py2ls 0.2.4__py3-none-any.whl → 0.2.4.2__py3-none-any.whl

py2ls/plot.py

@@ -10,8 +10,8 @@ from cycler import cycler
 import logging
 import os
 import re
-
-from .ips import fsave, fload, mkdir, listdir, figsave, strcmp, unique, get_os, ssplit
+from typing import Union
+from .ips import fsave, fload, mkdir, listdir, figsave, strcmp, unique, get_os, ssplit,plt_font
 from .stats import *
 from .netfinder import get_soup, fetch
 
@@ -152,6 +152,36 @@ def heatmap(
     yticklabels=True,  # Show row labels
     **kwargs,
 ):
+    """
+    plot heatmap or clustermap for a given dataset (DataFrame).
+
+    Parameters:
+    - data (pd.DataFrame): The input data to visualize.
+    - ax (matplotlib.Axes, optional): Axis object to plot on. If None and cluster=False, a new axis is created.
+    - kind (str, default="corr"): Type of heatmap to plot. Options:
+        - "corr": Correlation heatmap based on numeric columns.
+        - "direct": Direct visualization of the numeric data.
+        - "pivot": Creates a heatmap using the `pivot_table` method.
+    - columns (str or list, default="all"): Columns to include in the heatmap. For pivoting, this specifies the 'columns' argument.
+    - index (str, optional): For pivot heatmap, sets the 'index' argument.
+    - values (str, optional): For pivot heatmap, sets the 'values' argument.
+    - tri (str, default="u"): Specifies whether to show the 'upper' or 'lower' triangle in the heatmap.
+    - mask (bool, default=True): Whether to mask half of the correlation matrix.
+    - k (int, default=1): Controls how much of the triangle is masked in correlation heatmaps.
+    - annot (bool, default=True): If True, writes the data values in each cell.
+    - cmap (str, default="coolwarm"): The colormap for the heatmap.
+    - fmt (str, default=".2f"): String formatting code for annotating cells.
+    - cluster (bool, default=False): If True, a clustermap with hierarchical clustering is plotted.
+    - inplace (bool, default=False): If True, modifies the original data. Not currently used.
+    - figsize (tuple, default=(10, 8)): Size of the figure for the heatmap.
+    - row_cluster (bool, default=True): Perform clustering on rows.
+    - col_cluster (bool, default=True): Perform clustering on columns.
+    - dendrogram_ratio (tuple, default=(0.2, 0.1)): Adjust the size of the dendrograms.
+    - cbar_pos (tuple, default=(0.02, 1, 0.02, 0.1)): Adjust the position of the colorbar.
+    - xticklabels (bool, default=True): Show or hide the column labels.
+    - yticklabels (bool, default=True): Show or hide the row labels.
+    - **kwargs: Additional arguments passed to `sns.heatmap` or `sns.clustermap`.
+    """
     if ax is None and not cluster:
         ax = plt.gca()
     # Select numeric columns or specific subset of columns
@@ -162,7 +192,8 @@ def heatmap(
 
     kinds = ["corr", "direct", "pivot"]
     kind = strcmp(kind, kinds)[0]
-    if kind == "corr":
+    print(kind)
+    if "corr" in kind:  # correlation
         # Compute the correlation matrix
         data4heatmap = df_numeric.corr()
         # Generate mask for the upper triangle if mask is True
@@ -254,11 +285,26 @@ def heatmap(
             )
             # Return the Axes object for further customization if needed
             return ax
-    elif kind == "direct":
+    elif "dir" in kind:  # direct
         data4heatmap = df_numeric
-    elif kind == "pivot":
-        print('need 3 param: e.g., index="Task", columns="Model", values="Score"')
-        data4heatmap = data.pivot(index=index, columns=columns, values=values)
+    elif "pi" in kind:  # pivot
+        try:
+            print(
+                f'pivot: \n\tneed at least 3 param: e.g., index="Task", columns="Model", values="Score"'
+            )
+            data4heatmap = data.pivot(index=index, columns=columns, values=values)
+        except:
+            print(
+                f'pivot_table: \n\tneed at least 4 param: e.g., index="Task", columns="Model", values="Score",aggfunc="mean"'
+            )
+            aggfunc = "mean"
+            for k_, v_ in kwargs.items():
+                if "agg" in k_.lower():
+                    aggfunc = v_
+            kwargs.pop(k_, None)
+            data4heatmap = data.pivot_table(
+                index=index, columns=columns, values=values, aggfunc=aggfunc
+            )
     else:
         print(f'"{kind}" is not supported')
     # Remove conflicting kwargs
@@ -1816,8 +1862,10 @@ def figsets(*args, **kwargs):
     matplotlib.rc("text", usetex=False)
 
     fig = plt.gcf()
-    fontsize = 11
-    fontname = "Arial"
+    fontsize = kwargs.get("fontsize",11)
+    plt.rcParams["font.size"]=fontsize
+    fontname = kwargs.pop("fontname","Arial") 
+    fontname=plt_font(fontname) # 显示中文
     sns_themes = ["white", "whitegrid", "dark", "darkgrid", "ticks"]
     sns_contexts = ["notebook", "talk", "poster"]  # now available "paper"
     scienceplots_styles = [
@@ -1843,6 +1891,7 @@ def figsets(*args, **kwargs):
     ]
 
     def set_step_1(ax, key, value):
+        nonlocal fontsize, fontname
         if ("fo" in key) and (("size" in key) or ("sz" in key)):
             fontsize = value
             plt.rcParams.update({"font.size": fontsize})
@@ -1885,15 +1934,15 @@ def figsets(*args, **kwargs):
             if ("x" in key.lower()) and (
                 "tic" not in key.lower() and "tk" not in key.lower()
             ):
-                ax.set_xlabel(value, fontname=fontname)
+                ax.set_xlabel(value, fontname=fontname,fontsize=fontsize)
             if ("y" in key.lower()) and (
                 "tic" not in key.lower() and "tk" not in key.lower()
             ):
-                ax.set_ylabel(value, fontname=fontname)
+                ax.set_ylabel(value, fontname=fontname,fontsize=fontsize)
             if ("z" in key.lower()) and (
                 "tic" not in key.lower() and "tk" not in key.lower()
             ):
-                ax.set_zlabel(value, fontname=fontname)
+                ax.set_zlabel(value, fontname=fontname,fontsize=fontsize)
         if key == "xlabel" and isinstance(value, dict):
             ax.set_xlabel(**value)
         if key == "ylabel" and isinstance(value, dict):
@@ -2096,6 +2145,7 @@ def figsets(*args, **kwargs):
             plt.set_cmap(value)
 
     def set_step_2(ax, key, value):
+        nonlocal fontsize, fontname
         if key == "figsize":
             pass
         if "xlim" in key.lower():
@@ -2135,9 +2185,9 @@ def figsets(*args, **kwargs):
                     ax.grid(visible=False)
         if "tit" in key.lower():
             if "sup" in key.lower():
-                plt.suptitle(value)
+                plt.suptitle(value,fontname=fontname,fontsize=fontsize)
             else:
-                ax.set_title(value)
+                ax.set_title(value,fontname=fontname,fontsize=fontsize)
         if key.lower() in ["spine", "adjust", "ad", "sp", "spi", "adj", "spines"]:
             if isinstance(value, bool) or (value in ["go", "do", "ja", "yes"]):
                 if value:
@@ -2873,13 +2923,26 @@ def plot_xy(
     x=None,
     y=None,
     ax=None,
-    kind: str = None,  # Specify the kind of plot
+    kind: Union[str, list] = None,  # Specify the kind of plot
+    verbose=False,
+    **kwargs,
+):
+    # You can call the original plotxy function if needed
+    # or simply replicate the functionality here
+    return plotxy(data, x, y, ax, kind, verbose, **kwargs)
+
+
+def plotxy(
+    data: pd.DataFrame = None,
+    x=None,
+    y=None,
+    ax=None,
+    kind: Union[str, list] = None,  # Specify the kind of plot
     verbose=False,
-    # kws_figsets:dict=None,
     **kwargs,
 ):
     """
-    e.g., plot_xy(data=data_log, x="Component_1", y="Component_2", hue="Cluster",kind='scater)
+    e.g., plotxy(data=data_log, x="Component_1", y="Component_2", hue="Cluster",kind='scater)
     Create a variety of plots based on the kind parameter.
 
     Parameters:
@@ -2942,10 +3005,10 @@ def plot_xy(
             kws_figsets = v_arg
             kwargs.pop(k_arg, None)
             break
-    kws_text = {}
+    kws_add_text = {}
     for k_arg, v_arg in kwargs.items():
-        if "add" in k_arg and all(["t" in k_arg, "x" in k_arg]):  # add_text
-            kws_text = v_arg
+        if "add" in k_arg and "text" in k_arg:  # add_text
+            kws_add_text = v_arg
             kwargs.pop(k_arg, None)
             break
 
@@ -2993,6 +3056,7 @@ def plot_xy(
             ax = stdshade(ax=ax, **kwargs)
         elif k == "scatterplot":
             kws_scatter = kwargs.pop("kws_scatter", kwargs)
+            hue = kwargs.pop("hue", None)
             palette = kws_scatter.pop(
                 "palette",
                 (
@@ -3029,7 +3093,8 @@ def plot_xy(
             ax = sns.rugplot(data=data, x=x, ax=ax, **kws_rug)
         elif k == "stripplot":
             kws_strip = kwargs.pop("kws_strip", kwargs)
-            ax = sns.stripplot(data=data, x=x, y=y, ax=ax, **kws_strip)
+            dodge = kws_strip.pop("dodge", True)
+            ax = sns.stripplot(data=data, x=x, y=y, ax=ax, dodge=dodge, **kws_strip)
         elif k == "swarmplot":
             kws_swarm = kwargs.pop("kws_swarm", kwargs)
             ax = sns.swarmplot(data=data, x=x, y=y, ax=ax, **kws_swarm)
@@ -3050,6 +3115,8 @@ def plot_xy(
             ax = sns.barplot(data=data, x=x, y=y, ax=ax, **kws_bar)
         elif k == "countplot":
             kws_count = kwargs.pop("kws_count", kwargs)
+            if not kws_count.get("hue",None):
+                kws_count.pop("palette",None) 
             ax = sns.countplot(data=data, x=x, ax=ax, **kws_count)
         elif k == "regplot":
             kws_reg = kwargs.pop("kws_reg", kwargs)
@@ -3062,7 +3129,8 @@ def plot_xy(
             ax = sns.lineplot(ax=ax, data=data, x=x, y=y, **kws_line)
 
         figsets(ax=ax, **kws_figsets)
-        add_text(ax=ax, **kws_text)
+        print(kws_add_text)
+        add_text(ax=ax, **kws_add_text) if kws_add_text else None
         print(k, " ⤵ ")
         print(default_settings[k])
         print(
@@ -3077,14 +3145,14 @@ def plot_xy(
 
 
 def volcano(
-    data,
-    x,
-    y,
+    data:pd.DataFrame,
+    x:str,
+    y:str,
     gene_col=None,
     top_genes=5,
     thr_x=np.log2(1.5),
     thr_y=-np.log10(0.05),
-    colors=("#e70b0b", "#0d26e3", "#b8bbbe"),
+    colors=("#00BFFF", "#9d9a9a", "#FF3030"),
     s=20,
     fill=True,  # plot filled scatter
     facecolor="none",
@@ -3094,8 +3162,8 @@ def volcano(
     legend=False,
     ax=None,
     verbose=False,
-    kws_arrow=None,
-    kws_text=None,
+    kws_text=dict(fontsize=10, color="k"),
+    kws_arrow=dict(style="-", color="k", lw=0.5),
     **kwargs,
 ):
     """
@@ -3220,55 +3288,55 @@ def volcano(
             fontname = kws_text.pop("fontname", "Arial")
             textcolor = kws_text.pop("color", "k")
             fontsize = kws_text.pop("fontsize", 10)
-        for i in range(sele_gene.shape[0]):
-            if isinstance(textcolor, list):  # be consistant with dots's color
-                textcolor = colors[0] if sele_gene[x].iloc[i] > 0 else colors[1]
-            texts.append(
-                plt.text(
-                    x=sele_gene[x].iloc[i],
-                    y=sele_gene[y].iloc[i],
-                    s=sele_gene[gene_col].iloc[i],
-                    fontdict={
-                        "fontsize": fontsize,
-                        "color": textcolor,
-                        "fontname": fontname,
-                    },
+            for i in range(sele_gene.shape[0]):
+                if isinstance(textcolor, list):  # be consistant with dots's color
+                    textcolor = colors[0] if sele_gene[x].iloc[i] > 0 else colors[1]
+                texts.append(
+                    plt.text(
+                        x=sele_gene[x].iloc[i],
+                        y=sele_gene[y].iloc[i],
+                        s=sele_gene[gene_col].iloc[i],
+                        fontdict={
+                            "fontsize": fontsize,
+                            "color": textcolor,
+                            "fontname": fontname,
+                        },
+                    )
                 )
-            )
 
-        arrowstyles = [
-            "-",
-            "->",
-            "-[",
-            "|->",
-            "<-",
-            "<->",
-            "<|-",
-            "<|-|>",
-            "-|>",
-            "-[ ",
-            "fancy",
-            "simple",
-            "wedge",
-        ]
-        arrowstyle = kws_arrow.pop("style", "-")
-        arrowcolor = kws_arrow.pop("color", "0.5")
-        arrowlinewidth = kws_arrow.pop("lw", 0.5)
-        shrinkA = kws_arrow.pop("shrinkA", 5)
-        shrinkB = kws_arrow.pop("shrinkB", 5)
-        arrowstyle = strcmp(arrowstyle, arrowstyles)[0]
-        adjust_text(
-            texts,
-            expand_text=(1.05, 1.2),
-            arrowprops=dict(
-                arrowstyle=arrowstyle,
-                color=arrowcolor,
-                lw=arrowlinewidth,
-                shrinkA=shrinkA,
-                shrinkB=shrinkB,
-                **kws_arrow,
-            ),
-        )
+                arrowstyles = [
+                    "-",
+                    "->",
+                    "-[",
+                    "|->",
+                    "<-",
+                    "<->",
+                    "<|-",
+                    "<|-|>",
+                    "-|>",
+                    "-[ ",
+                    "fancy",
+                    "simple",
+                    "wedge",
+                ]
+                arrowstyle = kws_arrow.pop("style", "-")
+                arrowcolor = kws_arrow.pop("color", "0.5")
+                arrowlinewidth = kws_arrow.pop("lw", 0.5)
+                shrinkA = kws_arrow.pop("shrinkA", 5)
+                shrinkB = kws_arrow.pop("shrinkB", 5)
+                arrowstyle = strcmp(arrowstyle, arrowstyles)[0]
+                adjust_text(
+                    texts,
+                    expand_text=(1.05, 1.2),
+                    arrowprops=dict(
+                        arrowstyle=arrowstyle,
+                        color=arrowcolor,
+                        lw=arrowlinewidth,
+                        shrinkA=shrinkA,
+                        shrinkB=shrinkB,
+                        **kws_arrow,
+                    ),
+                )
 
     figsets(**kws_figsets)
 

{py2ls-0.2.4.dist-info → py2ls-0.2.4.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: py2ls
-Version: 0.2.4
+Version: 0.2.4.2
 Summary: py(thon)2(too)ls
 Author: Jianfeng
 Author-email: Jianfeng.Liu0413@gmail.com

{py2ls-0.2.4.dist-info → py2ls-0.2.4.2.dist-info}/RECORD

@@ -173,6 +173,7 @@ py2ls/LICENSE,sha256=UOZ1F5fFDe3XXvG4oNnkL1-Ecun7zpHzRxjp-XsMeAo,11324
 py2ls/README.md,sha256=CwvJWAnSXnCnrVHlnEbrxxi6MbjbE_MT6DH2D53S818,11572
 py2ls/__init__.py,sha256=Nn8jTIvySX7t7DMJ8VNRVctTStgXGjHldOIdZ35PdW8,165
 py2ls/batman.py,sha256=E7gYofbDzN7S5oCmO_dd5Z1bxxhoYMJSD6s-VaF388E,11398
+py2ls/bio.py,sha256=5q7T_LXmDg0MJoKXwO0kWnfbpshXNvUR5kCnYyLqm2w,10711
 py2ls/brain_atlas.py,sha256=w1o5EelRjq89zuFJUNSz4Da8HnTCwAwDAZ4NU4a-bAY,5486
 py2ls/chat.py,sha256=Yr22GoIvoWhpV3m4fdwV_I0Mn77La346_ymSinR-ORA,3793
 py2ls/correlators.py,sha256=RbOaJIPLCHJtUm5SFi_4dCJ7VFUPWR0PErfK3K26ad4,18243
@@ -203,23 +204,24 @@ py2ls/data/styles/style6.json,sha256=tu-MYOT9x5Rorc-2IK6sy-J-frmz0RNdm65XAsDQKX4
 py2ls/data/styles/style7.json,sha256=StdUFwIVrS7T_6CDrADHMorzc0WZFWBM7IyYdO1TPHg,4447
 py2ls/data/styles/style8.json,sha256=8XUgkZtew8ebvjbAHlDHCSWUqNra3ktDvMCO4vNh-CM,4456
 py2ls/data/styles/style9.json,sha256=PLxvntbH_kfzZlnCTtCEAUVBGi5m6Lngb9C01rArQog,4769
-py2ls/data/usages_pd.json,sha256=A76y7lr28BUBdggFN_50r-4My3Q51M_3y0ZcQ4LHSco,15077
+py2ls/data/usages_pd copy.json,sha256=cS2fYSKvSC274uAw1l6eMPGzLMvZt184dfbcuUiErmw,197313
+py2ls/data/usages_pd.json,sha256=4DgbPahF4G5Hd6G0TQurb6dBRVey67lpKdgK6A01Tww,266818
 py2ls/data/usages_sns.json,sha256=3OTu6T7n9HbQaFkz-UPMJ_9-Ug6Xjf7q5aDIvZ_6cHk,9246
 py2ls/db2ls.py,sha256=MMfFX47aIPIyu7fU9aPvX9lbPRPYOpJ_VXwlnWk-8qo,13615
 py2ls/doc.py,sha256=xN3g1OWfoaGUhikbJ0NqbN5eKy1VZVvWwRlhHMgyVEc,4243
 py2ls/export_requirements.py,sha256=x2WgUF0jYKz9GfA1MVKN-MdsM-oQ8yUeC6Ua8oCymio,2325
-py2ls/fetch_update.py,sha256=jh2MQHREpCqzYhDmEnMpuIvQVf4_wD9pDdIziXoFE3E,4055
+py2ls/fetch_update.py,sha256=9LXj661GpCEFII2wx_99aINYctDiHni6DOruDs_fdt8,4752
 py2ls/freqanalysis.py,sha256=F4218VSPbgL5tnngh6xNCYuNnfR-F_QjECUUxrPYZss,32594
 py2ls/ich2ls.py,sha256=3E9R8oVpyYZXH5PiIQgT3CN5NxLe4Dwtm2LwaeacE6I,21381
-py2ls/ips.py,sha256=92b5_p1EM0VRsEylXln7oaI7eLmtcC3GkBcEHFTUkIU,199481
+py2ls/ips.py,sha256=46nrt6RRl8Lc-tMh03dRqxF4nUlLfMElnETE1ipu-DM,210309
 py2ls/netfinder.py,sha256=LwBkGITB_4BTNtY6RlKdEZVFW6epzMWlnqy2g03KtyU,56117
 py2ls/ocr.py,sha256=5lhUbJufIKRSOL6wAWVLEo8TqMYSjoI_Q-IO-_4u3DE,31419
-py2ls/plot.py,sha256=dxZeD27TZMzccN8_kyqSJf72PdZJk45gLuTYAeDq81I,131906
+py2ls/plot.py,sha256=A4NiRDItVyrc80qPtLgT1mpzvebU_iMVVownjsu_YFc,135976
 py2ls/setuptools-70.1.0-py3-none-any.whl,sha256=2bi3cUVal8ip86s0SOvgspteEF8SKLukECi-EWmFomc,882588
 py2ls/sleep_events_detectors.py,sha256=bQA3HJqv5qnYKJJEIhCyhlDtkXQfIzqksnD0YRXso68,52145
 py2ls/stats.py,sha256=DMoJd8Z5YV9T1wB-4P52F5K5scfVK55DT8UP4Twcebo,38627
 py2ls/translator.py,sha256=zBeq4pYZeroqw3DT-5g7uHfVqKd-EQptT6LJ-Adi8JY,34244
 py2ls/wb_detector.py,sha256=7y6TmBUj9exCZeIgBAJ_9hwuhkDh1x_-yg4dvNY1_GQ,6284
-py2ls-0.2.4.dist-info/METADATA,sha256=-i9MH0eTedNkRUR6XQuj6rikJRNwp9U2eA1CskY6X1Y,20036
-py2ls-0.2.4.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-py2ls-0.2.4.dist-info/RECORD,,
+py2ls-0.2.4.2.dist-info/METADATA,sha256=_YQg86nAdjPWqkaIrH6p9nSPhjNHbY1AU0BGV6o3wU0,20038
+py2ls-0.2.4.2.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+py2ls-0.2.4.2.dist-info/RECORD,,