py2ls 0.2.4.4__py3-none-any.whl → 0.2.4.5__py3-none-any.whl

py2ls/bio.py

@@ -324,7 +324,7 @@ def find_condition(data:pd.DataFrame, columns=["characteristics_ch1","title"]):
     # 详细看看每个信息的有哪些类, 其中有数字的, 要去除
     for col in columns:
         print(f"{"="*10} {col} {"="*10}")
-        display(ips.flatten([ips.ssplit(i, by="numer")[0] for i in data[col]]))
+        display(ips.flatten([ips.ssplit(i, by="numer")[0] for i in data[col]],verbose=False))
 
 def add_condition(
     data: pd.DataFrame,
@@ -581,7 +581,7 @@ def batch_effect(
     return df_corrected
 
 def get_common_genes(elment1, elment2):
-    common_genes=ips.shared(elment1, elment2)
+    common_genes=ips.shared(elment1, elment2,verbose=False)
     return common_genes
 
 def counts2expression(
@@ -667,7 +667,7 @@ def counts2expression(
             
             length.index=length.index.astype(str).str.strip()
             counts.columns = counts.columns.astype(str).str.strip()
-            shared_genes=ips.shared(length.index, counts.columns)
+            shared_genes=ips.shared(length.index, counts.columns,verbose=False)
             length=length.loc[shared_genes]
             counts=counts.loc[:,shared_genes]
             columns_org = counts.columns.tolist()
@@ -842,6 +842,7 @@ def scope_genes(gene_list: list, scopes:str=None, fields: str = "symbol", specie
 
 def get_enrichr(gene_symbol_list, 
                 gene_sets:str, 
+                download:bool = False,
                 species='Human', 
                 dir_save="./", 
                 plot_=False, 
@@ -854,6 +855,7 @@ def get_enrichr(gene_symbol_list,
                 title=None,# 'KEGG'
                 cutoff=0.05,
                 cmap="coolwarm",
+                size=5,
                 **kwargs):
     """
     Note: Enrichr uses a list of Entrez gene symbols as input.
@@ -878,16 +880,22 @@ def get_enrichr(gene_symbol_list,
         lib_support_names = gp.get_library_name()
         # correct input gene_set name
         gene_sets_name=ips.strcmp(gene_sets,lib_support_names)[0]
+        
         # download it
-        gene_sets = gp.get_library(name=gene_sets_name, organism=species)
-    print(f"gene_sets get ready: {gene_sets_name}")
+        if download:
+            gene_sets = gp.get_library(name=gene_sets_name, organism=species)
+        else:
+            gene_sets = gene_sets_name # 避免重复下载
+    print(f"\ngene_sets get ready: {gene_sets_name}")
 
     # gene symbols are uppercase
     gene_symbol_list=[str(i).upper() for i in gene_symbol_list]
 
     # # check how shared genes
-    if check_shared:
-        shared_genes=ips.shared(ips.flatten(gene_symbol_list,verbose=False), ips.flatten(gene_sets,verbose=False))
+    if check_shared and isinstance(gene_sets, dict):
+        shared_genes=ips.shared(ips.flatten(gene_symbol_list,verbose=False), 
+                                ips.flatten(gene_sets,verbose=False),
+                                verbose=False)
     
     #! enrichr 
     try:
@@ -903,13 +911,13 @@ def get_enrichr(gene_symbol_list,
         return None
     
     results_df = enr.results
-    print(f"got enrichr reslutls; shape: {results_df.shape}")
+    print(f"got enrichr reslutls; shape: {results_df.shape}\n")
     results_df["-log10(Adjusted P-value)"] = -np.log10(results_df["Adjusted P-value"])
     results_df.sort_values("-log10(Adjusted P-value)", inplace=True, ascending=False)
 
     if plot_:
         if palette is None:
-            palette=plot.get_color(n_top, cmap="coolwarm")[::-1]
+            palette=plot.get_color(n_top, cmap=cmap)[::-1]
         #! barplot
         if n_top<5:
             height_=4
@@ -921,11 +929,12 @@ def get_enrichr(gene_symbol_list,
             height_=7
         elif 15<=n_top<20:
             height_=8
-        elif 25<=n_top<30:
+        elif 20<=n_top<30:
             height_=9
         else:
             height_=int(n_top/3)
-        plt.figure(figsize=[5, height_])
+        plt.figure(figsize=[10, height_])
+
         ax1=plot.plotxy(
             data=results_df.head(n_top),
             kind="barplot",
@@ -935,18 +944,17 @@ def get_enrichr(gene_symbol_list,
             palette=palette,
             legend=None,
         )
+        plot.figsets(ax=ax1, **kws_figsets)
         if dir_save: 
             ips.figsave(f"{dir_save} enr_barplot.pdf")
-        plot.figsets(ax=ax1, **kws_figsets)
         plt.show()
 
         #! dotplot 
         cutoff_curr = cutoff
         step=0.05
         cutoff_stop = 0.5
-        while cutoff_curr <=cutoff_stop:
+        while cutoff_curr <= cutoff_stop:
             try:
-                print(kws_figsets)
                 if cutoff_curr!=cutoff:
                     plt.clf()
                 ax2 = gp.dotplot(enr.res2d, 
@@ -957,7 +965,8 @@ def get_enrichr(gene_symbol_list,
                                 cmap=cmap,
                                 cutoff=cutoff_curr,
                                 top_term=n_top,
-                                figsize=[6, height_])
+                                size=size,
+                                figsize=[10, height_])
                 if len(ax2.collections)>=n_top: 
                     print(f"cutoff={cutoff_curr} done! ")
                     break 
@@ -975,6 +984,420 @@ def get_enrichr(gene_symbol_list,
 
     return results_df
 
+def plot_enrichr(results_df,
+                 kind="bar",# 'barplot', 'dotplot'
+                 cutoff=0.05,
+                 show_ring=False,
+                 xticklabels_rot=0,
+                 title=None,# 'KEGG'
+                 cmap="coolwarm",
+                 n_top=10,
+                 size=5,
+                 ax=None,
+                 **kwargs):
+    kws_figsets = {}
+    for k_arg, v_arg in kwargs.items():
+        if "figset" in k_arg:
+            kws_figsets = v_arg
+            kwargs.pop(k_arg, None)
+            break
+    if isinstance(cmap,str):
+        palette = plot.get_color(n_top, cmap=cmap)[::-1]
+    elif isinstance(cmap,list):
+        palette=cmap
+
+    if n_top<5:
+        height_=4
+    elif 5<=n_top<10:
+        height_=5
+    elif 5<=n_top<10:
+        height_=6
+    elif 10<=n_top<15:
+        height_=7
+    elif 15<=n_top<20:
+        height_=8
+    elif 20<=n_top<30:
+        height_=9
+    else:
+        height_=int(n_top/3)
+    if ax is None:
+        _,ax=plt.subplots(1,1,figsize=[10, height_])
+    #! barplot
+    if 'bar' in kind.lower():
+        ax=plot.plotxy(
+            data=results_df.head(n_top),
+            kind="barplot",
+            x="-log10(Adjusted P-value)",
+            y="Term",
+            hue="Term",
+            palette=palette,
+            legend=None,
+        )
+        plot.figsets(ax=ax, **kws_figsets)
+        return ax,results_df
+    #! dotplot
+    elif 'dot' in kind.lower():
+        #! dotplot 
+        cutoff_curr = cutoff
+        step=0.05
+        cutoff_stop = 0.5
+        while cutoff_curr <= cutoff_stop:
+            try:
+                if cutoff_curr!=cutoff:
+                    plt.clf()
+                ax = gp.dotplot(results_df, 
+                                column="Adjusted P-value",
+                                show_ring=show_ring,
+                                xticklabels_rot=xticklabels_rot,
+                                title=title,
+                                cmap=cmap,
+                                cutoff=cutoff_curr,
+                                top_term=n_top,
+                                size=size,
+                                figsize=[10, height_])
+                if len(ax.collections)>=n_top: 
+                    print(f"cutoff={cutoff_curr} done! ")
+                    break 
+                if cutoff_curr==cutoff_stop:
+                    break
+                cutoff_curr+=step
+            except Exception as e:
+                cutoff_curr+=step
+                print(f"Warning: trying cutoff={cutoff_curr}, cutoff={cutoff_curr-step} failed: {e} ")
+        plot.figsets(ax=ax, **kws_figsets)
+        return ax,results_df
+    #! barplot with counts
+    elif 'count' in kind.lower():
+        # 从overlap中提取出个数
+        results_df["count"] = results_df["Overlap"].apply(
+        lambda x: int(x.split("/")[0]) if isinstance(x, str) else x)
+        df_=results_df.sort_values(by="count", ascending=False)
+        ax=plot.plotxy(
+            data=df_.head(n_top),
+            kind="barplot",
+            x="count",
+            y="Term",
+            hue="Term",
+            palette=palette,
+            legend=None,
+            ax=ax
+        )
+        
+        plot.figsets(ax=ax, **kws_figsets)
+        return ax,df_
+
+def plot_bp_cc_mf(
+    deg_gene_list,
+    gene_sets=[
+        "GO_Biological_Process_2023",
+        "GO_Cellular_Component_2023",
+        "GO_Molecular_Function_2023",
+    ],
+    species="human",
+    n_top=10,
+    plot_=True,
+    ax=None,
+    palette=plot.get_color(3),
+    ** kwargs,
+):
+
+    def res_enrichr_2_count(res_enrichr, n_top=10):
+        """把enrich resulst 提取出count,并排序"""
+        res_enrichr["Count"] = res_enrichr["Overlap"].apply(
+            lambda x: int(x.split("/")[0]) if isinstance(x, str) else x
+        )
+        res_enrichr.sort_values(by="Count", ascending=False, inplace=True)
+
+        return res_enrichr.head(n_top)#[["Term", "Count"]]
+
+    res_enrichr_BP = get_enrichr(
+        deg_gene_list, gene_sets[0], species=species, plot_=False
+    )
+    res_enrichr_CC = get_enrichr(
+        deg_gene_list, gene_sets[1], species=species, plot_=False
+    )
+    res_enrichr_MF = get_enrichr(
+        deg_gene_list, gene_sets[2], species=species, plot_=False
+    )
+
+    df_BP = res_enrichr_2_count(res_enrichr_BP, n_top=n_top)
+    df_BP["Ontology"] = ["BP"] * n_top
+
+    df_CC = res_enrichr_2_count(res_enrichr_CC, n_top=n_top)
+    df_CC["Ontology"] = ["CC"] * n_top
+
+    df_MF = res_enrichr_2_count(res_enrichr_MF, n_top=n_top)
+    df_MF["Ontology"] = ["MF"] * n_top
+    
+    # 合并
+    df2plot = pd.concat([df_BP, df_CC, df_MF])
+    n_top=n_top*3
+    if n_top < 5:
+        height_ = 4
+    elif 5 <= n_top < 10:
+        height_ = 5 
+    elif 10 <= n_top < 15:
+        height_ = 6
+    elif 15 <= n_top < 20:
+        height_ = 7
+    elif 20 <= n_top < 30:
+        height_ = 8
+    elif 30 <= n_top < 40:
+        height_ = int(n_top / 4)
+    else:
+        height_ = int(n_top / 5)
+    if ax is None:
+        _,ax=plt.subplots(1,1,figsize=[10, height_])
+    # 作图
+    if df2plot["Term"].tolist()[0].endswith(")"):
+        df2plot["Term"] = df2plot["Term"].apply(lambda x: x.split("(")[0][:-1])
+    if plot_:
+        ax = plot.plotxy(
+            data=df2plot,
+            x="Count",
+            y="Term",
+            hue="Ontology",
+            kind="bar",
+            palette=palette,
+            ax=ax,
+            **kwargs
+        )
+    return ax, df2plot
+
+def get_library_name():
+    return gp.get_library_name()
+
+def get_gsva(
+    data_gene_samples: pd.DataFrame,  # index(gene),columns(samples)
+    gene_sets: str,
+    species:str="Human",
+    dir_save:str="./",
+    plot_:bool=False,
+    n_top:int=30,
+    check_shared:bool=True,
+    cmap="coolwarm",
+    min_size=1,
+    max_size=1000,
+    kcdf="Gaussian",# 'Gaussian' for continuous data
+    method='gsva',
+    seed=1,
+    **kwargs,
+):
+    kws_figsets = {}
+    for k_arg, v_arg in kwargs.items():
+        if "figset" in k_arg:
+            kws_figsets = v_arg
+            kwargs.pop(k_arg, None)
+            break
+    species_org = species
+    # organism (str) – Select one from { ‘Human’, ‘Mouse’, ‘Yeast’, ‘Fly’, ‘Fish’, ‘Worm’ }
+    organisms = ["Human", "Mouse", "Yeast", "Fly", "Fish", "Worm"]
+    species = ips.strcmp(species, organisms)[0]
+    if species_org.lower() != species.lower():
+        print(f"species was corrected to {species}, becasue only support {organisms}")
+    if os.path.isfile(gene_sets):
+        gene_sets_name = os.path.basename(gene_sets)
+        gene_sets = ips.fload(gene_sets)
+    else:
+        lib_support_names = gp.get_library_name()
+        # correct input gene_set name
+        gene_sets_name = ips.strcmp(gene_sets, lib_support_names)[0]
+        # download it
+        gene_sets = gp.get_library(name=gene_sets_name, organism=species)
+    print(f"gene_sets get ready: {gene_sets_name}")
+
+    # gene symbols are uppercase
+    gene_symbol_list = [str(i).upper() for i in data_gene_samples.index]
+    data_gene_samples.index=gene_symbol_list
+    # display(data_gene_samples.head(3))
+    # # check how shared genes
+    if check_shared:
+        ips.shared(
+            ips.flatten(gene_symbol_list, verbose=False),
+            ips.flatten(gene_sets, verbose=False),
+            verbose=False
+        )
+    gsva_results = gp.gsva(
+        data=data_gene_samples,  #  matrix should have genes as rows and samples as columns
+        gene_sets=gene_sets,
+        outdir=None,
+        kcdf=kcdf,  # 'Gaussian' for continuous data
+        min_size=min_size,
+        method=method,
+        max_size=max_size,
+        verbose=True,
+        seed=seed,
+        # no_plot=False,
+    )
+    gsva_res = gsva_results.res2d.copy()
+    gsva_res["ES_abs"] = gsva_res["ES"].apply(np.abs)
+    gsva_res = gsva_res.sort_values(by="ES_abs", ascending=False)
+    gsva_res = (
+        gsva_res.drop_duplicates(subset="Term").drop(columns="ES_abs")
+        # .iloc[:80, :]
+        .reset_index(drop=True)
+    )
+    gsva_res = gsva_res.sort_values(by="ES", ascending=False)
+    if plot_:
+        if gsva_res.shape[0]>=2*n_top:
+            gsva_res_plot=pd.concat([gsva_res.head(n_top),gsva_res.tail(n_top)])
+        else:
+            gsva_res_plot = gsva_res
+        if isinstance(cmap,str):
+            palette = plot.get_color(n_top*2, cmap=cmap)[::-1]
+        elif isinstance(cmap,list):
+            if len(cmap)==2:
+                palette = [cmap[0]]*n_top+[cmap[1]]*n_top
+            else:
+                palette=cmap
+        # ! barplot
+        if n_top < 5:
+            height_ = 3
+        elif 5 <= n_top < 10:
+            height_ = 4 
+        elif 10 <= n_top < 15:
+            height_ = 5
+        elif 15 <= n_top < 20:
+            height_ = 6
+        elif 20 <= n_top < 30:
+            height_ = 7
+        elif 30 <= n_top < 40:
+            height_ = int(n_top / 3.5)
+        else:
+            height_ = int(n_top / 3)
+        plt.figure(figsize=[10, height_])
+        ax2 = plot.plotxy(
+            data=gsva_res_plot,
+            x="ES",
+            y="Term",
+            hue="Term",
+            palette=palette,
+            kind=["bar"],
+            figsets=dict(yticklabel=[], ticksloc="b", boxloc="b", ylabel=None),
+        )
+        # 改变labels的位置
+        for i, bar in enumerate(ax2.patches):
+            term = gsva_res_plot.iloc[i]["Term"]
+            es_value = gsva_res_plot.iloc[i]["ES"]
+
+            # Positive ES values: Align y-labels to the left
+            if es_value > 0:
+                ax2.annotate(
+                    term,
+                    xy=(0, bar.get_y() + bar.get_height() / 2),
+                    xytext=(-5, 0),  # Move to the left
+                    textcoords="offset points",
+                    ha="right",
+                    va="center",  # Align labels to the right
+                    fontsize=10,
+                    color="black",
+                )
+            # Negative ES values: Align y-labels to the right
+            else:
+                ax2.annotate(
+                    term,
+                    xy=(0, bar.get_y() + bar.get_height() / 2),
+                    xytext=(5, 0),  # Move to the right
+                    textcoords="offset points",
+                    ha="left",
+                    va="center",  # Align labels to the left
+                    fontsize=10,
+                    color="black",
+                )
+        plot.figsets(ax=ax2, **kws_figsets)
+        if dir_save:
+            ips.figsave(dir_save + f"GSVA_{gene_sets_name}.pdf")
+        plt.show()
+    return gsva_res.reset_index(drop=True)
+
+def plot_gsva(gsva_res, # output from bio.get_gsva()
+              n_top=10,
+              ax=None,            
+              x="ES",
+              y="Term",
+              hue="Term",
+              cmap="coolwarm",
+              **kwargs
+              ):
+    kws_figsets = {}
+    for k_arg, v_arg in kwargs.items():
+        if "figset" in k_arg:
+            kws_figsets = v_arg
+            kwargs.pop(k_arg, None)
+            break
+    # ! barplot
+    if n_top < 5:
+        height_ = 4
+    elif 5 <= n_top < 10:
+        height_ = 5 
+    elif 10 <= n_top < 15:
+        height_ = 6
+    elif 15 <= n_top < 20:
+        height_ = 7
+    elif 20 <= n_top < 30:
+        height_ = 8
+    elif 30 <= n_top < 40:
+        height_ = int(n_top / 3.5)
+    else:
+        height_ = int(n_top / 3)
+    if ax is None:
+        _,ax=plt.subplots(1,1,figsize=[10, height_])
+    gsva_res = gsva_res.sort_values(by=x, ascending=False)
+
+    if gsva_res.shape[0]>=2*n_top:
+        gsva_res_plot=pd.concat([gsva_res.head(n_top),gsva_res.tail(n_top)])
+    else:
+        gsva_res_plot = gsva_res
+    if isinstance(cmap,str):
+        palette = plot.get_color(n_top*2, cmap=cmap)[::-1]
+    elif isinstance(cmap,list):
+        if len(cmap)==2:
+            palette = [cmap[0]]*n_top+[cmap[1]]*n_top
+        else:
+            palette=cmap
+
+    ax = plot.plotxy(
+        ax=ax,
+        data=gsva_res_plot,
+        x=x,
+        y=y,
+        hue=hue,
+        palette=palette,
+        kind=["bar"],
+        figsets=dict(yticklabel=[], ticksloc="b", boxloc="b", ylabel=None),
+    )
+    # 改变labels的位置
+    for i, bar in enumerate(ax.patches):
+        term = gsva_res_plot.iloc[i]["Term"]
+        es_value = gsva_res_plot.iloc[i]["ES"]
+
+        # Positive ES values: Align y-labels to the left
+        if es_value > 0:
+            ax.annotate(
+                term,
+                xy=(0, bar.get_y() + bar.get_height() / 2),
+                xytext=(-5, 0),  # Move to the left
+                textcoords="offset points",
+                ha="right",
+                va="center",  # Align labels to the right
+                fontsize=10,
+                color="black",
+            )
+        # Negative ES values: Align y-labels to the right
+        else:
+            ax.annotate(
+                term,
+                xy=(0, bar.get_y() + bar.get_height() / 2),
+                xytext=(5, 0),  # Move to the right
+                textcoords="offset points",
+                ha="left",
+                va="center",  # Align labels to the left
+                fontsize=10,
+                color="black",
+            )
+    plot.figsets(ax=ax, **kws_figsets)
+    return ax
+
 
 #! https://string-db.org/help/api/
 
@@ -1296,7 +1719,12 @@ def plot_ppi(
     )
     plot.figsets(ax=ax,**kws_figsets)
     ax.axis("off")
-    net.write_html(dir_save)
+    if dir_save:
+        if not os.path.basename(dir_save):
+            dir_save="_.html"
+        net.write_html(dir_save)
+        nx.write_graphml(G, dir_save.replace(".html",".graphml"))  # Export to GraphML
+        print(f"could be edited in Cytoscape \n{dir_save.replace(".html",".graphml")}")
     return G,ax
 
 

py2ls/ips.py

@@ -554,14 +554,14 @@ def shared(*args, strict=True, n_shared=2, verbose=True):
         # Get elements that appear in at least n_shared lists
         shared_elements = [item for item, count in element_count.items() if count >= n_shared]
 
-    shared_elements = flatten(shared_elements) 
+    shared_elements = flatten(shared_elements, verbose=verbose) 
     if verbose:
         elements2show = shared_elements if len(shared_elements)<10 else shared_elements[:5]
         print(f"{' '*2}{len(shared_elements)} elements shared: {' '*2}{elements2show}")
         print("********* checking shared elements *********")
     return shared_elements
 
-def flatten(nested: Any, unique_list=True,verbose=True):
+def flatten(nested: Any, unique_list=True, verbose=True):
     """
     Recursively flattens a nested structure (lists, tuples, dictionaries, sets) into a single list.
     Parameters:
@@ -2840,7 +2840,7 @@ def listdir(
 # print(result)
 # df=listdir("/", contains='sss',sort_by='name',ascending=False)
 # print(df.fname.to_list(),"\n",df.fpath.to_list())
-def list_func(lib_name, opt="call"):
+def listfunc(lib_name, opt="call"):
     if opt == "call":
         funcs = [func for func in dir(lib_name) if callable(getattr(lib_name, func))]
     else:

py2ls/plot.py

@@ -2220,6 +2220,9 @@ def figsets(*args, **kwargs):
                 legend = ax.get_legend()
                 if legend is not None:
                     legend.remove()
+        if any(['colorbar' in key.lower(),'cbar' in key.lower()]) and "loc" in key.lower():
+            cbar = ax.collections[0].colorbar  # Access the colorbar from the plot
+            cbar.ax.set_position(value)  # [left, bottom, width, height] [0.475, 0.15, 0.04, 0.25]
 
     for arg in args:
         if isinstance(arg, matplotlib.axes._axes.Axes):
@@ -2708,15 +2711,45 @@ def adjust_spines(ax=None, spines=["left", "bottom"], distance=2):
 # And then plot the data:
 
 
-def add_colorbar(im, width=None, pad=None, **kwargs):
-    # usage: add_colorbar(im, width=0.01, pad=0.005, label="PSD (dB)", shrink=0.8)
-    l, b, w, h = im.axes.get_position().bounds  # get boundaries
-    width = width or 0.1 * w  # get width of the colorbar
-    pad = pad or width  # get pad between im and cbar
-    fig = im.axes.figure  # get figure of image
-    cax = fig.add_axes([l + w + pad, b, width, h])  # define cbar Axes
-    return fig.colorbar(im, cax=cax, **kwargs)  # draw cbar
+# def add_colorbar(im, width=None, pad=None, **kwargs):
+#     # usage: add_colorbar(im, width=0.01, pad=0.005, label="PSD (dB)", shrink=0.8)
+#     l, b, w, h = im.axes.get_position().bounds  # get boundaries
+#     width = width or 0.1 * w  # get width of the colorbar
+#     pad = pad or width  # get pad between im and cbar
+#     fig = im.axes.figure  # get figure of image
+#     cax = fig.add_axes([l + w + pad, b, width, h])  # define cbar Axes
+#     return fig.colorbar(im, cax=cax, **kwargs)  # draw cbar
+
+def add_colorbar(im, 
+                 cmap="viridis", 
+                 vmin=-1,
+                 vmax=1,
+                 orientation='vertical', 
+                 width_ratio=0.05, 
+                 pad_ratio=0.02, 
+                 shrink=1.0, 
+                 **kwargs):
+    import matplotlib as mpl
+    if all([cmap, vmin, vmax]):
+        norm = mpl.colors.Normalize(vmin=vmin, vmax=vmax)
+    else:
+        norm=False
+    sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
+    sm.set_array([])
+    l, b, w, h = im.axes.get_position().bounds  # position: left, bottom, width, height
+    if orientation == 'vertical':
+        width = width_ratio * w
+        pad = pad_ratio * w
+        cax = im.figure.add_axes([l + w + pad, b, width, h * shrink])  # Right of the image
+    else:
+        height = width_ratio * h
+        pad = pad_ratio * h
+        cax = im.figure.add_axes([l, b - height - pad, w * shrink, height])  # Below the image
+    cbar=im.figure.colorbar(sm, cax=cax, orientation=orientation, **kwargs)
+    return cbar 
 
+# Usage:
+# add_colorbar(im, width_ratio=0.03, pad_ratio=0.01, orientation='horizontal', label="PSD (dB)")
 
 def generate_xticks_with_gap(x_len, hue_len):
     """
@@ -3129,7 +3162,7 @@ def plotxy(
             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)
+            ax = sns.countplot(data=data, x=x,y=y, ax=ax, **kws_count)
         elif k == "regplot":
             kws_reg = kwargs.pop("kws_reg", kwargs)
             ax = sns.regplot(data=data, x=x, y=y, ax=ax, **kws_reg)

{py2ls-0.2.4.4.dist-info → py2ls-0.2.4.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: py2ls
-Version: 0.2.4.4
+Version: 0.2.4.5
 Summary: py(thon)2(too)ls
 Author: Jianfeng
 Author-email: Jianfeng.Liu0413@gmail.com

{py2ls-0.2.4.4.dist-info → py2ls-0.2.4.5.dist-info}/RECORD

@@ -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=J-zGAgHiSQwDyUvjMKDOsJZoeTkqGaXcHDYHtMd84SQ,53879
+py2ls/bio.py,sha256=7q-zIxGU76g9AABUcrCLW2GrowTw-ljN_8zKbjdi7p0,67677
 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 +214,16 @@ 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=USmQKEZuqnjJyP5dhXzFG8yMrhrH6L8yt9jFtttuqLI,227772
+py2ls/ips.py,sha256=4CmSK5Ye4eHPSkTbrbS9KZ20mz-GA7xw2vEa1o1fI4k,227789
 py2ls/ml2ls.py,sha256=XSe2-sLNzUVSvVRkeRGfhrB_q8C49SDK1sekYC1Bats,50277
 py2ls/netfinder.py,sha256=RJFr80tGEJiuwEx99IBOhI5-ZuXnPdWnGUYpF7XCEwI,56426
 py2ls/ocr.py,sha256=5lhUbJufIKRSOL6wAWVLEo8TqMYSjoI_Q-IO-_4u3DE,31419
-py2ls/plot.py,sha256=MepTGqtxqHnc_pTixvEXjQHGPTETcTeI1FGXMxBB8L8,144556
+py2ls/plot.py,sha256=h-pcdlQN7Aqqgxw52Rsq5Wvu8LzgiYwO1F6CBvKpTkg,145989
 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-0.2.4.4.dist-info/METADATA,sha256=OS59HPIjSXN6Zdy5X0AxSfyvQba6SuK66h74n7nVDno,20038
-py2ls-0.2.4.4.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-py2ls-0.2.4.4.dist-info/RECORD,,
+py2ls-0.2.4.5.dist-info/METADATA,sha256=z1aLD2Jcfn3klBZIptJYjHcdwMRZ4hOe9GdjsmI8bBU,20038
+py2ls-0.2.4.5.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+py2ls-0.2.4.5.dist-info/RECORD,,