py2ls 0.2.4.1__py3-none-any.whl → 0.2.4.3__py3-none-any.whl

py2ls/plot.py

@@ -10,13 +10,15 @@ from cycler import cycler
 import logging
 import os
 import re
-from typing import List, Optional, Union
-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
 
 # Suppress INFO messages from fontTools
-logging.getLogger("fontTools").setLevel(logging.WARNING)
+logging.getLogger("fontTools").setLevel(logging.ERROR)
+logging.getLogger('matplotlib').setLevel(logging.ERROR)
+
 
 
 def add_text(ax=None, height_offset=0.5, fmt=".1f", **kwargs):
@@ -1862,8 +1864,10 @@ 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 = [
@@ -1889,6 +1893,7 @@ 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})
@@ -1931,15 +1936,15 @@ 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):
@@ -2142,6 +2147,7 @@ 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():
@@ -2181,9 +2187,9 @@ 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:
@@ -2919,7 +2925,7 @@ def plot_xy(
     x=None,
     y=None,
     ax=None,
-    kind: Union(str, list) = None,  # Specify the kind of plot
+    kind: Union[str, list] = None,  # Specify the kind of plot
     verbose=False,
     **kwargs,
 ):
@@ -2933,7 +2939,7 @@ def plotxy(
     x=None,
     y=None,
     ax=None,
-    kind: Union(str, list) = None,  # Specify the kind of plot
+    kind: Union[str, list] = None,  # Specify the kind of plot
     verbose=False,
     **kwargs,
 ):
@@ -3111,6 +3117,8 @@ def plotxy(
             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)
@@ -3123,6 +3131,7 @@ def plotxy(
             ax = sns.lineplot(ax=ax, data=data, x=x, y=y, **kws_line)
 
         figsets(ax=ax, **kws_figsets)
+        print(kws_add_text)
         add_text(ax=ax, **kws_add_text) if kws_add_text else None
         print(k, " ⤵ ")
         print(default_settings[k])
@@ -3138,14 +3147,14 @@ def plotxy(
 
 
 def volcano(
-    data,
-    x,
-    y,
+    data:pd.DataFrame,
+    x:str,
+    y:str,
     gene_col=None,
-    top_genes=5,
+    top_genes=[5, 5], # [down-regulated, up-regulated]
     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",
@@ -3155,8 +3164,12 @@ def volcano(
     legend=False,
     ax=None,
     verbose=False,
-    kws_arrow=None,
-    kws_text=None,
+    kws_text=dict(fontsize=10, color="k"),
+    kws_bbox=dict(facecolor='none', 
+                  alpha=0.5, 
+                  edgecolor='black',
+                  boxstyle='round,pad=0.3'),# '{}' to hide
+    kws_arrow={},
     **kwargs,
 ):
     """
@@ -3172,7 +3185,7 @@ def volcano(
         Column name for y-axis values (e.g., -log10(FDR)).
     gene_col : str, optional
         Column name for gene names. If provided, gene names will be displayed. Default is None.
-    top_genes : int, optional
+    top_genes : int, list, optional
         Number of top genes to label based on y-axis values. Default is 5.
     thr_x : float, optional
         Threshold for x-axis values. Default is 0.585.
@@ -3232,14 +3245,22 @@ def volcano(
         colors[2],
         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
+
+    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
+    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])
+    sele_gene = pd.concat([down_reg_genes, up_reg_genes])
 
-    # Selecting top significant points for labeling
-    sele_gene = (
-        data.query("color != @colors[2]")  # Exclude gray points
-        .groupby("color", axis=0)
-        .apply(lambda x: x.sort_values(y, ascending=False).head(top_genes))
-        .droplevel(level=0)
-    )
     palette = {colors[0]: colors[0], colors[1]: colors[1], colors[2]: colors[2]}
     # Plot setup
     if ax is None:
@@ -3270,9 +3291,9 @@ def volcano(
     )
 
     # Add threshold lines for x and y axes
-    plt.axhline(y=thr_y, color="black", linestyle="--")
-    plt.axvline(x=-thr_x, color="black", linestyle="--")
-    plt.axvline(x=thr_x, color="black", linestyle="--")
+    ax.axhline(y=thr_y, color="black", linestyle="--",lw=1)
+    ax.axvline(x=-thr_x, color="black", linestyle="--",lw=1)
+    ax.axvline(x=thr_x, color="black", linestyle="--",lw=1)
 
     # Add gene labels for selected significant points
     if gene_col:
@@ -3281,56 +3302,62 @@ 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,
-                    },
+            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,
                 )
             )
 
-        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-0.2.4.1.dist-info → py2ls-0.2.4.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: py2ls
-Version: 0.2.4.1
+Version: 0.2.4.3
 Summary: py(thon)2(too)ls
 Author: Jianfeng
 Author-email: Jianfeng.Liu0413@gmail.com

{py2ls-0.2.4.1.dist-info → py2ls-0.2.4.3.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=FnEf4RV4LBUQfLefWIpIFszVRYeXjnRlc5261DINIdg,18835
 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=fBBco8wQFc6u4KxJ32xwrMh1SZeNz4o8ohiUB5WMKOs,199755
+py2ls/ips.py,sha256=yYSpbHIGDfLK2SXtTX4f--H5oa885pggXePEbhiNRsw,220887
 py2ls/netfinder.py,sha256=LwBkGITB_4BTNtY6RlKdEZVFW6epzMWlnqy2g03KtyU,56117
 py2ls/ocr.py,sha256=5lhUbJufIKRSOL6wAWVLEo8TqMYSjoI_Q-IO-_4u3DE,31419
-py2ls/plot.py,sha256=m8SxFSS1ogwRNQ-O9l-BJWqjGPmjGbsegU56kXG0krw,135132
+py2ls/plot.py,sha256=B_npRfO2rZJJjcYSQ7YMZt2LZTG0mU08JCDnM6zAVx4,136956
 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-0.2.4.1.dist-info/METADATA,sha256=xxXfqGzklXZ1eGESjgYcm1ptiKIRl_Nk0AlfUIyYSIU,20038
-py2ls-0.2.4.1.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-py2ls-0.2.4.1.dist-info/RECORD,,
+py2ls-0.2.4.3.dist-info/METADATA,sha256=S4Il5phQ0Vx8U7VrlEUopkX-hfwcKKQi-qkfD2EYI1g,20038
+py2ls-0.2.4.3.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+py2ls-0.2.4.3.dist-info/RECORD,,