gwaslab 3.5.0__py3-none-any.whl → 3.5.2__py3-none-any.whl

gwaslab/viz_plot_mqqplot.py

@@ -139,6 +139,7 @@ def mqqplot(insumstats,
           anno_gtf_path=None,
           anno_adjust=False,
           anno_max_iter=100,
+          arrow_kwargs=None,
           arm_offset=None,
           arm_scale=1,
           anno_height=1,
@@ -243,7 +244,8 @@ def mqqplot(insumstats,
         anno_args=dict()
     if colors is None:
         colors=["#597FBD","#74BAD3"]
-    
+    if arrow_kwargs is None:
+        arrow_kwargs=dict()
     if region is not None:
         if marker_size == (5,20):
             marker_size=(45,65)
@@ -262,7 +264,7 @@ def mqqplot(insumstats,
         
     if region_marker_shapes is None:
         # 9 shapes
-        region_marker_shapes = ['o', 's','^','D','*','P','X','h','8']
+        region_marker_shapes = ['o', '^','s','D','*','P','X','h','8']
     if region_grid_line is None:
         region_grid_line = {"linewidth": 2,"linestyle":"--"}
     if region_lead_grid_line is None:
@@ -638,6 +640,14 @@ def mqqplot(insumstats,
             linewidth=1
             if len(region_ref) == 1:
                 palette = {100+i:region_ld_colors[i] for i in range(len(region_ld_colors))}
+                scatter_args["markers"]= {(i+1):m for i,m in enumerate(region_marker_shapes[:2])}
+                if region_ref[0] is None:
+                    id_to_hide = sumstats["scaled_P"].idxmax()
+                    sumstats.loc[id_to_hide,"s"] = -100
+                else:
+                    sumstats.loc[sumstats["SNPID"]==region_ref[0],"s"] = -100
+                marker_size=(0,marker_size[1])
+                style="SHAPE"
             else:
                 palette = {}
                 region_color_maps = []
@@ -650,12 +660,14 @@ def mqqplot(insumstats,
                         # 1 + 5 + 1
                         region_ld_colors_single = [region_ld_colors[0]] + output_hex_colors + [output_hex_colors[-1]]
                     region_color_maps.append(region_ld_colors_single)
-                # gradient colors
+                
+                # gradient color dict
                 for i, hex_colors in enumerate(region_color_maps):
                     for j, hex_color in enumerate(hex_colors):
                         palette[(i+1)*100 + j ] = hex_color
 
                 edgecolor="none"
+                # create a marker shape dict
                 scatter_args["markers"]= {(i+1):m for i,m in enumerate(region_marker_shapes[:len(region_ref)])}
                 style="SHAPE"
 
@@ -1002,6 +1014,7 @@ def mqqplot(insumstats,
                                 region_anno_bbox_args=region_anno_bbox_args,
                                 skip=skip,
                                 anno_height=anno_height,
+                                arrow_kwargs=arrow_kwargs,
                                 snpid=snpid,
                                 chrom=chrom,
                                 pos=pos,
@@ -1393,14 +1406,19 @@ def _process_xtick(ax1, chrom_df, xtick_chr_dict, fontsize, font_family, log=Log
 
 def _process_ytick(ax1, fontsize, font_family, ax4, log=Log(),verbose=True):
     log.write(" -Processing Y labels...",verbose=verbose)
-    ax1_yticklabels = ax1.get_yticklabels()
+    #ax1_yticklabels = ax1.get_yticklabels()
+    #print(ax1_yticklabels)
+    #plt.draw()
+    #ax1_yticks = ax1.get_yticks()
+    #print(ax1_yticks)
     #ax1.set_yticklabels(ax1_yticklabels,fontsize=fontsize,family=font_family) 
-    ax1_yticks = ax1.get_yticks()
-    ax1.set_yticks(ax1_yticks,ax1_yticklabels,fontsize=fontsize,family=font_family) 
+    ax1.tick_params(axis='y', labelsize=fontsize,labelfontfamily=font_family)
+    #ax1.set_yticks(ax1_yticks,ax1_yticklabels,fontsize=fontsize,family=font_family) 
     if ax4 is not None:
-        ax4_yticklabels = ax4.get_yticklabels()
-        ax4_yticks = ax4.get_yticks()
-        ax4.set_yticks(ax4_yticks,ax4_yticklabels, fontsize=fontsize,family=font_family) 
+        #ax4_yticklabels = ax4.get_yticklabels()
+        #ax4_yticks = ax4.get_yticks()
+        ax4.tick_params(axis='y', labelsize=fontsize,labelfontfamily=font_family)
+        #ax4.set_yticks(ax4_yticks,ax4_yticklabels, fontsize=fontsize,family=font_family) 
     return ax1, ax4
 
 def _process_xlabel(region, xlabel, ax1, gtf_path, mode, fontsize, font_family,  ax3=None , log=Log(),verbose=True):

gwaslab/viz_plot_phe_heatmap.py

@@ -203,7 +203,7 @@ def _gwheatmap(
             linewidth=linewidth,
             edgecolor = edgecolor,
             zorder=2,
-            ax=ax1)   
+            ax=ax1, **scatter_kwargs)   
     
     handles, labels = ax1.get_legend_handles_labels()
     new_labels = []

gwaslab/viz_plot_regional2.py

@@ -93,6 +93,7 @@ def _plot_regional(
             ax1, lead_id_single = _pinpoint_lead(sumstats = sumstats,
                                         ax1 = ax1, 
                                         region_ref=region_ref_single,
+                                        region_ref_total_n = len(region_ref), 
                                         lead_color = palette[(index+1)*100 + len(region_ld_threshold)+2], 
                                         marker_size= marker_size,
                                         region_marker_shapes=region_marker_shapes,
@@ -130,7 +131,9 @@ def _plot_regional(
                             region_ref=region_ref,
                             region_ld_threshold=region_ld_threshold, 
                             region_ref_index_dic=region_ref_index_dic,
-                            palette=palette)
+                            region_marker_shapes=region_marker_shapes,
+                            palette=palette,
+                            fig=fig)
         else:
             cbar=None
 
@@ -300,7 +303,7 @@ def _get_lead_id(sumstats=None, region_ref=None, log=None, verbose=True):
 
     return lead_id
 
-def _pinpoint_lead(sumstats,ax1,region_ref, lead_color, marker_size, log, verbose, region_marker_shapes):
+def _pinpoint_lead(sumstats,ax1,region_ref, region_ref_total_n, lead_color, marker_size, log, verbose, region_marker_shapes):
     
     if region_ref is None:
         log.write(" -Extracting lead variant..." , verbose=verbose)
@@ -308,12 +311,19 @@ def _pinpoint_lead(sumstats,ax1,region_ref, lead_color, marker_size, log, verbos
     else:
         lead_id = _get_lead_id(sumstats, region_ref, log, verbose)
     
+    if region_ref_total_n <2:
+        # single-ref mode
+        marker_shape = region_marker_shapes[sumstats.loc[lead_id,"SHAPE"]]
+    else:
+        # multi-ref mode
+        marker_shape = region_marker_shapes[sumstats.loc[lead_id,"SHAPE"]-1]
+
     if lead_id is not None:
         ax1.scatter(sumstats.loc[lead_id,"i"],sumstats.loc[lead_id,"scaled_P"],
                 color=lead_color,
                 zorder=3,
-                marker= region_marker_shapes[sumstats.loc[lead_id,"SHAPE"]-1],
-                s=marker_size[1]+2,
+                marker= marker_shape,
+                s=marker_size[1]*1.5,
                 edgecolor="black")
 
     return ax1, lead_id
@@ -322,14 +332,15 @@ def _add_region_title(region_title, ax1,region_title_args):
     ax1.text(0.015,0.97, region_title, transform=ax1.transAxes, va="top", ha="left", region_ref=None, **region_title_args )
     return ax1
 
-def _add_ld_legend(sumstats, ax1, region_ld_threshold, region_ref,region_ref_index_dic,palette =None, position=1):
+def _add_ld_legend(sumstats, ax1, region_ld_threshold, region_ref,region_ref_index_dic,region_marker_shapes,fig, palette =None, position=1):
     
     width_pct = "11%"
     height_pct = "{}%".format( 14 + 7 * len(region_ref))
     axins1 = inset_axes(ax1,
             width=width_pct,  # width = 50% of parent_bbox width
             height=height_pct,  # height : 5%
-            loc='upper right',axes_kwargs={"frameon":True,"facecolor":"white","zorder":999999})
+            loc='upper right',
+            axes_kwargs={"frameon":True,"facecolor":"white","zorder":999999})
     
     ld_ticks = [0]+region_ld_threshold+[1]
 
@@ -345,7 +356,7 @@ def _add_ld_legend(sumstats, ax1, region_ld_threshold, region_ref,region_ref_ind
                 a = Rectangle((x,y),width, height, fill = True, color = hex_color , linewidth = 2)
                 #patches.append(a)
                 axins1.add_patch(a)
-
+    
     # y snpid
     yticks_position = 0.1 + 0.2 *np.arange(0,len(region_ref))
     axins1.set_yticks(yticks_position, ["{}".format(x) for x in region_ref])
@@ -354,9 +365,31 @@ def _add_ld_legend(sumstats, ax1, region_ld_threshold, region_ref,region_ref_ind
     # x ld thresholds
     axins1.set_xticks(ticks=ld_ticks) 
     axins1.set_xticklabels([str(i) for i in ld_ticks]) 
-    axins1.set_xlim(0,1)    
 
+    xmin, xmax = 0, 1
+    axins1.set_xlim(xmin,xmax)    
+
+    ############### ##############plot marker ############## ##############
+    for group_index, ref in enumerate(region_ref):
+        x= -0.1
+        y= 0.1 + 0.2 * group_index
+        
+        if len(region_ref) <2:
+            # single-ref mode
+            marker = region_marker_shapes[group_index+1]
+        else:
+            # multi-ref mode
+            marker = region_marker_shapes[group_index]
+        
+        # ([x0,y0][x1,y1])
+        data_to_point =(axins1.bbox.get_points()[1][0]-axins1.bbox.get_points()[0][0]) / (xmax - xmin)
+        s =  data_to_point * 0.075
+        c =  palette[(region_ref_index_dic[region_ref[group_index]]+1)*100 + len(ld_ticks)-1]
+        axins1.scatter(x, y, s=s, marker=marker,c=c, edgecolors="black", linewidths = 1,  clip_on=False, zorder=100)
+    
+    axins1.set_xlim(0,1)   
     axins1.set_aspect('equal', adjustable='box')
+    axins1.tick_params(axis="y", pad=np.sqrt(data_to_point * 0.11))
     axins1.set_title('LD $r^{2}$ with variant',loc="center",y=-0.2)
     cbar = axins1
     return ax1, cbar
@@ -664,6 +697,9 @@ def process_vcf(sumstats,
     sumstats[final_shape_col] = 1
     sumstats[final_rsq_col] = 0.0
     
+    if len(region_ref)==1:
+        sumstats.loc[lead_id, final_shape_col] +=1 
+
     for i in range(len(region_ref)):
         ld_single = "LD_{}".format(i)
         current_rsq = "RSQ_{}".format(i)
@@ -672,7 +708,6 @@ def process_vcf(sumstats,
         sumstats.loc[a_ngt_b, final_ld_col] = 100 * (i+1) + sumstats.loc[a_ngt_b, ld_single]
         sumstats.loc[a_ngt_b, final_rsq_col] = sumstats.loc[a_ngt_b, current_rsq]
         sumstats.loc[a_ngt_b, final_shape_col] = i + 1
-
     ####################################################################################################
     log.write("Finished loading reference genotype successfully!", verbose=verbose)
     return sumstats

gwaslab/viz_plot_scatter_with_reg.py

@@ -0,0 +1,229 @@
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+import scipy.stats as ss
+import seaborn as sns
+import gc
+import math
+import scipy.stats as ss
+from matplotlib.patches import Rectangle
+from adjustText import adjust_text
+from gwaslab.viz_aux_save_figure import save_figure
+from gwaslab.util_in_get_sig import getsig
+from gwaslab.util_in_get_sig import annogene
+from gwaslab.g_Log import Log
+from gwaslab.util_in_correct_winnerscurse import wc_correct
+from gwaslab.util_in_correct_winnerscurse import wc_correct_test
+from gwaslab.g_Sumstats import Sumstats
+from gwaslab.io_process_args import _merge_and_sync_dic
+from gwaslab.io_process_args import _extract_kwargs
+
+def scatter(df, 
+            x, 
+            y,
+            mode="0",
+            reg_box=None,
+            is_reg=True,
+            fdr=False,
+            allele_match=False,
+            r_se=False,
+            is_45_helper_line=False,
+            plt_args=None,
+            xylabel_prefix="Per-allele effect size in ",
+            helper_line_args=None,
+            font_args=None,
+            fontargs=None,
+            build="19",
+            r_or_r2="r",
+            err_kwargs=None,
+            legend_args=None,
+            log = Log(),
+            save=False,
+            reg_xmin=None,
+            verbose=True,
+            save_args=None,
+            scatter_kwargs=None,
+            font_kwargs=None,
+            plt_kwargs=None,
+            null_beta=0,
+            engine="plt",
+            **kwargs):
+    
+    if save_args is None:
+        save_args = {"dpi":300,"facecolor":"white"}
+    if reg_box is None:
+        reg_box = dict(boxstyle='round', facecolor='white', alpha=1,edgecolor="None")
+    if err_kwargs is None:
+        err_kwargs={"ecolor":"#cccccc","elinewidth":1}
+    if font_kwargs is None:
+        font_kwargs={'fontsize':12,'family':'sans','fontname':'Arial'}
+    if helper_line_args is None:
+        helper_line_args={"color":'black', "linestyle":'-',"lw":1}
+    if plt_kwargs is None:
+        plt_kwargs={"figsize":(8,8),"dpi":300}
+    if scatter_kwargs is None:
+        scatter_kwargs={"s":20}
+    if reg_xmin is None:
+        reg_xmin = df[x].min()
+    
+    save_kwargs =      _extract_kwargs("save", save_args, locals())
+    err_kwargs =       _extract_kwargs("err", err_kwargs, locals())
+    plt_kwargs =       _extract_kwargs("plt", plt_kwargs,  locals())
+    scatter_kwargs =   _extract_kwargs("scatter", scatter_kwargs, locals())
+    font_kwargs =      _extract_kwargs("font",font_kwargs, locals())
+
+    log.write("Start to create scatter plot...", verbose=verbose)
+    fig,ax = plt.subplots(**plt_kwargs) 
+
+   # plot x=0,y=0, and a 45 degree line
+    xl,xh=ax.get_xlim()
+    yl,yh=ax.get_ylim()
+
+    #ax.axhline(y=0, zorder=1,**helper_line_args)
+    #ax.axvline(x=0, zorder=1,**helper_line_args)
+    
+    #for spine in ['top', 'right']:
+    #    ax.spines[spine].set_visible(False)
+    
+    log.write(" -Creating scatter plot : {} - {}...".format(x, y), verbose=verbose)
+    if engine=="plt":
+        ax.scatter(df[x],df[y],**scatter_kwargs)
+    elif engine=="sns":
+        sns.scatterplot(data=df,x=x,y=y,ax=ax,**scatter_kwargs)
+    ###regression line##############################################################################################################################
+    ax, reg = confire_regression_line(x, y,
+                                 is_reg,
+                                 reg_box, 
+                                 df, 
+                                 ax, 
+                                 mode,
+                                 xl,
+                                 yl,
+                                 xh,
+                                 yh, 
+                                 null_beta, 
+                                 r_se, 
+                                is_45_helper_line,
+                                helper_line_args, 
+                                font_kwargs,
+                                log, 
+                                verbose, reg_xmin)
+    
+    save_figure(fig = fig, save = save, keyword="scatter", save_args=save_args, log = log, verbose=verbose)
+
+    return fig, ax, reg
+
+
+def confire_regression_line(x, y, is_reg, reg_box, df,  ax, mode,xl,yl,xh,yh, null_beta, r_se, 
+                            is_45_helper_line,helper_line_args, font_kwargs,
+                            log, verbose, reg_xmin):
+    # if N <3
+    if len(df)<3: 
+        is_reg=False
+    
+    if is_reg is True:
+        # reg 
+        # slope, intercept, r, p, slope_se, intercept_se
+        if mode=="0":
+            reg = ss.linregress(df[x],df[y])
+            # estimate se for r
+            if r_se==True:
+                log.write(" -Estimating SE for rsq using Jackknife method.", verbose=verbose)
+                r_se_jackknife = jackknife_r(df,x,y,log,verbose)
+                r_se_jackknife_string = " ({:.2f})".format(r_se_jackknife)
+            else:
+                r_se_jackknife_string= ""
+        else:
+            reg = ss.linregress(df[x],df[y])
+            r_se_jackknife_string= ""
+
+        #### calculate p values based on selected value , default = 0 
+        create_reg_log(reg, log, verbose)
+
+        reg_string = create_reg_string(reg, 
+                    r_se_jackknife_string)
+        
+        ax.text(0.99,0.01, reg_string, va="bottom",ha="right",transform=ax.transAxes,bbox=reg_box,**font_kwargs)
+        
+        ax = create_helper_line(ax, reg[0], is_45_helper_line, helper_line_args, reg_xmin=reg_xmin)
+        ax = create_reg_line(ax, reg, reg_xmin=reg_xmin)
+
+    return ax, reg
+
+#############################################################################################################################################################################
+def create_reg_log(reg,log, verbose):
+    #t_score = (reg[0]-null_beta) / reg[4]
+    #degree = len(df.dropna())-2
+    p =  reg[3]
+    #ss.t.sf(abs(t_score), df=degree)*2
+    log.write(" -Beta = ", reg[0], verbose=verbose)
+    log.write(" -Beta_se = ", reg[4], verbose=verbose)
+    log.write(" -H0 beta =  0",", default p = ", "{:.2e}".format(reg[3]), verbose=verbose)
+    log.write(" -Peason correlation coefficient =  ", "{:.2f}".format(reg[2]), verbose=verbose)
+    log.write(" -r2 =  ", "{:.2f}".format(reg[2]**2), verbose=verbose)
+
+def create_helper_line(ax, 
+                       slope,
+                       is_45_helper_line, 
+                       helper_line_args,
+                       reg_xmin=0):
+    
+    if is_45_helper_line is True:
+        xl,xh=ax.get_xlim()
+        yl,yh=ax.get_ylim()
+        if slope >0:
+            ax.axline([min(xl,yl),min(xl,yl)], [max(xh, yh),max(xh, yh)],zorder=1,**helper_line_args)
+        else:
+            ax.axline([min(xl,yl),-min(xl,yl)], [max(xh, yh),-max(xh, yh)],zorder=1,**helper_line_args)
+
+    return ax
+
+def create_reg_line(ax, reg, reg_xmin=0):
+    xy1 = (reg_xmin,reg[0]*reg_xmin+reg[1])
+    ax.axline(xy1=xy1,slope=reg[0],color="#cccccc",linestyle='--',zorder=1)
+    return ax
+
+def create_reg_string(reg,  
+                      r_se_jackknife_string):
+    p = reg[2]
+    try:
+        p12=str("{:.2e}".format(p)).split("e")[0]
+        pe =str(int("{:.2e}".format(p).split("e")[1]))
+    except:
+        p12="0"
+        pe="0"
+
+    p_text="$p = " + p12 + " \\times  10^{"+pe+"}$"
+    p_latex= f'{p_text}'
+
+    reg_string = "$y =$ "+"{:.2f}".format(reg[1]) +" $+$ "+ "{:.2f}".format(reg[0])+" $x$, "+ p_latex + ", $r =$" +"{:.2f}".format(reg[2])+r_se_jackknife_string
+    
+    return reg_string
+
+def jackknife_r(df,x,y,log,verbose):
+    """Jackknife estimation of se for rsq
+    """
+
+    # dropna
+    df_nona = df.loc[:,[x,y]].dropna()
+    # non-empty entries
+    n=len(df)
+    # assign row number
+    df_nona["_NROW"] = range(n)
+    # a list to store r2
+    r_list=[]
+    # estimate r
+    for i in range(n):
+        # exclude 1 record
+        records_to_use = df_nona["_NROW"]!=i
+        # estimate r
+        reg_jackknife = ss.linregress(df_nona.loc[records_to_use, x],df_nona.loc[records_to_use,y])
+        # add r_i to list
+        r_list.append(reg_jackknife[2])
+
+    # convert list to array
+    rs = np.array(r_list)
+    # https://en.wikipedia.org/wiki/Jackknife_resampling
+    r_se = np.sqrt( (n-1)/n * np.sum((rs - np.mean(rs))**2) )
+    log.write(" -R se (jackknife) = {:.2e}".format(r_se), verbose=verbose)
+    return r_se

gwaslab/viz_plot_stackedregional.py

@@ -143,7 +143,7 @@ def plot_stacked_mqq(objects,
     mqq_args_for_each_plot = _sort_args(mqq_args, n_plot)
     ##########################################################################################################################################
     # get x axis dict
-    if mode=="m":
+    if mode=="m" or mode=="r":
         _posdiccul = _get_chrom_dic(sumstats_list,chrom="CHR",pos="POS",chrpad=0.02)
     else:
         _posdiccul=None

gwaslab/viz_plot_trumpetplot.py

@@ -281,7 +281,7 @@ def plottrumpet(mysumstats,
     sumstats["ABS_BETA"] = sumstats[beta].abs()
 
     ##################################################################################################
-    size_norm = (sumstats["ABS_BETA"].min(), sumstats["ABS_BETA"].max())
+    size_norm = (sumstats[size].min(), sumstats[size].max())
     ## if highlight  ##################################################################################################
     dots = sns.scatterplot(data=sumstats,
                     x=maf,

{gwaslab-3.5.0.dist-info → gwaslab-3.5.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gwaslab
-Version: 3.5.0
+Version: 3.5.2
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/
@@ -20,7 +20,7 @@ Requires-Dist: scipy>=1.12
 Requires-Dist: pySAM==0.22.1
 Requires-Dist: Biopython>=1.79
 Requires-Dist: adjustText<=0.8,>=0.7.3
-Requires-Dist: liftover>=1.1.13
+Requires-Dist: liftover<=1.3.1,>=1.1.13
 Requires-Dist: scikit-allel>=1.3.5
 Requires-Dist: pyensembl==2.2.3
 Requires-Dist: gtfparse==1.3.0
@@ -51,7 +51,7 @@ Warning: Known issues of GWASLab are summarized in [https://cloufield.github.io/
 ### install via pip
 
 ```
-pip install gwaslab==3.4.46
+pip install gwaslab==3.5.0
 ```
 
 ```python

{gwaslab-3.5.0.dist-info → gwaslab-3.5.2.dist-info}/RECORD

@@ -1,22 +1,23 @@
-gwaslab/__init__.py,sha256=7TKJaODdpeuQKibL7gIEa4MtyQ0pmrU-vIHQ-Et27lQ,2433
+gwaslab/__init__.py,sha256=pP_OQwkaXMJokVVU_o6AXnJEBs2HtaMtpcHIls3ezO8,2486
 gwaslab/bd_common_data.py,sha256=2voBqMrIsII1TN5T6uvyDax90fWcJK1Stmo1ZHNGGsE,13898
 gwaslab/bd_config.py,sha256=TP-r-DPhJD3XnRYZbw9bQHXaDIkiRgK8bG9HCt-UaLc,580
 gwaslab/bd_download.py,sha256=cDDk2C5IvjeAzvPvVYGTkI4Ss33DUtEDjGo8eAbQRvY,15663
-gwaslab/bd_get_hapmap3.py,sha256=asNjQYeGfQi8u3jnfenRvDdKMs5ptql5wpcUzqMlwUI,3937
+gwaslab/bd_get_hapmap3.py,sha256=FQpwbhWUPFT152QtiLevEkkN4YcVDIeKzoK0Uz1NlRo,4108
 gwaslab/cache_manager.py,sha256=HOTnSkCOyGEPLRl90WT8D_6pAdI8d8AzenMIDGuCeWc,28113
 gwaslab/g_Log.py,sha256=C3Zv-_6c3C9ms8bgQ-ytplz22sjk7euqXYkWr9zNeAs,1573
 gwaslab/g_Phenotypes.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-gwaslab/g_Sumstats.py,sha256=6bzc7Sf23fIZRP85h-hQJC8DsBl3YLZNBUKJaOboHJQ,36639
+gwaslab/g_Sumstats.py,sha256=eqEpHEH5fnBMsOIufVzwaRp0_vCsuHvGEUe5OzNL41s,36969
 gwaslab/g_SumstatsPair.py,sha256=20snPb4SlI6ftMGVjgxAuyxsxYRQF-GzzlBSnoB-3Lo,8851
 gwaslab/g_SumstatsT.py,sha256=u_DighLMnMxwTLnqm-B58pA0G6WXRj6pudPyKMVKjSU,2133
 gwaslab/g_Sumstats_summary.py,sha256=FECvvFXJVKaCX5dggBvvk9YvJ6AbdbcLfjltysX7wEE,6380
 gwaslab/g_meta.py,sha256=htWlgURWclm9R6UqFcX1a93WN27xny7lGUeyJZOtszQ,2583
 gwaslab/g_vchange_status.py,sha256=w3zsYYOcCaI3PTeboonvkQjudzUAfVIgATzRdiPViZs,1939
-gwaslab/g_version.py,sha256=ll9kIVGycz_99ofwzsFd_semBDePvcEjIqqCgWdVa_8,1885
+gwaslab/g_version.py,sha256=GO-TBEpIUgE6esSkU-I4E8yS1MrCnzKwbYKM7htcJcw,1885
 gwaslab/hm_casting.py,sha256=FqP4EQl83Q2OKLw004OgLIvUH795TVCGwziLk5jsHqY,11368
 gwaslab/hm_harmonize_sumstats.py,sha256=_sZ8soikAxDokw-dcr_CLguBB8OmTmPPS04MfmsJc_Q,79509
 gwaslab/hm_rsid_to_chrpos.py,sha256=ODWREO0jPN0RAfNzL5fRzSRANfhiksOvUVPuEsFZQqA,6552
 gwaslab/io_preformat_input.py,sha256=J8Ny4OPMaLVdo2nP8lTM-c5A8LSdqphSrp9G4i9JjDQ,24097
+gwaslab/io_process_args.py,sha256=KnQWMBwEZjQpCsVMKPrR1qQzeXCg542YdXsP0KwKat8,906
 gwaslab/io_read_ldsc.py,sha256=wsYXpH50IchBKd2dhYloSqc4YgnDkiwMsAweaCoN5Eo,12471
 gwaslab/io_read_tabular.py,sha256=EG-C6KhCutt4J4LlOMgXnqzJvU-EZXzVhMvaDFnHrMM,2380
 gwaslab/io_to_formats.py,sha256=8FmbQjWUIsz_V1Lb80TuwRIXKBgs5t42j25Znougk1Y,29401
@@ -28,7 +29,7 @@ gwaslab/ldsc_parse.py,sha256=MBnfgcWlV4oHp9MoDRh1mpilaHhAR15Af77hMFn4-5k,10564
 gwaslab/ldsc_regressions.py,sha256=yzbGjgNV7u-SWXNPsh9S8y9mK97Bim_Nmad9G9V18ZU,30078
 gwaslab/ldsc_sumstats.py,sha256=O0olsDxKlh1MJ1gAuEN1t40rxhajOEwOQ20ak7xoDrI,26245
 gwaslab/qc_check_datatype.py,sha256=kW68uk4dTLOU2b1dHoVat6n0loundDysAjIqxsXW28Q,3379
-gwaslab/qc_fix_sumstats.py,sha256=rb1Iv05o0tYGGTiXXXJphkx-xVQNKAtlwkDfY-D0yPs,97979
+gwaslab/qc_fix_sumstats.py,sha256=u0YfC70zop2roUfq6mLMNL49m8AHPF2G-j8dKqW25yY,98261
 gwaslab/run_script.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 gwaslab/util_abf_finemapping.py,sha256=LRcopjtkT-iXtKPAJIzR4qjPdhD7nrS_BGit4EW89FM,3054
 gwaslab/util_ex_calculate_ldmatrix.py,sha256=Z_spxbq6SHDS0v84I59YTTF40iyLQIOZbt0dmEcNJjw,15417
@@ -53,24 +54,27 @@ gwaslab/util_in_get_density.py,sha256=kpKXH69acMkeYVG5vs-VbJC3COhmuLBfYco-wuOxgj
 gwaslab/util_in_get_sig.py,sha256=53NOh7KueLY3vJPTNhhb37KPAIgLEfcP3k2zIV61lc4,39845
 gwaslab/util_in_meta.py,sha256=5K9lIZcIgUy0AERqHy1GvMN2X6dp45JUUgopuDLgt4o,11284
 gwaslab/util_in_snphwe.py,sha256=-KpIDx6vn_nah6H55IkV2OyjXQVXV13XyBL069WE1wM,1751
-gwaslab/viz_aux_annotate_plot.py,sha256=i-Fvg_4H6LZvENM6F_yH9-sVSxjD_9LwVhlvgHusW6w,25006
+gwaslab/vis_plot_credible sets.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+gwaslab/viz_aux_annotate_plot.py,sha256=gA-s8a90dsl3MB5CIapdI_DecD9h2FmuqMgy07kMYJI,25207
 gwaslab/viz_aux_chromatin.py,sha256=7cGmej5EkKO7fxR1b5w8r1oRRl9ofVzFRG52SCYWtz0,4109
-gwaslab/viz_aux_quickfix.py,sha256=HnhVvY0GP0EN0gLJ-B11OYiE5PWDcdKGUpQ3QZeu0lE,18592
+gwaslab/viz_aux_property.py,sha256=UIaivghnLXYpTwkKnXRK0F28Jbn9L6OaICk3K73WZaU,33
+gwaslab/viz_aux_quickfix.py,sha256=cGX5i3WBmvKIiqck8V00caDg-pvKOO709Ux3DBXsUrM,18693
 gwaslab/viz_aux_reposition_text.py,sha256=iRIP-Rkltlei068HekJcVubiqPrunBqvAoSQ1eHk04M,4304
-gwaslab/viz_aux_save_figure.py,sha256=GdUXNBOelsWqtTXm8pEZzeGGwDxHYnBkyrGwLOK16ew,2723
+gwaslab/viz_aux_save_figure.py,sha256=x_b4DlTSmHJddfQgoYoReCi4QQbQEtcwCWTKfGetfTA,2768
 gwaslab/viz_plot_compare_af.py,sha256=qtXW45-Sq_ugK8ZfqBYMpmf58SKi3lB3YyHnzn_akcE,5344
-gwaslab/viz_plot_compare_effect.py,sha256=60KlfRGj1TSc0-NCaInZ7GMiAUveXe4qDCjIW-RHJNE,51304
+gwaslab/viz_plot_compare_effect.py,sha256=kq-rVWygHEeTBMOtd_jk8nK85ClZHU-ADSf4nI2gTKo,66604
 gwaslab/viz_plot_forestplot.py,sha256=xgOnefh737CgdQxu5naVyRNBX1NQXPFKzf51fbh6afs,6771
 gwaslab/viz_plot_miamiplot.py,sha256=rCFEp7VNuVqeBBG3WRkmFAtFklbF79BvIQQYiSY70VY,31238
 gwaslab/viz_plot_miamiplot2.py,sha256=xiFCgFX8hEySmCJORpEurMVER9eEXQyy_Ik7mLkbi9g,16015
-gwaslab/viz_plot_mqqplot.py,sha256=nIwS3fMAXv_LVn7l9koSFZiZbcKCyuVq6Qg5fMzrEps,67049
-gwaslab/viz_plot_phe_heatmap.py,sha256=vCCPAiTyBBVklZahXG_zmyxXPgm0d7ArVha7A6gJaok,9514
+gwaslab/viz_plot_mqqplot.py,sha256=mfmHseYHIFoEfSKBX46ps6abSQ6t9xDNahLDLLj4K8I,67924
+gwaslab/viz_plot_phe_heatmap.py,sha256=qoXVeFTIm-n8IinNbDdPFVBSz2yGCGK6QzTstXv6aj4,9532
 gwaslab/viz_plot_qqplot.py,sha256=psQgVpP29686CEZkzQz0iRbApzqy7aE3GGiBcazVvNw,7247
-gwaslab/viz_plot_regional2.py,sha256=tBoGox-4ngL5o_twdIjk_VW6Iam3JDyrPKuttm6_4Sg,36862
+gwaslab/viz_plot_regional2.py,sha256=g9cGI5sPAH32WR0ICvZB1wMG5butMgpdxYtxZUfG6fE,38314
 gwaslab/viz_plot_regionalplot.py,sha256=8u-5-yfy-UaXhaxVVz3Y5k2kBAoqzczUw1hyyD450iI,37983
 gwaslab/viz_plot_rg_heatmap.py,sha256=PidUsgOiEVt6MfBPCF3_yDhOEytZ-I1q-ZD6_0pFrV4,13713
-gwaslab/viz_plot_stackedregional.py,sha256=IRugpwLjqKdwuSVTQtCM36Rk4Gpv6MxdsGIWVj6vk8w,16651
-gwaslab/viz_plot_trumpetplot.py,sha256=ZHdc6WcVx0-oKoj88yglRkmB4bS9pOiEMcuwKW35Yvo,42672
+gwaslab/viz_plot_scatter_with_reg.py,sha256=PmUZDQl2q4Dme3HLPXEwf_TrMjwJADA-uFXNDBWUEa4,8333
+gwaslab/viz_plot_stackedregional.py,sha256=HfNUhwxevbwSoauE0ysG020U7YFVy4111nkIWdaJ4Q8,16664
+gwaslab/viz_plot_trumpetplot.py,sha256=uuEdHNr2ZBXJkOMA6uu0OzKFh0de-BxOnPsUAYqwqOU,42660
 gwaslab/data/formatbook.json,sha256=N2nJs80HH98Rsu9FxaSvIQO9J5yIV97WEtAKjRqYwiY,38207
 gwaslab/data/reference.json,sha256=IrjwFnXjrpVUp3zYfcYClpibJE9Y-94gtrC1Aw8sXxg,12332
 gwaslab/data/chrx_par/chrx_par_hg19.bed.gz,sha256=LocZg_ozhZjQiIpgWCO4EYCW9xgkEKpRy1m-YdIpzQs,83
@@ -79,9 +83,9 @@ gwaslab/data/hapmap3_SNPs/hapmap3_db150_hg19.snplist.gz,sha256=qD9RsC5S2h6l-OdpW
 gwaslab/data/hapmap3_SNPs/hapmap3_db151_hg38.snplist.gz,sha256=Y8ZT2FIAhbhlgCJdE9qQVAiwnV_fcsPt72usBa7RSBM,10225828
 gwaslab/data/high_ld/high_ld_hla_hg19.bed.gz,sha256=R7IkssKu0L4WwkU9SrS84xCMdrkkKL0gnTNO_OKbG0Y,219
 gwaslab/data/high_ld/high_ld_hla_hg38.bed.gz,sha256=76CIU0pibDJ72Y6UY-TbIKE9gEPwTELAaIbCXyjm80Q,470
-gwaslab-3.5.0.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-gwaslab-3.5.0.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
-gwaslab-3.5.0.dist-info/METADATA,sha256=SocHVFBOrjeEchxsvVLUgI4CZPwSypppxfSE7o7yp1I,7751
-gwaslab-3.5.0.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
-gwaslab-3.5.0.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
-gwaslab-3.5.0.dist-info/RECORD,,
+gwaslab-3.5.2.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+gwaslab-3.5.2.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
+gwaslab-3.5.2.dist-info/METADATA,sha256=KYa_HwVvvyGlZeookgHHJAUgfde0d5YqitViCSmEU8M,7758
+gwaslab-3.5.2.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+gwaslab-3.5.2.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
+gwaslab-3.5.2.dist-info/RECORD,,

{gwaslab-3.5.0.dist-info → gwaslab-3.5.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.2.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any