py2ls 0.2.4.5__py3-none-any.whl → 0.2.4.7__py3-none-any.whl

py2ls/bio.py

@@ -166,9 +166,23 @@ def get_probe(
     if platform_id is None:
         df_meta = get_meta(geo=geo, dataset=dataset, verbose=False)
         platform_id = df_meta["platform_id"].unique().tolist()
-        platform_id = platform_id[0] if len(platform_id) == 1 else platform_id
         print(f"Platform: {platform_id}")
-    df_probe = geo[dataset].gpls[platform_id].table
+    if len(platform_id) > 1:
+        df_probe= geo[dataset].gpls[platform_id[0]].table
+        # df_probe=pd.DataFrame()
+        # # Iterate over each platform ID and collect the probe tables
+        # for platform_id_ in platform_id:
+        #     if platform_id_ in geo[dataset].gpls:
+        #         df_probe_ = geo[dataset].gpls[platform_id_].table
+        #         if not df_probe_.empty:
+        #             df_probe=pd.concat([df_probe, df_probe_])
+        #         else:
+        #             print(f"Warning: Probe table for platform {platform_id_} is empty.")
+        #     else:
+        #         print(f"Warning: Platform ID {platform_id_} not found in dataset {dataset}.")
+    else:
+        df_probe= geo[dataset].gpls[platform_id[0]].table
+    
     if df_probe.empty:
         print(
             f"Warning: cannot find the probe info. 看一下是不是在单独的文件中包含了probe信息"
@@ -215,9 +229,12 @@ def get_data(geo: dict, dataset: str = "GSE25097", verbose=False):
     df_expression = get_expression_data(geo, dataset=dataset)
     if not df_expression.select_dtypes(include=["number"]).empty:
         # 如果数据全部是counts类型的话, 则使用TMM进行normalize
-        if 'counts' in get_data_type(df_expression): 
-            print(f"{dataset}'s type is raw read counts, nomalized(transformed) via 'TMM'")
-            df_expression=counts2expression(df_expression.T).T 
+        if 'counts' in get_data_type(df_expression):
+            try:
+                df_expression=counts2expression(df_expression.T).T 
+                print(f"{dataset}'s type is raw read counts, nomalized(transformed) via 'TMM'")
+            except Exception as e: 
+                print("raw counts data")
     if any([df_probe.empty, df_expression.empty]):
         print(
             f"got empty values, check the probe info. 看一下是不是在单独的文件中包含了probe信息"
@@ -814,7 +831,11 @@ def counts_deseq(counts_sam_gene: pd.DataFrame,
     #     .reset_index()
     #     .rename(columns={"index": "gene"})
     # )
-    return dds, diff,stat_res
+    df_norm=pd.DataFrame(dds.layers['normed_counts'])
+    df_norm.index=counts_sam_gene.index
+    df_norm.columns=counts_sam_gene.columns
+    print("res[0]: dds\nres[1]:diff\nres[2]:stat_res\nres[3]:df_normalized")
+    return dds, diff, stat_res,df_norm
 
 def scope_genes(gene_list: list, scopes:str=None, fields: str = "symbol", species="human"):
     """
@@ -1005,25 +1026,25 @@ def plot_enrichr(results_df,
         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
+    if n_top < 5:
+        height_ = 3
+    elif 5 <= n_top < 10:
+        height_ = 3 
+    elif 10 <= n_top < 15:
+        height_ = 3
+    elif 15 <= n_top < 20:
+        height_ =4
+    elif 20 <= n_top < 30:
+        height_ = 5
+    elif 30 <= n_top < 40:
+        height_ = int(n_top / 6)
     else:
-        height_=int(n_top/3)
-    if ax is None:
-        _,ax=plt.subplots(1,1,figsize=[10, height_])
+        height_ = int(n_top / 8) 
+
     #! barplot
     if 'bar' in kind.lower():
+        if ax is None:
+            _,ax=plt.subplots(1,1,figsize=[10, height_])
         ax=plot.plotxy(
             data=results_df.head(n_top),
             kind="barplot",
@@ -1035,6 +1056,7 @@ def plot_enrichr(results_df,
         )
         plot.figsets(ax=ax, **kws_figsets)
         return ax,results_df
+
     #! dotplot
     elif 'dot' in kind.lower():
         #! dotplot 
@@ -1066,16 +1088,20 @@ def plot_enrichr(results_df,
                 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():
+        if ax is None:
+            _,ax=plt.subplots(1,1,figsize=[10, height_])
         # 从overlap中提取出个数
-        results_df["count"] = results_df["Overlap"].apply(
+        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)
+        df_=results_df.sort_values(by="Count", ascending=False)
+
         ax=plot.plotxy(
             data=df_.head(n_top),
             kind="barplot",
-            x="count",
+            x="Count",
             y="Term",
             hue="Term",
             palette=palette,
@@ -1094,11 +1120,12 @@ def plot_bp_cc_mf(
         "GO_Molecular_Function_2023",
     ],
     species="human",
+    download=False,
     n_top=10,
     plot_=True,
     ax=None,
     palette=plot.get_color(3),
-    ** kwargs,
+    **kwargs,
 ):
 
     def res_enrichr_2_count(res_enrichr, n_top=10):
@@ -1111,13 +1138,13 @@ def plot_bp_cc_mf(
         return res_enrichr.head(n_top)#[["Term", "Count"]]
 
     res_enrichr_BP = get_enrichr(
-        deg_gene_list, gene_sets[0], species=species, plot_=False
+        deg_gene_list, gene_sets[0], species=species, plot_=False,download=download
     )
     res_enrichr_CC = get_enrichr(
-        deg_gene_list, gene_sets[1], species=species, plot_=False
+        deg_gene_list, gene_sets[1], species=species, plot_=False,download=download
     )
     res_enrichr_MF = get_enrichr(
-        deg_gene_list, gene_sets[2], species=species, plot_=False
+        deg_gene_list, gene_sets[2], species=species, plot_=False,download=download
     )
 
     df_BP = res_enrichr_2_count(res_enrichr_BP, n_top=n_top)
@@ -1149,6 +1176,7 @@ def plot_bp_cc_mf(
     if ax is None:
         _,ax=plt.subplots(1,1,figsize=[10, height_])
     # 作图
+    display(df2plot)
     if df2plot["Term"].tolist()[0].endswith(")"):
         df2plot["Term"] = df2plot["Term"].apply(lambda x: x.split("(")[0][:-1])
     if plot_:
@@ -1164,8 +1192,15 @@ def plot_bp_cc_mf(
         )
     return ax, df2plot
 
-def get_library_name():
-    return gp.get_library_name()
+def get_library_name(by=None, verbose=False):
+    lib_names=gp.get_library_name()
+    if by is None:
+        if verbose:
+            [print(i) for i in lib_names]
+        return lib_names
+    else:
+        return ips.flatten(ips.strcmp(by, lib_names, get_rank=True,verbose=verbose),verbose=verbose)
+    
 
 def get_gsva(
     data_gene_samples: pd.DataFrame,  # index(gene),columns(samples)
@@ -1398,7 +1433,385 @@ def plot_gsva(gsva_res, # output from bio.get_gsva()
     plot.figsets(ax=ax, **kws_figsets)
     return ax
 
+def get_prerank(
+    rnk: pd.DataFrame,
+    gene_sets: str,
+    download: bool = False,
+    species="Human",
+    threads=8,  # Number of CPU cores to use
+    permutation_num=1000,  # Number of permutations for significance 
+    min_size=1,  # Minimum gene set size
+    max_size=2000,  # Maximum gene set size
+    seed=1,  # Seed for reproducibility
+    verbose=True,  # Verbosity
+    dir_save="./",
+    plot_=False,
+    size=5,
+    cutoff=0.25,
+    show_ring=False,
+    cmap="coolwarm",
+    check_shared=True,
+    **kwargs,
+):
+    """
+    Note: Enrichr uses a list of Entrez gene symbols as input.
+
+    """
+    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
+        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}")
+
+    #! prerank
+    try:
+        pre_res = gp.prerank(
+            rnk=rnk,
+            gene_sets=gene_sets,
+            threads=threads,  # Number of CPU cores to use
+            permutation_num=permutation_num,  # Number of permutations for significance
+            min_size=min_size,  # Minimum gene set size
+            max_size=max_size,  # Maximum gene set size
+            seed=seed,  # Seed for reproducibility
+            verbose=verbose,  # Verbosity
+        )
+    except ValueError as e:
+        print(f"\n{'!'*10}  Error  {'!'*10}\n{' '*4}{e}\n{'!'*10}  Error  {'!'*10}")
+        return None
+    df_prerank = pre_res.res2d
+    if plot_:
+        #! gseaplot
+        # # (1) easy way
+        # terms = df_prerank.Term
+        # axs = pre_res.plot(terms=terms[0])
+        # (2) # to make more control on the plot, use
+        terms = df_prerank.Term
+        axs = pre_res.plot(
+            terms=terms[:7],
+            # legend_kws={"loc": (1.2, 0)},  # set the legend loc
+            # show_ranking=True,  # whether to show the second yaxis
+            figsize=(3, 4),
+        )
+        ips.figsave(dir_save + f"prerank_gseaplot_{gene_sets}.pdf")
+        #!dotplot
+        from gseapy import dotplot
+
+        # to save your figure, make sure that ``ofname`` is not None
+        ax = dotplot(
+            df_prerank,
+            column="NOM p-val",  # FDR q-val",
+            cmap=cmap,
+            size=size,
+            figsize=(10, 5),
+            cutoff=cutoff,
+            show_ring=show_ring,
+        )
+        ips.figsave(dir_save + f"prerank_dotplot_{gene_sets}.pdf")
+
+        #! network plot
+        from gseapy import enrichment_map
+        import networkx as nx
+
+        for top_term in range(5, 50):
+            try:
+                # return two dataframe
+                nodes, edges = enrichment_map(
+                    df=df_prerank,
+                    columns="FDR q-val",
+                    cutoff=0.25,  # 0.25 when "FDR q-val"; 0.05 when "Nom p-value"
+                    top_term=top_term,
+                )
+                # build graph
+                G = nx.from_pandas_edgelist(
+                    edges,
+                    source="src_idx",
+                    target="targ_idx",
+                    edge_attr=["jaccard_coef", "overlap_coef", "overlap_genes"],
+                )
+                # to check if nodes.Hits_ratio or nodes.NES doesn’t match the number of nodes
+                if len(list(nodes.Hits_ratio)) == len(G.nodes):
+                    node_sizes = list(nodes.Hits_ratio * 1000)
+                else:
+                    raise ValueError(
+                        "The size of node_size list does not match the number of nodes in the graph."
+                    )
+
+                layout = "circular"
+                fig, ax = plt.subplots(figsize=(8, 8))
+                if layout == "spring":
+                    pos = nx.layout.spring_layout(G)
+                elif layout == "circular":
+                    pos = nx.layout.circular_layout(G)
+                elif layout == "shell":
+                    pos = nx.layout.shell_layout(G)
+                elif layout == "spectral":
+                    pos = nx.layout.spectral_layout(G)
+
+                # node_size = nx.get_node_attributes()
+                # draw node
+                nx.draw_networkx_nodes(
+                    G,
+                    pos=pos,
+                    cmap=plt.cm.RdYlBu,
+                    node_color=list(nodes.NES),
+                    node_size=list(nodes.Hits_ratio * 1000),
+                )
+                # draw node label
+                nx.draw_networkx_labels(
+                    G,
+                    pos=pos,
+                    labels=nodes.Term.to_dict(),
+                    font_size=8,
+                    verticalalignment="bottom",
+                )
+                # draw edge
+                edge_weight = nx.get_edge_attributes(G, "jaccard_coef").values()
+                nx.draw_networkx_edges(
+                    G,
+                    pos=pos,
+                    width=list(map(lambda x: x * 10, edge_weight)),
+                    edge_color="#CDDBD4",
+                )
+                ax.set_axis_off()
+                print(f"{gene_sets}(top_term={top_term})")
+                plot.figsets(title=f"{gene_sets}(top_term={top_term})")
+                ips.figsave(dir_save + f"prerank_network_{gene_sets}.pdf")
+                break
+            except:
+                print(f"not work {top_term}")
+    return df_prerank
+def plot_prerank(
+    results_df,
+    kind="bar",  # 'barplot', 'dotplot'
+    cutoff=0.25,
+    show_ring=False,
+    xticklabels_rot=0,
+    title=None,  # 'KEGG'
+    cmap="coolwarm",
+    n_top=10,
+    size=5, # when size is None in network, by "NES"
+    facecolor=None,# default by "NES"
+    linewidth=None,# default by "NES"
+    linecolor=None,# default by "NES"
+    linealpha=None, # default by "NES"
+    alpha=None,# default by "NES"
+    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 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 / 5)
+    else:
+        height_ = int(n_top / 6)
+    results_df["-log10(Adjusted P-value)"]=results_df["FDR q-val"].apply(lambda x : -np.log10(x))
+    results_df["Count"] = results_df["Lead_genes"].apply(lambda x: len(x.split(";")))
+    #! barplot
+    if "bar" in kind.lower():
+        df_=results_df.sort_values(by="-log10(Adjusted P-value)",ascending=False)
+        if ax is None:
+            _, ax = plt.subplots(1, 1, figsize=[10, height_])
+        ax = plot.plotxy(
+            data=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, 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="NOM p-val",
+                    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 "co" in kind.lower():
+        if ax is None:
+            _, ax = plt.subplots(1, 1, figsize=[10, height_])
+        # 从overlap中提取出个数
+        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,
+            **kwargs,
+        )
+
+        plot.figsets(ax=ax, **kws_figsets)
+        return ax, df_
+    #! scatter with counts
+    elif "sca" in kind.lower():
+        if isinstance(cmap, str):
+            palette = plot.get_color(n_top, cmap=cmap)
+        elif isinstance(cmap, list):
+            palette = cmap
+        if ax is None:
+            _, ax = plt.subplots(1, 1, figsize=[10, height_])
+        # 从overlap中提取出个数
+        df_ = results_df.sort_values(by="Count", ascending=False)
+        ax = plot.plotxy(
+            data=df_.head(n_top),
+            kind="scatter",
+            x="Count",
+            y="Term",
+            hue="Count",
+            size="Count",
+            sizes=[10,50],
+            palette=palette,
+            legend=None,
+            ax=ax,
+            **kwargs,
+        )
 
+        plot.figsets(ax=ax, **kws_figsets)
+        return ax, df_
+    elif "net" in kind.lower():
+        #! network plot
+        from gseapy import enrichment_map
+        import networkx as nx
+        from matplotlib import cm
+        # try:
+        if cutoff>=1 or cutoff is None:
+            print(f"cutoff is {cutoff} => Without applying filter")
+            nodes, edges = enrichment_map(
+                df=results_df,
+                columns="NOM p-val",
+                cutoff=1.1,  # 0.25 when "FDR q-val"; 0.05 when "Nom p-value"
+                top_term=n_top,
+            )
+        else:
+            cutoff_curr = cutoff
+            step = 0.05
+            cutoff_stop = 1.0
+            while cutoff_curr <= cutoff_stop:
+                try:
+                    # return two dataframe
+                    nodes, edges = enrichment_map(
+                        df=results_df,
+                        columns="NOM p-val",
+                        cutoff=cutoff_curr,  # 0.25 when "FDR q-val"; 0.05 when "Nom p-value"
+                        top_term=n_top,
+                    )
+
+                    if nodes.shape[0] >= 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"{e}: trying cutoff={cutoff_curr}"
+                    )
+
+        print("size: by 'NES'") if size is None else print("")
+        print("linewidth: by 'NES'") if linewidth is None else print("")
+        print("linecolor: by 'NES'") if linecolor is None else print("")
+        print("linealpha: by 'NES'") if linealpha is None else print("")
+        print("facecolor: by 'NES'")  if facecolor is None else print("")
+        print("alpha: by '-log10(Adjusted P-value)'")  if alpha is None else print("")
+        edges.sort_values(by="jaccard_coef", ascending=False,inplace=True)
+        colormap = cm.get_cmap(cmap)  # Get the 'coolwarm' colormap
+        G,ax=plot_ppi(
+            interactions=edges,
+            player1="src_name",
+            player2="targ_name",
+            weight="jaccard_coef",
+            size=[
+                    node["NES"] * 300 for _, node in nodes.iterrows()
+                ] if size is None else size,  #  size nodes by NES
+            facecolor=[colormap(node["NES"]) for _, node in nodes.iterrows()] if facecolor is None else facecolor,  # Color by FDR q-val
+            linewidth=[node["NES"] * 300 for _, node in nodes.iterrows()] if linewidth is None else linewidth,
+            linecolor=[node["NES"] * 300 for _, node in nodes.iterrows()] if linecolor is None else linecolor,
+            linealpha=[node["NES"] * 300 for _, node in nodes.iterrows()] if linealpha is None else linealpha,
+            alpha=[node["NES"] * 300 for _, node in nodes.iterrows()] if alpha is None else alpha,
+            **kwargs
+            )
+        # except Exception as e:
+        #     print(f"not work {n_top},{e}")
+        return ax, G, nodes, edges
+
+    
 #! https://string-db.org/help/api/
 
 import pandas as pd
@@ -1527,16 +1940,22 @@ def plot_ppi(
     n_rank=[5, 10],  # Nodes in each rank for the concentric layout
     dist_node = 10,  # Distance between each rank of circles
     layout="degree", 
-    size='auto',#700,
+    size=None,#700,
+    sizes=(50,500),# min and max of size
     facecolor="skyblue",
     cmap='coolwarm',
     edgecolor="k",
     edgelinewidth=1.5,
     alpha=.5,
+    alphas=(0.1, 1.0),# min and max of alpha
     marker="o",
     node_hideticks=True,
     linecolor="gray",
+    line_cmap='coolwarm',
     linewidth=1.5,
+    linewidths=(0.5,5),# min and max of linewidth
+    linealpha=1.0,
+    linealphas=(0.1,1.0),# min and max of linealpha
     linestyle="-",
     line_arrowstyle='-',
     fontsize=10,
@@ -1565,7 +1984,7 @@ def plot_ppi(
     for col in [player1, player2, weight]:
         if col not in interactions.columns:
             raise ValueError(f"Column '{col}' is missing from the interactions DataFrame.")
-    
+    interactions.sort_values(by=[weight], inplace=True)
     # Initialize Pyvis network
     net = Network(height="750px", width="100%", bgcolor=bgcolor, font_color=fontcolor)
     net.force_atlas_2based(
@@ -1584,34 +2003,71 @@ def plot_ppi(
     G = nx.Graph()
     for _, row in interactions.iterrows():
         G.add_edge(row[player1], row[player2], weight=row[weight])
+    # G = nx.from_pandas_edgelist(interactions, source=player1, target=player2, edge_attr=weight)
+
 
     # Calculate node degrees
     degrees = dict(G.degree())
     norm = Normalize(vmin=min(degrees.values()), vmax=max(degrees.values()))
     colormap = cm.get_cmap(cmap)  # Get the 'coolwarm' colormap
 
+    if not ips.isa(facecolor, 'color'):
+        print("facecolor: based on degrees")
+        facecolor = [colormap(norm(deg)) for deg in degrees.values()]  # Use colormap
+    num_nodes = G.number_of_nodes()
+    #* size
     # Set properties based on degrees
     if not isinstance(size, (int,float,list)):
+        print("size: based on degrees")
         size = [deg * 50 for deg in degrees.values()]  # Scale sizes
-    if not ips.isa(facecolor, 'color'):
-        facecolor = [colormap(norm(deg)) for deg in degrees.values()]  # Use colormap
-    if size is None:
-        size = [700] * G.number_of_nodes()  # Default size for all nodes
-    elif isinstance(size, (int, float)):
-        size = [size] * G.number_of_nodes()  # If a scalar, apply to all nodes
-    # else:
-    #     size = size.tolist()  # Ensure size is a list
-    if len(size)>G.number_of_nodes():
-        size=size[:G.number_of_nodes()]
-
-    for node in G.nodes():
+    size = (size[:num_nodes] if len(size) > num_nodes else size) if isinstance(size, list) else [size] * num_nodes
+    if isinstance(size, list) and len(ips.flatten(size,verbose=False))!=1:
+        # Normalize sizes
+        min_size, max_size = sizes  # Use sizes tuple for min and max values
+        min_degree, max_degree = min(size), max(size)
+        if max_degree > min_degree:  # Avoid division by zero
+            size = [
+                min_size + (max_size - min_size) * (sz - min_degree) / (max_degree - min_degree)
+                for sz in size
+            ]
+        else:
+            # If all values are the same, set them to a default of the midpoint
+            size = [(min_size + max_size) / 2] * len(size)
+
+    #* facecolor
+    facecolor = (facecolor[:num_nodes] if len(facecolor) > num_nodes else facecolor) if isinstance(facecolor, list) else [facecolor] * num_nodes
+    # * facealpha
+    if isinstance(alpha, list):
+        alpha = (alpha[:num_nodes] if len(alpha) > num_nodes else alpha + [alpha[-1]] * (num_nodes - len(alpha)))
+        min_alphas, max_alphas = alphas  # Use alphas tuple for min and max values
+        if len(alpha) > 0:
+            # Normalize alpha based on the specified min and max
+            min_alpha, max_alpha = min(alpha), max(alpha)
+            if max_alpha > min_alpha:  # Avoid division by zero
+                alpha = [
+                    min_alphas + (max_alphas - min_alphas) * (ea - min_alpha) / (max_alpha - min_alpha)
+                    for ea in alpha
+                ]
+            else:
+                # If all alpha values are the same, set them to the average of min and max
+                alpha = [(min_alphas + max_alphas) / 2] * len(alpha)
+        else:
+            # Default to a full opacity if no edges are provided
+            alpha = [1.0] * num_nodes  
+    else:
+        # If alpha is a single value, convert it to a list and normalize it
+        alpha = [alpha] * num_nodes  # Adjust based on alphas
+
+    for i, node in enumerate(G.nodes()):
         net.add_node(
             node,
             label=node,
-            size=size[list(G.nodes()).index(node)] if isinstance(size,list) else size[0],
-            color=facecolor[list(G.nodes()).index(node)] if isinstance(facecolor,list) else facecolor,
+            size=size[i],
+            color=facecolor[i],
+            alpha=alpha[i],
             font={"size": fontsize, "color": fontcolor},
         )
+    print(f'nodes number: {i+1}')
 
     for edge in G.edges(data=True):
         net.add_edge(
@@ -1621,6 +2077,7 @@ def plot_ppi(
             color=edgecolor,
             width=edgelinewidth * edge[2]["weight"],
         )
+
     layouts = [
         "spring",
         "circular",
@@ -1632,7 +2089,8 @@ def plot_ppi(
         "degree"
     ]
     layout = ips.strcmp(layout, layouts)[0]
-    print(layout)
+    print(f"layout:{layout}, or select one in {layouts}")
+    
     # Choose layout
     if layout == "spring":
         pos = nx.spring_layout(G, k=k_value)
@@ -1658,7 +2116,9 @@ def plot_ppi(
         # Calculate node degrees and sort nodes by degree
         degrees = dict(G.degree())
         sorted_nodes = sorted(degrees.items(), key=lambda x: x[1], reverse=True)
-
+        norm = Normalize(vmin=min(degrees.values()), vmax=max(degrees.values()))
+        colormap = cm.get_cmap(cmap)
+        
         # Create positions for concentric circles based on n_layers and n_rank
         pos = {}
         n_layers=len(n_rank)+1 if n_layers is None else n_layers
@@ -1689,8 +2149,8 @@ def plot_ppi(
 
     # If ax is None, use plt.gca()
     if ax is None:
-        fig, ax = plt.subplots(1,1,figsize=figsize)
-
+        fig, ax = plt.subplots(1,1,figsize=figsize) 
+    
     # Draw nodes, edges, and labels with customization options
     nx.draw_networkx_nodes(
         G,
@@ -1704,6 +2164,54 @@ def plot_ppi(
         hide_ticks=node_hideticks,
         node_shape=marker
     )
+
+    #* linewidth
+    if not isinstance(linewidth, list):
+        linewidth = [linewidth] * G.number_of_edges()
+    else:
+        linewidth = (linewidth[:G.number_of_edges()] if len(linewidth) > G.number_of_edges() else linewidth + [linewidth[-1]] * (G.number_of_edges() - len(linewidth)))
+        # Normalize linewidth if it is a list
+        if isinstance(linewidth, list):
+            min_linewidth, max_linewidth = min(linewidth), max(linewidth)
+            vmin, vmax = linewidths  # Use linewidths tuple for min and max values
+            if max_linewidth > min_linewidth:  # Avoid division by zero
+                # Scale between vmin and vmax
+                linewidth = [
+                    vmin + (vmax - vmin) * (lw - min_linewidth) / (max_linewidth - min_linewidth)
+                    for lw in linewidth
+                ]
+            else:
+                # If all values are the same, set them to a default of the midpoint
+                linewidth = [(vmin + vmax) / 2] * len(linewidth)
+        else:
+            # If linewidth is a single value, convert it to a list of that value
+            linewidth = [linewidth] * G.number_of_edges()
+    #* linecolor 
+    if not isinstance(linecolor, str):  
+        weights = [G[u][v]["weight"] for u, v in G.edges()]
+        norm = Normalize(vmin=min(weights), vmax=max(weights))
+        colormap = cm.get_cmap(line_cmap)
+        linecolor = [colormap(norm(weight)) for weight in weights]
+    else:
+        linecolor = [linecolor] * G.number_of_edges()
+
+    # * linealpha
+    if isinstance(linealpha, list):
+        linealpha = (linealpha[:G.number_of_edges()] if len(linealpha) > G.number_of_edges() else linealpha + [linealpha[-1]] * (G.number_of_edges() - len(linealpha)))
+        min_alpha, max_alpha = linealphas  # Use linealphas tuple for min and max values
+        if len(linealpha) > 0:
+            min_linealpha, max_linealpha = min(linealpha), max(linealpha)
+            if max_linealpha > min_linealpha:  # Avoid division by zero
+                linealpha = [
+                    min_alpha + (max_alpha - min_alpha) * (ea - min_linealpha) / (max_linealpha - min_linealpha)
+                    for ea in linealpha
+                ]
+            else:
+                linealpha = [(min_alpha + max_alpha) / 2] * len(linealpha)
+        else:
+            linealpha = [1.0] * G.number_of_edges() # 如果设置有误,则将它设置成1.0
+    else:
+        linealpha = [linealpha] * G.number_of_edges()  # Convert to list if single value
     nx.draw_networkx_edges(
         G, 
         pos, 
@@ -1712,8 +2220,9 @@ def plot_ppi(
         width=linewidth,
         style=linestyle,
         arrowstyle=line_arrowstyle, 
-        alpha=0.7
+        alpha=linealpha
     )
+ 
     nx.draw_networkx_labels(
         G, pos, ax=ax, font_size=fontsize, font_color=fontcolor,horizontalalignment=ha,verticalalignment=va
     )
@@ -1725,6 +2234,7 @@ def plot_ppi(
         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")}")
+        ips.figsave(dir_save.replace(".html",".pdf"))
     return G,ax