Fixed some issue of readme and added violin_box function (#714)

README.md

@@ -1,5 +1,5 @@
 <p align="center">
-  <img height="150" src="https://dynamo-release.readthedocs.io/en/latest/_static/logo_with_word.png" />
+  <img height="150" src="https://dynamo-release.readthedocs.io/en/latest/_static/logo.png" />
 </p>
 
 ##
@@ -21,7 +21,7 @@
 
 Inclusive model of expression dynamics with metabolic labeling based scRNA-seq / multiomics, vector field reconstruction, potential landscape mapping, differential geometry analyses, and most probably paths / *in silico* perturbation predictions.
 
-[Installation](https://dynamo-release.readthedocs.io/en/latest/ten_minutes_to_dynamo.html#how-to-install) - [Ten minutes to dynamo](https://dynamo-release.readthedocs.io/en/latest/ten_minutes_to_dynamo.html) - [Tutorials](https://dynamo-release.readthedocs.io/en/latest/notebooks/Differential_geometry.html) - [API](https://dynamo-release.readthedocs.io/en/latest/API.html) - [Citation](https://www.sciencedirect.com/science/article/pii/S0092867421015774?via%3Dihub) - [Theory](https://dynamo-release.readthedocs.io/en/latest/notebooks/Primer.html)
+[Installation](https://dynamo-release.readthedocs.io/en/latest/installation.html) - [Ten minutes to dynamo](https://dynamo-release.readthedocs.io/en/latest/user_guide/index.html) - [Tutorials](https://dynamo-release.readthedocs.io/en/latest/tutorials/index.html) - [API](https://dynamo-release.readthedocs.io/en/latest/api/index.html) - [Citation](https://dynamo-release.readthedocs.io/en/latest/references.html) - [Theory](https://dynamo-release.readthedocs.io/en/latest/introduction/index.html)
 
 ![Dynamo](https://user-images.githubusercontent.com/7456281/152110270-7ee1b0ed-1205-495d-9d65-59c7984d2fa2.png)
 

dynamo/data_io.py

@@ -48,6 +48,8 @@ def make_dir(path: str, can_exist: bool = True) -> bool:
         main_info("creating a new directory")
         os.makedirs(path)
         return True
+
+
 
 
 def convert2float(adata: AnnData, columns: List, var: bool = False) -> None:

dynamo/plot/__init__.py

@@ -79,6 +79,8 @@
     speed,
 )
 
+from .violin_box import violin_box
+
 __all__ = [
     "quiver_autoscaler",
     "save_fig",
@@ -161,4 +163,5 @@
     "sctransform_plot_fit",
     "plot_residual_var",
     "plot_dim_reduced_direct_graph",
+    "violin_box"
 ]

dynamo/plot/violin_box.py

@@ -0,0 +1,78 @@
+import pandas as pd
+import numpy as np
+import seaborn as sns
+import matplotlib.pyplot as plt
+from scipy.sparse import issparse
+
+def violin_box(adata, keys, groupby, ax=None, 
+               figsize=(4,4), show=True, 
+               max_strip_points=200):
+    import colorcet
+
+    # 获取 y 数据
+    y = None
+    if not adata.raw is None and keys in adata.raw.var_names:
+        y = adata.raw[:, keys].X
+    elif keys in adata.obs.columns:
+        y = adata.obs[keys].values
+    elif keys in adata.var_names:
+        y = adata[:, keys].X
+    else:
+        raise ValueError(f'{keys} not found in adata.raw.var_names, adata.var_names, or adata.obs.columns')
+
+    if issparse(y):
+        y = y.toarray().reshape(-1)
+    else:
+        y = y.reshape(-1)
+
+    # 获取 x 数据
+    x = adata.obs[groupby].values.reshape(-1)
+
+    # 创建绘图数据
+    plot_data = pd.DataFrame({groupby: x, keys: y})
+
+    # 创建图形和轴
+    if ax is None:
+        fig, ax = plt.subplots(1, 1, figsize=figsize)
+
+    # 获取或设置颜色
+    if f'{groupby}_colors' not in adata.uns or adata.uns[f'{groupby}_colors'] is None:
+        colors = ['#%02x%02x%02x' % tuple([int(k * 255) for k in i]) for i in colorcet.glasbey_bw_minc_20_maxl_70]
+        adata.uns[f'{groupby}_colors'] = colors[:len(adata.obs[groupby].unique())]
+
+    # 绘制小提琴图
+    sns.violinplot(x=groupby, y=keys, data=plot_data, hue=groupby, dodge=False,
+                   palette=adata.uns[f'{groupby}_colors'], scale="width", inner=None, ax=ax)
+
+    # 调整小提琴图
+    xlim, ylim = ax.get_xlim(), ax.get_ylim()
+    for violin in ax.collections:
+        bbox = violin.get_paths()[0].get_extents()
+        x0, y0, width, height = bbox.bounds
+        violin.set_clip_path(plt.Rectangle((x0, y0), width / 2, height, transform=ax.transData))
+
+    # 绘制箱线图
+    sns.boxplot(x=groupby, y=keys, data=plot_data, saturation=1, showfliers=False,
+                width=0.3, boxprops={'zorder': 3, 'facecolor': 'none'}, ax=ax)
+
+    # 限制 stripplot 的数据点数量
+    if len(plot_data) > max_strip_points:
+        plot_data = plot_data.sample(max_strip_points)
+
+    # 绘制 stripplot
+    old_len_collections = len(ax.collections)
+    sns.stripplot(x=groupby, y=keys, data=plot_data, hue=groupby,
+                  palette=adata.uns[f'{groupby}_colors'], dodge=False, ax=ax)
+
+    # 调整 stripplot 点的位置
+    for dots in ax.collections[old_len_collections:]:
+        dots.set_offsets(dots.get_offsets() + np.array([0.12, 0]))
+
+    ax.set_xlim(xlim)
+    ax.set_ylim(ylim)
+    plt.xticks(rotation=90)
+
+    if show:
+        plt.show()
+
+    return ax