py2ls 0.2.4.3__py3-none-any.whl → 0.2.4.4__py3-none-any.whl

py2ls/netfinder.py

@@ -742,7 +742,18 @@ def downloader(
                 counter_ = str(counter)
             new_filename = f"{base}_{counter_}{ext}"
             counter += 1
-        return new_filename
+        return new_filename 
+    
+    if url.startswith("ftp"):
+        import urllib.request
+
+        if dir_save is None:
+            dir_save = "./" 
+        dir_save+= os.path.basename(url)
+        print(dir_save)
+        urllib.request.urlretrieve(url, dir_save)
+        print(f"Downloaded file to: {dir_save}")
+        return None
 
     fpath_tmp, corrected_fname = None, None
     if not isinstance(kind, list):

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
+from .ips import fsave, fload, mkdir, listdir, figsave, strcmp, unique, get_os, ssplit,plt_font,flatten
 from .stats import *
 from .netfinder import get_soup, fetch
 
@@ -1897,6 +1897,16 @@ def figsets(*args, **kwargs):
         if ("fo" in key) and (("size" in key) or ("sz" in key)):
             fontsize = value
             plt.rcParams.update({"font.size": fontsize})
+            # Customize tick labels
+            ax.tick_params(axis='both', which='major', labelsize=fontsize)
+            for label in ax.get_xticklabels() + ax.get_yticklabels():
+                label.set_fontname(fontname)
+
+            # Optionally adjust legend font properties if a legend is included
+            if ax.get_legend():
+                for text in ax.get_legend().get_texts():
+                    text.set_fontsize(fontsize)
+                    text.set_fontname(fontname)
         # style
         if "st" in key.lower() or "th" in key.lower():
             if isinstance(value, str):
@@ -3145,15 +3155,20 @@ def plotxy(
             return g, ax
     return ax
 
+def norm_cmap(data, cmap="coolwarm", min_max=[0, 1]):
+    norm_ = plt.Normalize(min_max[0], min_max[1])
+    colormap = plt.get_cmap(cmap)
+    return colormap(norm_(data))
 
 def volcano(
     data:pd.DataFrame,
     x:str,
     y:str,
-    gene_col=None,
+    gene_col:str=None,
     top_genes=[5, 5], # [down-regulated, up-regulated]
-    thr_x=np.log2(1.5),
+    thr_x=np.log2(1.5), # default: 0.585
     thr_y=-np.log10(0.05),
+    sort_xy="x", #'y'
     colors=("#00BFFF", "#9d9a9a", "#FF3030"),
     s=20,
     fill=True,  # plot filled scatter
@@ -3169,7 +3184,7 @@ def volcano(
                   alpha=0.5, 
                   edgecolor='black',
                   boxstyle='round,pad=0.3'),# '{}' to hide
-    kws_arrow={},
+    kws_arrow=dict(color="k", lw=0.5),# '{}' to hide
     **kwargs,
 ):
     """
@@ -3239,29 +3254,39 @@ def volcano(
             kws_figsets = v_arg
             kwargs.pop(k_arg, None)
             break
-    # Color-coding based on thresholds using np.where
-    data["color"] = np.where(
+    
+    data=data.copy()
+    # filter nan
+    data = data.dropna(subset=[x, y])  # Drop rows with NaN in x or y
+    data.loc[:,"color"] = np.where(
         (data[x] > thr_x) & (data[y] > thr_y),
         colors[2],
-        np.where((data[x] < -thr_x) & (data[y] > thr_y), colors[0], colors[1]),
+        np.where((data[x] < -thr_x) & (data[y] > thr_y), 
+                 colors[0], 
+                 colors[1]),
     )
     top_genes=[top_genes, top_genes] if isinstance(top_genes,int) else top_genes
+    
+    # could custom how to select the top genes, x: x has priority
+    sort_by_x_y=[x,y] if sort_xy=="x" else [y,x]
+    ascending_up=[True, True] if sort_xy=="x" else [False, True]
+    ascending_down=[False, True] if sort_xy=="x" else [False, False]
 
     down_reg_genes = data[
         (data["color"] == colors[0]) & 
         (data[x].abs() > thr_x) & 
         (data[y] > thr_y)
-    ].sort_values(by=[y, x], ascending=[False, True]).head(top_genes[0])
-
-    # Selecting top upregulated genes based on both p-value and fold change
+    ].sort_values(by=sort_by_x_y, ascending=ascending_up).head(top_genes[0])
     up_reg_genes = data[
         (data["color"] == colors[2]) & 
         (data[x].abs() > thr_x) & 
         (data[y] > thr_y)
-    ].sort_values(by=[y, x], ascending=[False, False]).head(top_genes[1])
+    ].sort_values(by=sort_by_x_y, ascending=ascending_down).head(top_genes[1])
     sele_gene = pd.concat([down_reg_genes, up_reg_genes])
-
-    palette = {colors[0]: colors[0], colors[1]: colors[1], colors[2]: colors[2]}
+    
+    palette = {colors[0]: colors[0], 
+               colors[1]: colors[1], 
+               colors[2]: colors[2]}
     # Plot setup
     if ax is None:
         ax = plt.gca()
@@ -3279,7 +3304,7 @@ def volcano(
         data=data,
         x=x,
         y=y,
-        # hue="color",
+        hue="color",
         palette=palette,
         s=s,
         linewidths=edgelinewidth,
@@ -3298,65 +3323,57 @@ def volcano(
     # Add gene labels for selected significant points
     if gene_col:
         texts = []
-        if kws_text:
-            fontname = kws_text.pop("fontname", "Arial")
-            textcolor = kws_text.pop("color", "k")
-            fontsize = kws_text.pop("fontsize", 10)
-            arrowstyles = [
-                "->","<-","<->","<|-","-|>","<|-|>",
-                "-","-[","-[",
-                "fancy","simple","wedge",
-            ]
-            arrowstyle = kws_arrow.pop("style", "<|-")
-            arrowstyle = strcmp(arrowstyle, arrowstyles,scorer='strict')[0]
-            expand=kws_arrow.pop("expand",(1.05,1.1))
-            arrowcolor = kws_arrow.pop("color", "0.4")
-            arrowlinewidth = kws_arrow.pop("lw", 0.75)
-            shrinkA = kws_arrow.pop("shrinkA", 0)
-            shrinkB = kws_arrow.pop("shrinkB", 0)
-            mutation_scale = kws_arrow.pop("head", 10)
-            arrow_fill=kws_arrow.pop("fill", False)
-            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(
-                    ax.text(
-                        x=sele_gene[x].iloc[i],
-                        y=sele_gene[y].iloc[i],
-                        s=sele_gene[gene_col].iloc[i],
-                        bbox=kws_bbox if kws_bbox else None,
-                        fontdict={
-                            "fontsize": fontsize,
-                            "color": textcolor,
-                            "fontname": fontname,
-                        },
-                    )
-                )
-            print(arrowstyle)
-            adjust_text(
-                texts,
-                expand=expand,
-                min_arrow_len=5,
-                # force_explode=(0.1, 0.5), 
-                # force_text=(0.1, 0.5), 
-                # force_points=(0.1, 0.5),
-                # explode_radius=10,
-                # expand_text=(1, 1), 
-                # expand_points=(1, 1),
-                # ha='center', 
-                # va='top',
-                ax=ax,
-                arrowprops=dict(
-                    arrowstyle=arrowstyle,
-                    fill=arrow_fill,
-                    color=arrowcolor,
-                    lw=arrowlinewidth,
-                    shrinkA=shrinkA,
-                    shrinkB=shrinkB,
-                    mutation_scale=mutation_scale,
-                    **kws_arrow,
+        # if kws_text:
+        fontname = kws_text.pop("fontname", "Arial")
+        textcolor = kws_text.pop("color", "k")
+        fontsize = kws_text.pop("fontsize", 10)
+        arrowstyles = [
+            "->","<-","<->","<|-","-|>","<|-|>",
+            "-","-[","-[",
+            "fancy","simple","wedge",
+        ]
+        arrowstyle = kws_arrow.pop("style", "<|-")
+        arrowstyle = strcmp(arrowstyle, arrowstyles,scorer='strict')[0]
+        expand=kws_arrow.pop("expand",(1.05,1.1))
+        arrowcolor = kws_arrow.pop("color", "0.4")
+        arrowlinewidth = kws_arrow.pop("lw", 0.75)
+        shrinkA = kws_arrow.pop("shrinkA", 0)
+        shrinkB = kws_arrow.pop("shrinkB", 0)
+        mutation_scale = kws_arrow.pop("head", 10)
+        arrow_fill=kws_arrow.pop("fill", False)
+        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(
+                ax.text(
+                    x=sele_gene[x].iloc[i],
+                    y=sele_gene[y].iloc[i],
+                    s=sele_gene[gene_col].iloc[i],
+                    bbox=kws_bbox if kws_bbox else None,
+                    fontdict={
+                        "fontsize": fontsize,
+                        "color": textcolor,
+                        "fontname": fontname,
+                    },
                 )
             )
+        print(arrowstyle)
+        adjust_text(
+            texts,
+            expand=expand,
+            min_arrow_len=5, 
+            ax=ax,
+            arrowprops=dict(
+                arrowstyle=arrowstyle,
+                fill=arrow_fill,
+                color=arrowcolor,
+                lw=arrowlinewidth,
+                shrinkA=shrinkA,
+                shrinkB=shrinkB,
+                mutation_scale=mutation_scale,
+                **kws_arrow,
+            )
+        )
 
     figsets(**kws_figsets)
 
@@ -3446,3 +3463,181 @@ def sns_func_info(dir_save=None):
         dir_save + "sns_info.json",
         sns_info,
     )
+
+
+
+
+
+
+def venn(
+    lists:list,
+    labels:list,
+    ax=None,
+    colors=None,
+    edgecolor="0.25",
+    alpha=0.75,
+    linewidth=.75,
+    linestyle="-",
+    fontname='Arial',
+    fontsize=11,
+    fontweight="normal",
+    fontstyle="normal",
+    label_align="center",
+    label_baseline="center",
+    subset_fontsize=9,
+    subset_fontweight="normal",
+    subset_fontstyle="normal",
+    subset_label_format="{:d}",
+    shadow=False,
+    custom_texts=None,
+    hatches=None,
+    per_circle_styles=None,
+    **kwargs
+):
+    """
+    Advanced Venn diagram plotting function with extensive customization options.
+
+    Parameters:
+        lists: list of sets, 2 or 3 sets
+        labels: list of strings, labels for the sets
+        ax: matplotlib axis, optional
+        colors: list of colors, colors for the Venn diagram patches
+        edgecolor: string, color of the circle edges
+        alpha: float, transparency level for the patches
+        linewidth: float, width of the circle edges
+        linestyle: string, line style for the circles
+        fontname: string, font for set labels
+        fontsize: int, font size for set labels
+        fontweight: string, weight of the set label font (e.g., 'bold', 'light')
+        fontstyle: string, style of the set label font (e.g., 'italic')
+        label_align: string, horizontal alignment of set labels ('left', 'center', 'right')
+        label_baseline: string, vertical alignment of set labels ('top', 'center', 'bottom')
+        subset_fontsize: int, font size for subset labels (the numbers)
+        subset_fontweight: string, weight of subset label font
+        subset_fontstyle: string, style of subset label font
+        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 len(lists) == 2:
+        from matplotlib_venn import venn2, venn2_circles
+        v = venn2(subsets=lists, set_labels=labels, ax=ax, **kwargs)
+        venn_circles = venn2_circles(subsets=lists, ax=ax,color=edgecolor)
+        if not isinstance(linewidth,list):
+            linewidth=[linewidth]
+        if isinstance(linestyle,str):
+            linestyle=[linestyle]
+        linewidth=linewidth*2 if len(linewidth)==1 else linewidth
+        linestyle=linestyle*2 if len(linestyle)==1 else linestyle
+        for i in range(2):
+            venn_circles[i].set_lw(linewidth[i])
+            venn_circles[i].set_ls(linestyle[i])
+        # Apply styles to set labels
+        for i, text in enumerate(v.set_labels):
+            apply_text_style(text, fontname, fontsize, fontweight, fontstyle)
+
+        # 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
+                )
+    elif len(lists) == 3:
+        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])
+
+        # Apply styles to set labels
+        for i, text in enumerate(v.set_labels):
+            apply_text_style(text, fontname, fontsize, fontweight, fontstyle)
+
+        # 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
+                )
+    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):
+        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"],
+# )

{py2ls-0.2.4.3.dist-info → py2ls-0.2.4.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: py2ls
-Version: 0.2.4.3
+Version: 0.2.4.4
 Summary: py(thon)2(too)ls
 Author: Jianfeng
 Author-email: Jianfeng.Liu0413@gmail.com

{py2ls-0.2.4.3.dist-info → py2ls-0.2.4.4.dist-info}/RECORD

@@ -1,4 +1,4 @@
-py2ls/.DS_Store,sha256=9qxq9N5T7k6muGHxG5s6yEdEEYqEh8eDGT3w7LokxsU,6148
+py2ls/.DS_Store,sha256=JdpMN4cmDCbGxELP0b4LUPASIOzoxopMYybGVl8zlZ0,6148
 py2ls/.git/COMMIT_EDITMSG,sha256=AdtqRHle5Ej2EBNPJY79v-SB454v5UK4wuPCPFELiFQ,11
 py2ls/.git/FETCH_HEAD,sha256=VM-2Jiw6iPaGu0ftg9xwq76OyNPWV0iT1nL0VWiL1zI,100
 py2ls/.git/HEAD,sha256=KNJb-Cr0wOK3L1CVmyvrhZ4-YLljCl6MYD2tTdsrboA,21
@@ -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=YCofugnXLz17aY5kqXGtUpV8FzXPdgQdEwcjQ8bHDfg,4232
+py2ls/.git/index,sha256=O4t8fvweL1JsEypzrWigO2hAxCpfQwC4VOW3q8panRk,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=FnEf4RV4LBUQfLefWIpIFszVRYeXjnRlc5261DINIdg,18835
+py2ls/bio.py,sha256=J-zGAgHiSQwDyUvjMKDOsJZoeTkqGaXcHDYHtMd84SQ,53879
 py2ls/brain_atlas.py,sha256=w1o5EelRjq89zuFJUNSz4Da8HnTCwAwDAZ4NU4a-bAY,5486
 py2ls/chat.py,sha256=Yr22GoIvoWhpV3m4fdwV_I0Mn77La346_ymSinR-ORA,3793
 py2ls/correlators.py,sha256=RbOaJIPLCHJtUm5SFi_4dCJ7VFUPWR0PErfK3K26ad4,18243
@@ -182,6 +182,7 @@ py2ls/data/db2ls_sql_chtsht.json,sha256=ls9d7Sm8TLeujanWHfHlWhU85Qz1KnAizO_9X3wU
 py2ls/data/docs_links.json,sha256=kXgbbWo0b8bfV4n6iuuUNLnZipIyLzokUO6Lzmf7nO4,101829
 py2ls/data/email/email_html_template.html,sha256=UIg3aixWfdNsvVx-j2dX1M5N3G-6DgrnV1Ya1cLjiUQ,2809
 py2ls/data/lang_code_iso639.json,sha256=qZiU7H2RLJjDMXK22C-jhwzLJCI5vKmampjB1ys4ek4,2157
+py2ls/data/mygenes_fields_241022.txt,sha256=-7htEdtmqbSRTUKHHVmjUFLBwZZg9u3LFpn9OZMb1qg,11348
 py2ls/data/sns_info.json,sha256=pEzdg2bhMkwQHZpXx02_7zAP7NvRoCc0Le8PN6Uv0Vk,4074
 py2ls/data/styles/example/style1.pdf,sha256=Pt_qQJ5kiCSIPiz3TWSwEffHUdj75kKXnZ4MPqpEx4I,29873
 py2ls/data/styles/example/style2.pdf,sha256=0xduPLPulET38LEP2V2H_q70wqlrrBEo8ttqO-FMrfQ,25449
@@ -213,15 +214,16 @@ 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=yYSpbHIGDfLK2SXtTX4f--H5oa885pggXePEbhiNRsw,220887
-py2ls/netfinder.py,sha256=LwBkGITB_4BTNtY6RlKdEZVFW6epzMWlnqy2g03KtyU,56117
+py2ls/ips.py,sha256=USmQKEZuqnjJyP5dhXzFG8yMrhrH6L8yt9jFtttuqLI,227772
+py2ls/ml2ls.py,sha256=XSe2-sLNzUVSvVRkeRGfhrB_q8C49SDK1sekYC1Bats,50277
+py2ls/netfinder.py,sha256=RJFr80tGEJiuwEx99IBOhI5-ZuXnPdWnGUYpF7XCEwI,56426
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