **kwargs
     )
@@ -225,6 +299,7 @@ def scatter_trait(
     legend: dict = None,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ) -> None:
     data: AnnData = trait_adata.copy()
@@ -285,6 +360,7 @@ def scatter_trait(
                 output, f"cell_{trait_}_score_{layer_}.pdf" if layer_ is not None else f"cell_{trait_}_score.pdf"
             ) if output is not None else None,
             show=show,
+            close=close,
             **kwargs
         )
 
@@ -336,9 +412,10 @@ def volcano_base(
     y_name: Optional[str] = None,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ):
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     if palette is None:
         palette = ["#01c5c4", "#686d76", "#ff414d"]
@@ -352,7 +429,7 @@ def volcano_base(
     plt.axvline(axv_left_value, color='grey', linestyle='--')
     plt.axvline(axv_right_value, color='grey', linestyle='--')
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)
 
 
 def manhattan_causal_variant(
@@ -375,9 +452,9 @@ def manhattan_causal_variant(
     y_limit: Tuple[float, float] = (0, 1),
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ):
-
     df[chr_name] = df[chr_name].astype(chrtype)
 
     if is_sort:
@@ -390,7 +467,7 @@ def manhattan_causal_variant(
         colors = type_20_colors.copy()
         colors.extend(type_set_colors)
 
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     x_labels = []
     x_labels_pos = []
@@ -434,7 +511,7 @@ def manhattan_causal_variant(
     ax.set_xlim([0, len(df)])
     ax.set_ylim(y_limit)
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)
 
 
 def pseudo_time_score(
@@ -454,11 +531,12 @@ def pseudo_time_score(
     size: Union[float, collection] = 1.0,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ):
     from scipy.signal import savgol_filter
 
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     pseudo_times = df[x].values
     scores = df[y].values
@@ -482,4 +560,4 @@ def pseudo_time_score(
 
     plt.tight_layout()
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)

sciv/plot/_venn_.py

@@ -26,9 +26,10 @@ def three_venn(
     title: str = None,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ) -> None:
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     if colors is None:
         colors = type_set_colors[:3]
@@ -54,7 +55,7 @@ def three_venn(
 
     ax.axis('off')
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)
 
 
 def two_venn(
@@ -71,9 +72,10 @@ def two_venn(
     title: str = None,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ) -> None:
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     if colors is None:
         colors = type_set_colors[:2]
@@ -96,4 +98,4 @@ def two_venn(
 
     ax.axis('off')
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)

sciv/plot/_violin_.py

@@ -29,11 +29,12 @@ def violin_base(
     rotation: float = 65,
     line_width: float = 0.5,
     title: str = None,
-    split: bool = True,
+    split: bool = False,
     is_sort: bool = True,
     order_names: list = None,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ) -> None:
     # judge
@@ -50,7 +51,7 @@ def violin_base(
             f"The `hue` ({hue}) parameter must be in the `df` parameter data column name ({df_columns})")
         raise ValueError(f"The `hue` ({hue}) parameter must be in the `df` parameter data column name ({df_columns})")
 
-    fig, ax = plot_start(title, x_name, y_name, width, height, bottom, output, show)
+    fig, ax = plot_start(width, height, bottom, output, show)
 
     group_columns = [clusters]
 
@@ -98,15 +99,15 @@ def violin_base(
     )
 
     # set coordinate
-    for ax in g.axes.flat:
-        ax.spines['top'].set_linewidth(line_width)
-        ax.spines['right'].set_linewidth(line_width)
-        ax.spines['bottom'].set_linewidth(line_width)
-        ax.spines['left'].set_linewidth(line_width)
+    for _ax_ in g.axes.flat:
+        _ax_.spines['top'].set_linewidth(line_width)
+        _ax_.spines['right'].set_linewidth(line_width)
+        _ax_.spines['bottom'].set_linewidth(line_width)
+        _ax_.spines['left'].set_linewidth(line_width)
         # Set the rotation angle of the x-axis labels
-        ax.tick_params(axis='x', rotation=rotation)
+        _ax_.tick_params(axis='x', rotation=rotation)
 
-    plot_end(fig, output, show)
+    plot_end(fig, title, x_name, y_name, output, show, close)
 
 
 def violin_trait(
@@ -124,30 +125,29 @@ def violin_trait(
     rotation: float = 65,
     line_width: float = 0.1,
     bottom: float = 0.3,
-    split: bool = True,
+    split: bool = False,
     is_sort: bool = True,
     order_names: list = None,
     title: str = None,
     output: path = None,
     show: bool = True,
+    close: bool = False,
     **kwargs: Any
 ) -> None:
 
     data: DataFrame = trait_df.copy()
 
-    def trait_plot(trait_: Union[str, list], atac_cell_df_: DataFrame) -> None:
+    def trait_plot(_trait_: Union[str, list], _cell_df_: DataFrame) -> None:
         """
         show plot
-        :param trait_: trait name
-        :param atac_cell_df_:
+        :param _trait_: trait name
+        :param _cell_df_:
         :return: None
         """
-        ul.log(__name__).info("Plotting box {}".format(", ".join(trait_)))
+        ul.log(__name__).info("Plotting box {}".format(_trait_))
         # get gene score
-        _filename_: str = trait_ if isinstance(trait_, str) else "_".join(trait_)
-        trait_score = atac_cell_df_[
-            atac_cell_df_[trait_column_name] == trait_ if isinstance(trait_, str) else atac_cell_df_[
-                trait_column_name].isin(trait_)]
+        _filename_: str = _trait_
+        trait_score = _cell_df_[_cell_df_[trait_column_name] == _trait_]
         # Sort gene scores from small to large
         violin_base(
             df=trait_score,
@@ -169,6 +169,7 @@ def violin_trait(
             title=f"{title} {_filename_}" if title is not None else title,
             output=os.path.join(output, f"cell_{_filename_}_score_cat_{kind}.pdf") if output is not None else None,
             show=show,
+            close=close,
             **kwargs
         )
 
@@ -176,9 +177,10 @@ def violin_trait(
     trait_list = list(set(data[trait_column_name]))
     # judge trait
     if trait_name != "All":
-        if isinstance(trait_name, str) and trait_name not in trait_list:
-            ul.log(__name__).error(f"The {trait_name} trait/disease is not in the trait/disease list {trait_list}.")
-            raise ValueError(f"The {trait_name} trait/disease is not in the trait/disease list {trait_list}.")
+        if isinstance(trait_name, str):
+            if trait_name not in trait_list:
+                ul.log(__name__).error(f"The {trait_name} trait/disease is not in the trait/disease list {trait_list}.")
+                raise ValueError(f"The {trait_name} trait/disease is not in the trait/disease list {trait_list}.")
         else:
             for tn in trait_name:
                 if tn not in trait_list:

sciv/preprocessing/_scvi_.py

@@ -8,7 +8,7 @@ import numpy as np
 import pandas as pd
 
 from anndata import AnnData
-from torch import OutOfMemoryError
+from torch.cuda import OutOfMemoryError
 
 from .. import util as ul
 from ..tool import umap, tsne
@@ -134,7 +134,7 @@ 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", devices="cpu")
+                    model = scvi.external.POISSONVI.load(model_dir, adata=adata, accelerator="cpu", device="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/util/_core_.py

@@ -415,9 +415,6 @@ def check_gpu_availability(verbose: bool = True) -> bool:
 
 
 def plot_start(
-    title: str = None,
-    x_name: str = None,
-    y_name: str = None,
     width: float = 2,
     height: float = 2,
     bottom: float = 0,
@@ -431,6 +428,20 @@ def plot_start(
     fig, ax = plt.subplots(figsize=(width, height))
     fig.subplots_adjust(bottom=bottom)
 
+    return fig, ax
+
+
+def plot_end(
+    fig,
+    title: str = None,
+    x_name: str = None,
+    y_name: str = None,
+    output: str = None,
+    show: bool = True,
+    close: bool = False,
+    dpi: float = 300
+):
+
     if title is not None:
         plt.title(title)
 
@@ -438,12 +449,8 @@ def plot_start(
         plt.xlabel(x_name, rotation=0)
 
     if y_name is not None:
-        plt.xlabel(y_name, rotation=90)
-
-    return fig, ax
-
+        plt.ylabel(y_name, rotation=90)
 
-def plot_end(fig, output: str, show: bool, dpi: float = 300):
     if output is not None:
 
         if output.endswith(".pdf"):
@@ -451,7 +458,7 @@ def plot_end(fig, output: str, show: bool, dpi: float = 300):
             with PdfPages(output) as pdf:
                 pdf.savefig(fig)
 
-        elif output.endswith(".png") or output.endswith(".jpg"):
+        elif output.endswith(".png") or output.endswith(".jpg") or output.endswith(".svg"):
             plt.savefig(output, dpi=dpi)
         else:
             plt.savefig(f"{output}.png", dpi=dpi)
@@ -459,7 +466,8 @@ def plot_end(fig, output: str, show: bool, dpi: float = 300):
     if show:
         plt.show()
 
-    plt.close()
+    if close:
+        plt.close('all')
 
 
 def generate_hex_colors(num_colors):

{sciv-0.0.91.dist-info → sciv-0.0.93.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sciv
-Version: 0.0.91
+Version: 0.0.93
 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-0.0.93.dist-info/RECORD

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sciv-0.0.91.dist-info/RECORD

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