py2ls 0.2.4.5__py3-none-any.whl → 0.2.4.6__py3-none-any.whl

py2ls/plot.py

@@ -11,7 +11,7 @@ import logging
 import os
 import re
 from typing import Union
-from .ips import fsave, fload, mkdir, listdir, figsave, strcmp, unique, get_os, ssplit,plt_font,flatten
+from .ips import fsave, fload, mkdir, listdir, figsave, strcmp, unique, get_os, ssplit,flatten,plt_font
 from .stats import *
 from .netfinder import get_soup, fetch
 
@@ -1868,6 +1868,7 @@ def figsets(*args, **kwargs):
     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 = [
@@ -3498,37 +3499,106 @@ def sns_func_info(dir_save=None):
     )
 
 
-
-
-
-
+def get_color_overlap(*colors):
+    import matplotlib.colors as mcolors
+
+    """Blend multiple colors by averaging their RGB values."""
+    rgbs = [mcolors.to_rgb(color) for color in colors]
+    blended_rgb = [sum(channel) / len(channel) for channel in zip(*rgbs)]
+    return mcolors.to_hex(blended_rgb)
+
+
+def desaturate_color(color, saturation_factor=0.5):
+    """Reduce the saturation of a color by a given factor (between 0 and 1)."""
+    import matplotlib.colors as mcolors
+    import colorsys
+    # Convert the color to RGB
+    rgb = mcolors.to_rgb(color)
+    # Convert RGB to HLS (Hue, Lightness, Saturation)
+    h, l, s = colorsys.rgb_to_hls(*rgb)
+    # Reduce the saturation
+    s *= saturation_factor
+    # Convert back to RGB
+    return colorsys.hls_to_rgb(h, l, s)
+
+def textsets(text, fontname='Arial', fontsize=11, fontweight="normal", fontstyle="normal", 
+             fontcolor='k', backgroundcolor=None, shadow=False, ha="center", va="center"):
+    if text:  # Ensure text exists
+        if fontname:
+            text.set_fontname(plt_font(fontname))
+        if fontsize:
+            text.set_fontsize(fontsize)
+        if fontweight:
+            text.set_fontweight(fontweight)
+        if fontstyle:
+            text.set_fontstyle(fontstyle)
+        if fontcolor:
+            text.set_color(fontcolor)
+        if backgroundcolor:
+            text.set_backgroundcolor(backgroundcolor) 
+        text.set_horizontalalignment(ha)
+        text.set_verticalalignment(va) 
+        if shadow:
+            text.set_path_effects([
+                matplotlib.patheffects.withStroke(linewidth=3, foreground="gray")
+            ])
 def venn(
     lists:list,
-    labels:list,
+    labels:list=None,
     ax=None,
     colors=None,
-    edgecolor="0.25",
-    alpha=0.75,
-    linewidth=.75,
+    edgecolor=None,
+    alpha=0.5,
+    saturation=.75,
+    linewidth=0, # default no edge
     linestyle="-",
     fontname='Arial',
-    fontsize=11,
+    fontsize=10,
+    fontcolor='k',
     fontweight="normal",
     fontstyle="normal",
-    label_align="center",
-    label_baseline="center",
-    subset_fontsize=9,
+    ha="center",
+    va="center",
+    shadow=False,
+    subset_fontsize=10,
     subset_fontweight="normal",
     subset_fontstyle="normal",
-    subset_label_format="{:d}",
-    shadow=False,
+    subset_fontcolor='k',
+    backgroundcolor=None,
     custom_texts=None,
-    hatches=None,
-    per_circle_styles=None,
+    show_percentages=True,   # display percentage
+    fmt="{:.1%}",
+    ellipse_shape=False,  # 椭圆形
+    ellipse_scale=[1.5, 1],  #not perfect, 椭圆形的形状
     **kwargs
 ):
     """
     Advanced Venn diagram plotting function with extensive customization options.
+    Usage: 
+        # Define the two sets
+        set1 = [1, 2, 3, 4, 5]
+        set2 = [4, 5, 6, 7, 8]
+        set3 = [1, 2, 4, 7, 9, 10, 11, 6, 103]
+        _, axs = plt.subplots(1, 2)
+        venn(
+            [set1, set2],
+            ["Set A", "Set B"],
+            colors=["r", "b"],
+            edgecolor="r",
+            linewidth=0,
+            ax=axs[0],
+        )
+        venn(
+            [set1, set2, set3],
+            ["Set A", "Set B", "Set 3"],
+            colors=["r", "g", "b"],
+            saturation=0.8,
+            linewidth=[3, 5, 7],
+            linestyle=[":", "-", "--"],
+            # edgecolor="r",
+            # alpha=1,
+            ax=axs[1],
+        )
 
     Parameters:
         lists: list of sets, 2 or 3 sets
@@ -3551,126 +3621,218 @@ def venn(
         subset_label_format: string, format for subset labels (e.g., "{:.2f}" for floats)
         shadow: bool, add shadow effect to the patches
         custom_texts: list of custom texts to replace the subset labels
-        hatches: list of hatch patterns for the patches
-        per_circle_styles: dict, custom styles for each circle (e.g., {'circle_1': {'color': 'red'}})
         **kwargs: additional keyword arguments passed to venn2 or venn3
     """
     if ax is None:
         ax = plt.gca()
     lists=[set(flatten(i, verbose=False)) for i in lists]
     # Function to apply text styles to labels
-    def apply_text_style(text, fontname, fontsize, fontweight, fontstyle):
-        if text:  # Ensure text exists
-            if fontname:
-                text.set_fontname(fontname)
-            if fontsize:
-                text.set_fontsize(fontsize)
-            if fontweight:
-                text.set_fontweight(fontweight)
-            if fontstyle:
-                text.set_fontstyle(fontstyle)
-            # Alignment customization
-            text.set_horizontalalignment(label_align)
-            text.set_verticalalignment(label_baseline)
-
+    if colors is None:
+        colors=["r","b"] if len(lists)==2 else ["r","g","b"]
+    if labels is None:
+        labels=["set1","set2"] if len(lists)==2 else ["set1","set2","set3"]
+    if edgecolor is None:
+        edgecolor=colors
+    colors = [desaturate_color(color, saturation) for color in colors]
+    # Check colors and auto-calculate overlaps
     if len(lists) == 2:
+        def get_count_and_percentage(set_count, subset_count):
+            percent = subset_count / set_count if set_count > 0 else 0
+            return f"{subset_count}\n({fmt.format(percent)})" if show_percentages else f"{subset_count}"
+
         from matplotlib_venn import venn2, venn2_circles
+        # Auto-calculate overlap color for 2-set Venn diagram
+        overlap_color = get_color_overlap(colors[0], colors[1]) if colors else None
+        
+        # Draw the venn diagram
         v = venn2(subsets=lists, set_labels=labels, ax=ax, **kwargs)
-        venn_circles = venn2_circles(subsets=lists, ax=ax,color=edgecolor)
+        venn_circles = venn2_circles(subsets=lists, ax=ax)
+        set1,set2=lists[0],lists[1]
+        v.get_patch_by_id('10').set_color(colors[0])
+        v.get_patch_by_id('01').set_color(colors[1])
+        v.get_patch_by_id('11').set_color(get_color_overlap(colors[0], colors[1]) if colors else None)
+        # v.get_label_by_id('10').set_text(len(set1 - set2))
+        # v.get_label_by_id('01').set_text(len(set2 - set1))
+        # v.get_label_by_id('11').set_text(len(set1 & set2))
+        v.get_label_by_id('10').set_text(get_count_and_percentage(len(set1), len(set1 - set2)))
+        v.get_label_by_id('01').set_text(get_count_and_percentage(len(set2), len(set2 - set1)))
+        v.get_label_by_id('11').set_text(get_count_and_percentage(len(set1 | set2), len(set1 & set2)))
+
+
         if not isinstance(linewidth,list):
             linewidth=[linewidth]
         if isinstance(linestyle,str):
             linestyle=[linestyle]
+        if not isinstance(edgecolor, list):
+            edgecolor=[edgecolor]
         linewidth=linewidth*2 if len(linewidth)==1 else linewidth
         linestyle=linestyle*2 if len(linestyle)==1 else linestyle
+        edgecolor=edgecolor*2 if len(edgecolor)==1 else edgecolor 
         for i in range(2):
             venn_circles[i].set_lw(linewidth[i])
             venn_circles[i].set_ls(linestyle[i])
+            venn_circles[i].set_edgecolor(edgecolor[i])
+        # 椭圆
+        if ellipse_shape:
+            import matplotlib.patches as patches 
+            for patch in v.patches:
+                patch.set_visible(False)  # Hide original patches if using ellipses
+            center1 = v.get_circle_center(0)
+            center2 = v.get_circle_center(1)
+            ellipse1 = patches.Ellipse(
+                (center1.x, center1.y),
+                width=ellipse_scale[0],
+                height=ellipse_scale[1],
+                edgecolor=edgecolor[0] if edgecolor else colors[0],
+                facecolor=colors[0],
+                lw=linewidth if isinstance(linewidth, (int, float)) else 1.0,  # Ensure lw is a number
+                ls=linestyle[0],
+                alpha=alpha if isinstance(alpha, (int, float)) else 0.5  # Ensure alpha is a number
+            )
+            ellipse2 = patches.Ellipse(
+                (center2.x, center2.y),
+                width=ellipse_scale[0],
+                height=ellipse_scale[1],
+                edgecolor=edgecolor[1] if edgecolor else colors[1],
+                facecolor=colors[1],
+                lw=linewidth if isinstance(linewidth, (int, float)) else 1.0,  # Ensure lw is a number
+                ls=linestyle[0],
+                alpha=alpha if isinstance(alpha, (int, float)) else 0.5  # Ensure alpha is a number
+            )
+            ax.add_patch(ellipse1)
+            ax.add_patch(ellipse2)
         # Apply styles to set labels
         for i, text in enumerate(v.set_labels):
-            apply_text_style(text, fontname, fontsize, fontweight, fontstyle)
+            textsets(text, fontname=fontname, fontsize=fontsize, fontweight=fontweight, fontstyle=fontstyle,
+                     fontcolor=fontcolor,ha=ha,va=va,shadow=shadow)
 
         # Apply styles to subset labels
         for i, text in enumerate(v.subset_labels):
             if text:  # Ensure text exists
                 if custom_texts:  # Custom text handling
-                    text.set_text(custom_texts[i])
-                else:  # Default subset label formatting
-                    subset_size = (
-                        len(lists[i % 2])
-                        if i in [0, 1]
-                        else len(lists[0].intersection(lists[1]))
-                    )
-                    text.set_text(subset_label_format.format(subset_size))
-                apply_text_style(
-                    text, None, subset_fontsize, subset_fontweight, subset_fontstyle
-                )
+                    text.set_text(custom_texts[i]) 
+                textsets(text, fontname=fontname, fontsize=subset_fontsize, fontweight=subset_fontweight, fontstyle=subset_fontstyle,
+                     fontcolor=subset_fontcolor,ha=ha,va=va,shadow=shadow)
+
     elif len(lists) == 3:
+        def get_label(set_count, subset_count):
+            percent = subset_count / set_count if set_count > 0 else 0
+            return f"{subset_count}\n({fmt.format(percent)})" if show_percentages else f"{subset_count}"
+        
         from matplotlib_venn import venn3, venn3_circles
-        v = venn3(
-            subsets=lists, set_labels=labels, set_colors=colors, ax=ax, **kwargs
-        )
-        venn_circles = venn3_circles(
-            subsets=lists, ax=ax,color=edgecolor
-        )
-        if not isinstance(linewidth,list):
-            linewidth=[linewidth]
-        if isinstance(linestyle,str):
-            linestyle=[linestyle]
-        linewidth=linewidth*3 if len(linewidth)==1 else linewidth
-        linestyle=linestyle*3 if len(linestyle)==1 else linestyle
-        for i in range(3):
-            venn_circles[i].set_lw(linewidth[i])
-            venn_circles[i].set_ls(linestyle[i])
+        # Auto-calculate overlap colors for 3-set Venn diagram
+        colorAB = get_color_overlap(colors[0], colors[1]) if colors else None
+        colorAC = get_color_overlap(colors[0], colors[2]) if colors else None
+        colorBC = get_color_overlap(colors[1], colors[2]) if colors else None
+        colorABC = get_color_overlap(colors[0], colors[1], colors[2]) if colors else None
+        set1,set2,set3=lists[0],lists[1],lists[2]
+
+        # Draw the venn diagram
+        v = venn3(subsets=lists, set_labels=labels, ax=ax,**kwargs) 
+        v.get_patch_by_id('100').set_color(colors[0])
+        v.get_patch_by_id('010').set_color(colors[1])
+        v.get_patch_by_id('001').set_color(colors[2]) 
+        v.get_patch_by_id('110').set_color(colorAB)
+        v.get_patch_by_id('101').set_color(colorAC)
+        v.get_patch_by_id('011').set_color(colorBC)
+        v.get_patch_by_id('111').set_color(colorABC)
+        
+        # Correctly labeling subset sizes
+        # v.get_label_by_id('100').set_text(len(set1 - set2 - set3))
+        # v.get_label_by_id('010').set_text(len(set2 - set1 - set3))
+        # v.get_label_by_id('001').set_text(len(set3 - set1 - set2))
+        # v.get_label_by_id('110').set_text(len(set1 & set2 - set3))
+        # v.get_label_by_id('101').set_text(len(set1 & set3 - set2))
+        # v.get_label_by_id('011').set_text(len(set2 & set3 - set1))
+        # v.get_label_by_id('111').set_text(len(set1 & set2 & set3))
+        v.get_label_by_id('100').set_text(get_label(len(set1), len(set1 - set2 - set3)))
+        v.get_label_by_id('010').set_text(get_label(len(set2), len(set2 - set1 - set3)))
+        v.get_label_by_id('001').set_text(get_label(len(set3), len(set3 - set1 - set2)))
+        v.get_label_by_id('110').set_text(get_label(len(set1 | set2), len(set1 & set2 - set3)))
+        v.get_label_by_id('101').set_text(get_label(len(set1 | set3), len(set1 & set3 - set2)))
+        v.get_label_by_id('011').set_text(get_label(len(set2 | set3), len(set2 & set3 - set1)))
+        v.get_label_by_id('111').set_text(get_label(len(set1 | set2 | set3), len(set1 & set2 & set3)))
+
 
         # Apply styles to set labels
         for i, text in enumerate(v.set_labels):
-            apply_text_style(text, fontname, fontsize, fontweight, fontstyle)
+            textsets(text, fontname=fontname, fontsize=fontsize, fontweight=fontweight, fontstyle=fontstyle,
+                     fontcolor=fontcolor,ha=ha,va=va,shadow=shadow)
 
         # Apply styles to subset labels
         for i, text in enumerate(v.subset_labels):
             if text:  # Ensure text exists
                 if custom_texts:  # Custom text handling
                     text.set_text(custom_texts[i])
-                else:  # Default subset label formatting
-                    subset_size = (
-                        len(lists[i])
-                        if i < 3
-                        else len(lists[0].intersection(lists[1], lists[2]))
-                    )
-                    text.set_text(subset_label_format.format(subset_size))
-                apply_text_style(
-                    text, None, subset_fontsize, subset_fontweight, subset_fontstyle
-                )
+                textsets(text, fontname=fontname, fontsize=subset_fontsize, fontweight=subset_fontweight, fontstyle=subset_fontstyle,
+                     fontcolor=subset_fontcolor,ha=ha,va=va,shadow=shadow)
+
+        venn_circles = venn3_circles(subsets=lists, ax=ax)
+        if not isinstance(linewidth,list):
+            linewidth=[linewidth]
+        if isinstance(linestyle,str):
+            linestyle=[linestyle]
+        if not isinstance(edgecolor, list):
+            edgecolor=[edgecolor]
+        linewidth=linewidth*3 if len(linewidth)==1 else linewidth
+        linestyle=linestyle*3 if len(linestyle)==1 else linestyle
+        edgecolor=edgecolor*3 if len(edgecolor)==1 else edgecolor
+
+        # edgecolor=[to_rgba(i) for i in edgecolor]
+
+        for i in range(3): 
+            venn_circles[i].set_lw(linewidth[i])
+            venn_circles[i].set_ls(linestyle[i]) 
+            venn_circles[i].set_edgecolor(edgecolor[i]) 
+
+        #椭圆形
+        if ellipse_shape:
+            import matplotlib.patches as patches 
+            for patch in v.patches:
+                patch.set_visible(False)  # Hide original patches if using ellipses
+            center1 = v.get_circle_center(0)
+            center2 = v.get_circle_center(1)
+            center3 = v.get_circle_center(2) 
+            ellipse1 = patches.Ellipse(
+                (center1.x, center1.y),
+                width=ellipse_scale[0],
+                height=ellipse_scale[1],
+                edgecolor=edgecolor[0] if edgecolor else colors[0],
+                facecolor=colors[0],
+                lw=linewidth if isinstance(linewidth, (int, float)) else 1.0,  # Ensure lw is a number
+                ls=linestyle[0],
+                alpha=alpha if isinstance(alpha, (int, float)) else 0.5  # Ensure alpha is a number
+            )
+            ellipse2 = patches.Ellipse(
+                (center2.x, center2.y),
+                width=ellipse_scale[0],
+                height=ellipse_scale[1],
+                edgecolor=edgecolor[1] if edgecolor else colors[1],
+                facecolor=colors[1],
+                lw=linewidth if isinstance(linewidth, (int, float)) else 1.0,  # Ensure lw is a number
+                ls=linestyle[0],
+                alpha=alpha if isinstance(alpha, (int, float)) else 0.5  # Ensure alpha is a number
+            )
+            ellipse3 = patches.Ellipse(
+                (center3.x, center3.y),
+                width=ellipse_scale[0],
+                height=ellipse_scale[1],
+                edgecolor=edgecolor[1] if edgecolor else colors[1],
+                facecolor=colors[1],
+                lw=linewidth if isinstance(linewidth, (int, float)) else 1.0,  # Ensure lw is a number
+                ls=linestyle[0],
+                alpha=alpha if isinstance(alpha, (int, float)) else 0.5  # Ensure alpha is a number
+            )
+            ax.add_patch(ellipse1)
+            ax.add_patch(ellipse2)
+            ax.add_patch(ellipse3)
     else:
         raise ValueError("只支持2或者3个list")
-    # Set circle and patch customizations (edge color, transparency, hatches)
-    for i, patch in enumerate(v.patches):
+
+    # Set transparency level
+    for patch in v.patches:
         if patch:
-            if colors:
-                patch.set_facecolor(colors[i % len(colors)])
-            patch.set_edgecolor("none")
             patch.set_alpha(alpha)
-            if hatches:
-                patch.set_hatch(hatches[i % len(hatches)])
-            if shadow:
-                from matplotlib.patches import Shadow
-                shadow_patch = Shadow(patch, -0.02, -0.02, alpha=0.2)
-                ax.add_patch(shadow_patch)
-#  # usage:
-#  venn(
-#     [rf_features, svm_features, lasso_features],
-#     ["Random Forest", "SVM-RFE", "a"],
-#     ax=axs[0],  # Specify the axes
-#     colors=["#BDC8E0", "#E5C0C1", "#D0E9CB"],
-#     edgecolor="r", 
-#     alpha=1,
-#     linewidth=[1, 2, 18],# 分别设置字体大小
-#     linestyle=["-", "--", ":"], 
-#     fontsize=20,
-#     label_baseline="top",
-#     subset_label_format="{:.2f}%",
-#     subset_fontsize=18,
-#     shadow=False,
-#     # custom_texts=["a", "b", "c"],
-# )
+            if 'none' in edgecolor or 0 in linewidth:
+                patch.set_edgecolor("none")
+    return ax

{py2ls-0.2.4.5.dist-info → py2ls-0.2.4.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: py2ls
-Version: 0.2.4.5
+Version: 0.2.4.6
 Summary: py(thon)2(too)ls
 Author: Jianfeng
 Author-email: Jianfeng.Liu0413@gmail.com

{py2ls-0.2.4.5.dist-info → py2ls-0.2.4.6.dist-info}/RECORD

@@ -17,7 +17,7 @@ py2ls/.git/hooks/pre-receive.sample,sha256=pMPSuce7P9jRRBwxvU7nGlldZrRPz0ndsxAlI
 py2ls/.git/hooks/prepare-commit-msg.sample,sha256=6d3KpBif3dJe2X_Ix4nsp7bKFjkLI5KuMnbwyOGqRhk,1492
 py2ls/.git/hooks/push-to-checkout.sample,sha256=pT0HQXmLKHxt16-mSu5HPzBeZdP0lGO7nXQI7DsSv18,2783
 py2ls/.git/hooks/update.sample,sha256=jV8vqD4QPPCLV-qmdSHfkZT0XL28s32lKtWGCXoU0QY,3650
-py2ls/.git/index,sha256=O4t8fvweL1JsEypzrWigO2hAxCpfQwC4VOW3q8panRk,4232
+py2ls/.git/index,sha256=sPKeqbWaVtDr3kILep6S-tkzgNPfGUog5UQ5meN6K-8,4232
 py2ls/.git/info/exclude,sha256=ZnH-g7egfIky7okWTR8nk7IxgFjri5jcXAbuClo7DsE,240
 py2ls/.git/logs/HEAD,sha256=8ID7WuAe_TlO9g-ARxhIJYdgdL3u3m7-1qrOanaIUlA,3535
 py2ls/.git/logs/refs/heads/main,sha256=8ID7WuAe_TlO9g-ARxhIJYdgdL3u3m7-1qrOanaIUlA,3535
@@ -173,7 +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=7q-zIxGU76g9AABUcrCLW2GrowTw-ljN_8zKbjdi7p0,67677
+py2ls/bio.py,sha256=LN7OdnRziBwLLQ_p90Ytp7X3gf2941au-rGVbaI73Tw,86920
 py2ls/brain_atlas.py,sha256=w1o5EelRjq89zuFJUNSz4Da8HnTCwAwDAZ4NU4a-bAY,5486
 py2ls/chat.py,sha256=Yr22GoIvoWhpV3m4fdwV_I0Mn77La346_ymSinR-ORA,3793
 py2ls/correlators.py,sha256=RbOaJIPLCHJtUm5SFi_4dCJ7VFUPWR0PErfK3K26ad4,18243
@@ -214,16 +214,17 @@ py2ls/export_requirements.py,sha256=x2WgUF0jYKz9GfA1MVKN-MdsM-oQ8yUeC6Ua8oCymio,
 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=4CmSK5Ye4eHPSkTbrbS9KZ20mz-GA7xw2vEa1o1fI4k,227789
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