gwaslab 3.5.5__py3-none-any.whl → 3.5.7__py3-none-any.whl

gwaslab/viz_plot_regional2.py

@@ -36,12 +36,8 @@ def _plot_regional(
     region,
     vcf_path,
     marker_size,
-    fontsize,
     build,
-    chrom_df,
-    xtick_chr_dict,
     cut_line_color,
-    vcf_chr_dict = None,
     gtf_path="default",
     gtf_chr_dict = get_number_to_chr(),
     gtf_gene_name=None,
@@ -50,23 +46,29 @@ def _plot_regional(
     rr_chr_dict = get_number_to_chr(),
     rr_lim = (0,100),
     rr_ylabel = True,
-    rr_title=None,
     region_ld_legend=True,
     region_title=None,
     mode="mqq",
     region_step = 21,
     region_ref=None,
     region_ref_index_dic = None,
+    region_ref_alias = None,
     #region_ref_second=None,
     region_grid = False,
     region_grid_line = {"linewidth": 2,"linestyle":"--"},
     region_lead_grid = True,
     region_lead_grid_line = {"alpha":0.5,"linewidth" : 2,"linestyle":"--","color":"#FF0000"},
     region_title_args = None,
-    region_hspace=0.02,
     region_ld_threshold = [0.2,0.4,0.6,0.8],
-    region_ld_colors = ["#E4E4E4","#020080","#86CEF9","#24FF02","#FDA400","#FF0000","#FF0000"],
     region_marker_shapes=None,
+    cbar_fontsize=None,
+    cbar_scale=False,
+    cbar_bbox_to_anchor=None,
+    cbar_w_scale=1,
+    cbar_h_scale=1,
+    cbar_downward_offset =1.3, 
+    cbar_borderpad=None,
+    cbar_equal_aspect=False,
     palette=None,
     region_recombination = True,
     region_protein_coding=True,
@@ -75,8 +77,6 @@ def _plot_regional(
     track_font_family="Arial",
     taf=[4,0,0.95,1,1],
     # track_n, track_n_offset,font_ratio,exon_ratio,text_offset
-    tabix=None,
-    chrom="CHR",
     pos="POS",
     verbose=True,
     log=Log()
@@ -132,7 +132,16 @@ def _plot_regional(
                             region_ref=region_ref,
                             region_ld_threshold=region_ld_threshold, 
                             region_ref_index_dic=region_ref_index_dic,
+                            region_ref_alias=region_ref_alias, 
                             region_marker_shapes=region_marker_shapes,
+                            cbar_fontsize= cbar_fontsize,
+                            cbar_scale=cbar_scale,
+                            cbar_equal_aspect=cbar_equal_aspect,
+                            cbar_bbox_to_anchor=cbar_bbox_to_anchor,
+                            cbar_w_scale=cbar_w_scale,
+                            cbar_h_scale=cbar_h_scale,
+                            cbar_downward_offset =cbar_downward_offset, 
+                            cbar_borderpad=cbar_borderpad,
                             palette=palette,
                             region_legend_marker=region_legend_marker,
                             fig=fig)
@@ -154,6 +163,8 @@ def _plot_regional(
                                         build= build,
                                         rr_lim=rr_lim,
                                         rr_ylabel=rr_ylabel)
+    else:
+        ax4 = None
      
     ## regional plot : gene track ######################################################################
                 # calculate offset
@@ -205,7 +216,7 @@ def _plot_regional(
         if "r" in mode:
             if gtf_path is not None: 
                 ax3.set_xticks(np.linspace(gene_track_start_i+region[1], gene_track_start_i+region[2], num=region_step))
-                ax3.set_xticklabels(region_ticks,rotation=45,fontsize=fontsize,family="sans-serif")
+                ax3.set_xticklabels(region_ticks,rotation=45)
             
             if region_grid==True:
                 for i in np.linspace(gene_track_start_i+region[1], gene_track_start_i+region[2], num=region_step):
@@ -221,7 +232,7 @@ def _plot_regional(
         else:
             # set x ticks m plot
             ax1.set_xticks(np.linspace(gene_track_start_i+region[1], gene_track_start_i+region[2], num=region_step))
-            ax1.set_xticklabels(region_ticks,rotation=45,fontsize=fontsize,family="sans-serif")
+            ax1.set_xticklabels(region_ticks,rotation=45)
     
         ax1.set_xlim([gene_track_start_i+region[1], gene_track_start_i+region[2]])
 
@@ -345,25 +356,52 @@ 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,region_marker_shapes,fig, region_legend_marker=True,palette =None, position=1):
+def _add_ld_legend(sumstats, ax1, region_ld_threshold, region_ref,region_ref_index_dic,region_marker_shapes,fig, region_legend_marker=True,
+                   cbar_fontsize= None,cbar_scale=False,cbar_equal_aspect=True,cbar_w_scale=1,cbar_h_scale=1,palette =None, 
+                   cbar_downward_offset =1.2, cbar_borderpad=None,
+                   cbar_bbox_to_anchor=(0, 0, 1, 1),region_ref_alias=None):
+
+    scale = 1
+    if cbar_scale:
+        base_fontsize = 9
+        scale = cbar_fontsize / base_fontsize
+        scale = max(1,scale)
+    else:
+        scale = 1
+    
+    width_raw= 11 * (scale)*cbar_w_scale
+    height_raw=(7 + 7 * len(region_ref))*(scale)*cbar_h_scale
+
+    width_pct = "{}%".format(width_raw)
+    height_pct = "{}%".format( height_raw)
+
+    total_y_pixels =(ax1.bbox.get_points()[1][1]-ax1.bbox.get_points()[0][1]) 
+    downwards_offset = cbar_fontsize / (total_y_pixels/ fig.dpi * 72) * cbar_downward_offset
+    bbox_to_anchor = (cbar_bbox_to_anchor[0],cbar_bbox_to_anchor[1]-downwards_offset,cbar_bbox_to_anchor[2],cbar_bbox_to_anchor[3])
     
-    width_pct = "11%"
-    height_pct = "{}%".format( 14 + 7 * len(region_ref))
+    if cbar_borderpad is None:
+        borderpad=0.5*(scale)
+    else:
+        borderpad=cbar_borderpad
+
     axins1 = inset_axes(ax1,
             width=width_pct,  # width = 50% of parent_bbox width
             height=height_pct,  # height : 5%
+            bbox_to_anchor=bbox_to_anchor,
+            bbox_transform=ax1.transAxes,
+            borderpad=borderpad,
             loc='upper right',
-            axes_kwargs={"frameon":True,"facecolor":"white","zorder":999999})
-    
+            axes_kwargs={"frameon":True,"facecolor":"white","zorder":999999,"anchor":"NE"})
+
     ld_ticks = [0]+region_ld_threshold+[1]
 
     for index, ld_threshold in enumerate(ld_ticks):
         for group_index in range(len(region_ref)):
             if index < len(ld_ticks)-1:            
                 x=ld_threshold
-                y=0.2*group_index
+                y=0.2*group_index 
                 width=0.2
-                height=ld_ticks[index+1]-ld_ticks[index]
+                height=(ld_ticks[index+1]-ld_ticks[index]) 
                 hex_color = palette[(region_ref_index_dic[region_ref[group_index]]+1)*100 + index+1] # consistent color
                 
                 a = Rectangle((x,y),width, height, fill = True, color = hex_color , linewidth = 2)
@@ -371,22 +409,46 @@ def _add_ld_legend(sumstats, ax1, region_ld_threshold, region_ref,region_ref_ind
                 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])
-    axins1.set_ylim(0,0.2*len(region_ref))    
-    
+    if region_ref_alias is None:
+        region_ref_name = region_ref
+    else:
+        region_ref_name = [region_ref_alias[i] for i in region_ref]
+
+    yticks_position = (0.1 + 0.2 *np.arange(0,len(region_ref_name)))
+    axins1.set_yticks(yticks_position, ["{}".format(x) for x in region_ref_name])
+    axins1.set_ylim(0,0.2*len(region_ref_name))    
+    ymin, ymax=0,0.2*len(region_ref_name)
     # x ld thresholds
+    
     axins1.set_xticks(ticks=ld_ticks) 
     axins1.set_xticklabels([str(i) for i in ld_ticks]) 
-
     xmin, xmax = 0, 1
-    axins1.set_xlim(xmin,xmax)    
+    axins1.set_xlim(xmin,xmax)       
+
+    if cbar_equal_aspect==True:
+        axins1.set_aspect('equal', adjustable='box',anchor="NE")
 
     ############### ##############plot marker ############## ##############
     if region_legend_marker==True:
         for group_index, ref in enumerate(region_ref):
-            x= -0.1
-            y= 0.1 + 0.2 * group_index
+
+            data_to_point_y =((axins1.bbox.get_points()[1][1]-axins1.bbox.get_points()[0][1])*height_raw/(ymax -ymin))
+            data_to_point_x =((axins1.bbox.get_points()[1][0]-axins1.bbox.get_points()[0][0])*width_raw/(xmax -xmin))
+            y_to_x = data_to_point_y/data_to_point_x
+            x_to_y = 1/y_to_x
+            xyratio = min(y_to_x, x_to_y)
+            
+            marker_side_in_data = 0.075
+            if cbar_equal_aspect==True:
+                xyratio=1
+            
+            ## change markersize
+
+            if xyratio <1 :
+                x = 0 - (marker_side_in_data +0.03) * xyratio
+            else:
+                x = 0 - (marker_side_in_data +0.03)
+            y= (0.1 + 0.2 * group_index)
             
             if len(region_ref) <2:
                 # single-ref mode
@@ -398,21 +460,36 @@ def _add_ld_legend(sumstats, ax1, region_ld_threshold, region_ref,region_ref_ind
                 c =  palette[(region_ref_index_dic[region_ref[group_index]]+1)*100 + len(ld_ticks)-1]
             
             # ([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 * 0.15*0.11/(fig.dpi/72))**2 
+            #  y pixels / per data 1
+            
+            data_to_point_y =((axins1.bbox.get_points()[1][1]-axins1.bbox.get_points()[0][1])*height_raw/(ymax -ymin))
+            data_to_point_x =((axins1.bbox.get_points()[1][0]-axins1.bbox.get_points()[0][0])*width_raw/(xmax -xmin))
+            
+            if data_to_point_y < data_to_point_x:
+                length_raw = 1 #height_raw
+                data_to_point = data_to_point_y
+            else:
+                length_raw = 1 #width_raw
+                data_to_point = data_to_point_x
+
+            # pixels/data 1 -> font points/data 1  
+            #  (dpi / 72) = point_per_pixel
+            # y pixels / per data 1 / (dpi / 72)  -> y font points/data 1  
+            
+            font_points_per_data_1 = data_to_point/(fig.dpi/72)
+            s =  ((marker_side_in_data*2)* font_points_per_data_1 * length_raw/100 )**2     
             
             axins1.scatter(x, y, s=s, marker=marker,c=c, edgecolors="black", linewidths = 1,  clip_on=False, zorder=100)
-            axins1.tick_params(axis="y", pad=data_to_point* 0.11* 0.19/(fig.dpi/72))
-    
-    axins1.set_xlim(0,1)   
-    axins1.set_aspect('equal', adjustable='box')
-    #axins1.tick_params(axis="y", pad=data_to_point* 0.11* 0.19/(fig.dpi/72))
-    axins1.set_title('LD $r^{2}$ with variant',loc="center",y=-0.2)
+
+            pad = ((marker_side_in_data*2+0.02)* font_points_per_data_1 * length_raw/100)
+            tick_length=(abs(x)* font_points_per_data_1 * length_raw/100)
+            axins1.tick_params(axis="y", pad=pad-0.5*tick_length, length=tick_length) 
+
     cbar = axins1
     return ax1, cbar
 
 # -############################################################################################################################################################################
-def  _plot_recombination_rate(sumstats,pos, region, ax1, rr_path, rr_chr_dict, rr_header_dict, build,rr_lim,rr_ylabel=True):
+def  _plot_recombination_rate(sumstats,pos, region, ax1, rr_path, rr_chr_dict, rr_header_dict, build,rr_lim, rr_ylabel=True):
     ax4 = ax1.twinx()
     most_left_snp = sumstats["i"].idxmin()
     
@@ -479,12 +556,15 @@ def _plot_gene_track(
     stack_num_to_plot = max(taf[0],n_uniq_stack)
     ax3.set_ylim((-stack_num_to_plot*2-taf[1]*2,2+taf[1]*2))
     ax3.set_yticks([])
-    pixels_per_point = 72/fig.dpi
+    point_per_pixels = 72/fig.dpi
+    pixels_per_point = fig.dpi/72
+
     pixels_per_track = np.abs(ax3.transData.transform([0,0])[1] - ax3.transData.transform([0,1])[1])                   
     font_size_in_pixels= taf[2] * pixels_per_track
-    font_size_in_points =  font_size_in_pixels * pixels_per_point
-    linewidth_in_points=   pixels_per_track * pixels_per_point
+    font_size_in_points =  font_size_in_pixels * point_per_pixels
 
+    linewidth_in_points_per_track=   pixels_per_track * point_per_pixels
+    
     log.write(" -plotting gene track..", verbose=verbose)
     
     sig_gene_name = "Undefined"
@@ -517,8 +597,11 @@ def _plot_gene_track(
                 sig_gene_rights.append(gene_track_start_i+row["end"])
 
         # plot gene line
+        ## minimum width = 2 pixel 
+        gene_line_width = max(linewidth_in_points_per_track/10, 2/pixels_per_point)
+        
         ax3.plot((gene_track_start_i+row["start"],gene_track_start_i+row["end"]),
-                    (row["stack"]*2,row["stack"]*2),color=gene_color,linewidth=linewidth_in_points/10,solid_capstyle="butt")
+                    (row["stack"]*2,row["stack"]*2),color=gene_color,linewidth=gene_line_width,solid_capstyle="butt")
         
         # plot gene name
         if row["end"] >= region[2]:
@@ -549,9 +632,12 @@ def _plot_gene_track(
                 exon_color = region_lead_grid_line["color"]  
             else:
                 exon_color="#020080"
-        
+
+        ## minimum width = 8 pixel 
+        exon_line_width = max(linewidth_in_points_per_track * taf[3],  8/pixels_per_point) 
+
         ax3.plot((gene_track_start_i+row["start"],gene_track_start_i+row["end"]),
-                    (row["stack"]*2,row["stack"]*2),linewidth=linewidth_in_points*taf[3],color=exon_color,solid_capstyle="butt")
+                    (row["stack"]*2,row["stack"]*2),linewidth=exon_line_width,color=exon_color,solid_capstyle="butt")
 
     log.write(" -Finished plotting gene track..", verbose=verbose)
 
@@ -573,7 +659,6 @@ def process_vcf(sumstats,
                 region_ld_threshold, 
                 vcf_chr_dict,
                 tabix):
-
     log.write("Start to load reference genotype...", verbose=verbose)
     log.write(" -reference vcf path : "+ vcf_path, verbose=verbose)
 
@@ -631,7 +716,6 @@ def process_vcf(sumstats,
             # figure out lead variant
             lead_id = _get_lead_id(sumstats, region_ref_single, log, verbose)
         
-
         lead_series = None
         if lead_id is None:
             
@@ -685,6 +769,12 @@ def process_vcf(sumstats,
         else:
             log.write(" -Lead SNP not found in reference...", verbose=verbose)
             sumstats[rsq]=None
+            
+            # 
+            try:
+                sumstats.loc[lead_id,rsq]=1
+            except KeyError:
+                pass
         
         sumstats[rsq] = sumstats[rsq].astype("float")
         sumstats[ld_single] = 0
@@ -716,7 +806,7 @@ def process_vcf(sumstats,
     sumstats[final_ld_col]  = 0
     sumstats[final_shape_col] = 1
     sumstats[final_rsq_col] = 0.0
-    
+
     if len(region_ref)==1:
         if lead_id is not None:
             sumstats.loc[lead_id, final_shape_col] +=1 
@@ -729,6 +819,8 @@ 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
+    
+    sumstats = sumstats.dropna(subset=[pos,nea,ea])
     ####################################################################################################
     log.write("Finished loading reference genotype successfully!", verbose=verbose)
     return sumstats

gwaslab/viz_plot_rg_heatmap.py

@@ -37,7 +37,7 @@ def plot_rg(ldscrg,
         corrections=None,
         panno_texts=None,
         equal_aspect=True,
-        cmap = matplotlib.cm.get_cmap('RdBu'),
+        cmap = None,
         full_cell =None,
         log=Log(),
         panno_args=None,
@@ -57,6 +57,11 @@ def plot_rg(ldscrg,
     
     log.write("Start to create ldsc genetic correlation heatmap..." ,verbose=verbose)
     # configure arguments
+    if cmap is None:
+        try: #matplotlib <3.9
+            cmap = matplotlib.cm.get_cmap('RdBu')
+        except:
+            cmap = matplotlib.colormaps.get_cmap('RdBu')
     if fig_args is None:
         fig_args = {"dpi":300}
     if colorbar_args is None:

gwaslab/viz_plot_stackedregional.py

@@ -56,7 +56,7 @@ def plot_stacked_mqq(   objects,
                         gtf=None,
                         gene_track_height=0.5,
                         fig_args=None,
-                        region_hspace=0.05,
+                        region_hspace=0.07,
                         subplot_height=4,
                         region_lead_grids = None,
                         region_lead_grid_line=None,
@@ -113,10 +113,10 @@ def plot_stacked_mqq(   objects,
     if region_ld_legends is None:
         region_ld_legends = [0]
     if title_args is None:
-        title_args = {"family":"Arial"}
+        title_args = {"family":font_family}
     else:
         if "family" not in title_args.keys():
-            title_args["family"] = "Arial"
+            title_args["family"] = font_family
 
     if save is not None:
         if type(save) is not bool:
@@ -124,10 +124,17 @@ def plot_stacked_mqq(   objects,
                 if save[-3:]=="pdf" or save[-3:]=="svg":
                     log.write(" -Adjusting options for saving as pdf/svg...",verbose=verbose)
                     fig_args["dpi"]=72
+                    
                     if "scatter_args" not in  mqq_args.keys():
                         mqq_args["scatter_args"]={"rasterized":True}
                     else:
                         mqq_args["scatter_args"]["rasterized"] = True
+
+                    if mode=="r":
+                        if "scatter_args" not in  mqq_args.keys():
+                            mqq_args["scatter_args"]={"rasterized":False}
+                        else:
+                            mqq_args["scatter_args"]["rasterized"] = False
                 else:
                     fig_args["dpi"] = save_args["dpi"]
     # create figure and axes ##################################################################################################################
@@ -178,7 +185,6 @@ def plot_stacked_mqq(   objects,
     ##########################################################################################################################################
     mqq_args_for_each_plot = _sort_args(mqq_args, n_plot)
 
-
     ##########################################################################################################################################
     # get x axis dict
     if mode=="m" or mode=="r":
@@ -364,10 +370,15 @@ def _add_new_y_label(mode, fig, gene_track_height,n_plot,subplot_height ,fontsiz
     gene_track_height_ratio = gene_track_height/(gene_track_height + n_plot*subplot_height)
     ylabel_height = (1 - gene_track_height_ratio)*0.5 + gene_track_height_ratio
     if mode=="r":
-        fig.text(0.08, ylabel_height , "$-log_{10}(P)$", va='center', rotation='vertical',fontsize=fontsize,family=font_family)
+        fig.text(0.08, ylabel_height , "$\mathregular{-log_{10}(P)}$", va='center', rotation='vertical',
+                 fontsize=fontsize,
+                 family=font_family)
+        
         fig.text(0.93, ylabel_height, "Recombination rate(cM/Mb)", va='center', rotation=-90,fontsize=fontsize,family=font_family)
     elif mode=="m":
-        fig.text(0.08, ylabel_height , "$-log_{10}(P)$", va='center', rotation='vertical',fontsize=fontsize,family=font_family)    
+        fig.text(0.08, ylabel_height , "$\mathregular{-log_{10}(P)}$", va='center', rotation='vertical',
+                 fontsize=fontsize,
+                 family=font_family)    
 
 def _sort_args(mqq_args, n_plot):
     mqq_args_for_each_plot={i:{} for i in range(n_plot)}

{gwaslab-3.5.5.dist-info → gwaslab-3.5.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: gwaslab
-Version: 3.5.5
+Version: 3.5.7
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/
@@ -8,7 +8,7 @@ Project-URL: Github, https://github.com/Cloufield/gwaslab
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Requires-Python: <3.11,>=3.9
+Requires-Python: <3.13,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: LICENSE_before_v3.4.39

{gwaslab-3.5.5.dist-info → gwaslab-3.5.7.dist-info}/RECORD

@@ -1,4 +1,4 @@
-gwaslab/__init__.py,sha256=wyK0byyNw9vz6bcZDOA8r81-weibcnbNGggx_K6pT7s,2539
+gwaslab/__init__.py,sha256=2pIyLhHrPeyBYlcs3QsWElmUWPGIxoCf68awTk05YQk,2585
 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
@@ -6,16 +6,17 @@ gwaslab/bd_get_hapmap3.py,sha256=FQpwbhWUPFT152QtiLevEkkN4YcVDIeKzoK0Uz1NlRo,410
 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=M85hI9HkyzUV9RqCdIBpoIlD9uA7QDcdlq1M-Fpvv_M,37769
+gwaslab/g_Sumstats.py,sha256=QwXIqnjEd5v1jFRBFmeVlWJr3fO6Hx5hudLOgEf5fmc,39321
 gwaslab/g_SumstatsPair.py,sha256=71fPfwhr9pdH9pdyX17bSEu8ah_WVpTVU0nc_4uln4Y,8766
+gwaslab/g_SumstatsSet.py,sha256=AiTISWPfmu8NTGa8j9Yuts8DNw1pEUENYyPoS0HXp5I,29866
 gwaslab/g_SumstatsT.py,sha256=u_DighLMnMxwTLnqm-B58pA0G6WXRj6pudPyKMVKjSU,2133
 gwaslab/g_Sumstats_summary.py,sha256=FECvvFXJVKaCX5dggBvvk9YvJ6AbdbcLfjltysX7wEE,6380
 gwaslab/g_headers.py,sha256=Q37MZgc2G1bMzzJX94Kq6GoRYJyfUxQX50CvyIerXww,6524
 gwaslab/g_meta.py,sha256=Orj8WhFvbylDmaAp9Px_GRUoyEBVML8MLa9829sNM0o,2588
 gwaslab/g_vchange_status.py,sha256=w3zsYYOcCaI3PTeboonvkQjudzUAfVIgATzRdiPViZs,1939
-gwaslab/g_version.py,sha256=xQqOnBdKHR2JYgA4nuFyJcsmUNx3MbwJg640M-_N40Y,1889
+gwaslab/g_version.py,sha256=AdCrtpOcYXhFe4LFCH2xi4r0VT1oQG7Coqhyl842u8w,1889
 gwaslab/hm_casting.py,sha256=FqP4EQl83Q2OKLw004OgLIvUH795TVCGwziLk5jsHqY,11368
-gwaslab/hm_harmonize_sumstats.py,sha256=_sZ8soikAxDokw-dcr_CLguBB8OmTmPPS04MfmsJc_Q,79509
+gwaslab/hm_harmonize_sumstats.py,sha256=ymM33bwOOkLteiLXUuSSzURudgCrkVMTR7wUwXf1jQs,84381
 gwaslab/hm_rsid_to_chrpos.py,sha256=ODWREO0jPN0RAfNzL5fRzSRANfhiksOvUVPuEsFZQqA,6552
 gwaslab/io_preformat_input.py,sha256=cfoywijnk1z1QeTMOXL_lqcheI3GA_Ff4uOUNxAqCq4,25331
 gwaslab/io_process_args.py,sha256=0ljJOVGsD7qPuBLvdfvR7Vrh7zXPlvfPg-rhOw8xRpQ,1366
@@ -31,13 +32,13 @@ 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=mAM0LCMf9LseX44oeELG0croPlxfp7U8A8TH-Y5F6kQ,4453
-gwaslab/qc_fix_sumstats.py,sha256=u0YfC70zop2roUfq6mLMNL49m8AHPF2G-j8dKqW25yY,98261
+gwaslab/qc_fix_sumstats.py,sha256=4lXedhYGsd6BAoApBr7kEly_GbVdcXgBQXMB5X2iN70,98262
 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
 gwaslab/util_ex_calculate_prs.py,sha256=9uJ588Sdj4V0vw3OZ9NeLECwOvW67f0IdLandVPS5RY,9442
 gwaslab/util_ex_gwascatalog.py,sha256=--Gde9HrsikfYTeFqSaYz0gUODr9wmv_gV6GZGNlElg,7688
-gwaslab/util_ex_ldproxyfinder.py,sha256=wWNW9wITWozj23gT41LR00WxU-rrHpGKbxs2H_3jEyM,9431
+gwaslab/util_ex_ldproxyfinder.py,sha256=HadmnjEv5EvZCHR5SFSAbqxZWJryEErJftCS0WhZUbs,16898
 gwaslab/util_ex_ldsc.py,sha256=dMfL7hej0JzTOafPk6VYl5HUxB3eSp28wUKVWliIhlE,18937
 gwaslab/util_ex_plink_filter.py,sha256=pK1Yxtv9-J4rMOdVAG7VU9PktvI6-y4FxBiVEH0QuRs,1673
 gwaslab/util_ex_process_h5.py,sha256=ynFvo3zxgvOxWYL565v2IQf8P6iEuq7UlKQ_ULxrd6Y,2831
@@ -50,10 +51,11 @@ gwaslab/util_in_calculate_gc.py,sha256=MWOXVzJv7SZx4i2_ncRiqsiEOADc7EfghaUzgGy4j
 gwaslab/util_in_calculate_power.py,sha256=JfHJFg3tNF0f4NHgWlzVW2mSxCiP07mAHIyEfVfxTak,10360
 gwaslab/util_in_convert_h2.py,sha256=a8Cbudt3xn9WP2bPc-7ysuowB-LYub8j8GeDXl7Lk7Q,6483
 gwaslab/util_in_correct_winnerscurse.py,sha256=Gp--yAQ8MMzdkWIvXP9C1BHVjZc-YzqHfYWhAj19w9w,2110
-gwaslab/util_in_fill_data.py,sha256=wQwx3vtN1gJzJKc_FUZRk5xLLza1OeUa90z7d9G1Iis,14934
-gwaslab/util_in_filter_value.py,sha256=DXAjIei9OkD-4C3CSkMEu-9vwVB5-vvLP4wospzlDEE,24252
+gwaslab/util_in_fill_data.py,sha256=ZXdxRD7oUpQ-uG_5EVsS994rA1n3PqLbZ2TxOKz379w,15762
+gwaslab/util_in_filter_value.py,sha256=KnHazy2Z3wSLULFRfp-Sm7TQ2gGLqU6kxnkhETgVPPg,26501
 gwaslab/util_in_get_density.py,sha256=kpKXH69acMkeYVG5vs-VbJC3COhmuLBfYco-wuOxgjc,3934
 gwaslab/util_in_get_sig.py,sha256=53NOh7KueLY3vJPTNhhb37KPAIgLEfcP3k2zIV61lc4,39845
+gwaslab/util_in_merge.py,sha256=KB5VKRTUUZ1XGYUxgCP_l3cWYanjthMdwiZ_DincCZQ,2020
 gwaslab/util_in_meta.py,sha256=5K9lIZcIgUy0AERqHy1GvMN2X6dp45JUUgopuDLgt4o,11284
 gwaslab/util_in_snphwe.py,sha256=-KpIDx6vn_nah6H55IkV2OyjXQVXV13XyBL069WE1wM,1751
 gwaslab/viz_aux_annotate_plot.py,sha256=3PyBioC-3ZBzqKT2JRv6vp-hZUXSqTTePIT5cblEvnQ,25334
@@ -61,21 +63,22 @@ gwaslab/viz_aux_chromatin.py,sha256=aWZaXOSvGyZY7wQcoFDaqHRYCSHZbi_K4Q70HruN9ts,
 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=x_b4DlTSmHJddfQgoYoReCi4QQbQEtcwCWTKfGetfTA,2768
+gwaslab/viz_aux_save_figure.py,sha256=HwIRDMYpeXfkBgb7mqzLN7OVPMz163U-ZVOlQJABzeg,2811
 gwaslab/viz_plot_compare_af.py,sha256=qtXW45-Sq_ugK8ZfqBYMpmf58SKi3lB3YyHnzn_akcE,5344
 gwaslab/viz_plot_compare_effect.py,sha256=kq-rVWygHEeTBMOtd_jk8nK85ClZHU-ADSf4nI2gTKo,66604
 gwaslab/viz_plot_credible_sets.py,sha256=KxB7_bkDrLMgs6sk8HAnZWkllIRH-lEDCz5n5_Jnw68,3550
+gwaslab/viz_plot_effect.py,sha256=7p3YnGcgIG0ajwQSNCiHlmX9BvEeClwvQ-DhPe5LzSI,9750
 gwaslab/viz_plot_forestplot.py,sha256=xgOnefh737CgdQxu5naVyRNBX1NQXPFKzf51fbh6afs,6771
 gwaslab/viz_plot_miamiplot.py,sha256=rCFEp7VNuVqeBBG3WRkmFAtFklbF79BvIQQYiSY70VY,31238
-gwaslab/viz_plot_miamiplot2.py,sha256=nA8xAI0ou3rBobm3DygOQSpunhZWwXVilKVd0v4Jfac,16213
-gwaslab/viz_plot_mqqplot.py,sha256=AdEqATd6kpdwP_rQbwDIP6usJG3OUOSzfr43h3TKpmM,68710
+gwaslab/viz_plot_miamiplot2.py,sha256=tr3vRq6NLmoVoOSYbUkvXMHRONLLrvqjkRYN1iSX5-I,16214
+gwaslab/viz_plot_mqqplot.py,sha256=VIlAFL0lq4nEzqMh17I9d9u6HjCX3Jku69XHwIm1Fmw,69836
 gwaslab/viz_plot_phe_heatmap.py,sha256=qoXVeFTIm-n8IinNbDdPFVBSz2yGCGK6QzTstXv6aj4,9532
 gwaslab/viz_plot_qqplot.py,sha256=psQgVpP29686CEZkzQz0iRbApzqy7aE3GGiBcazVvNw,7247
-gwaslab/viz_plot_regional2.py,sha256=rvvIU60pOJFiDReQFd_Q2MkthuwvNOUkptV1swP9uJM,39444
+gwaslab/viz_plot_regional2.py,sha256=EcLHhdWMj3YPtN-YOkXG9W6qf-lktTFlRMFRRQvY9kA,43106
 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_rg_heatmap.py,sha256=z-G4gxK5-H_e13jV8RQnNzXPrKSQ0c7q41-KpMrA-cs,13861
 gwaslab/viz_plot_scatter_with_reg.py,sha256=PmUZDQl2q4Dme3HLPXEwf_TrMjwJADA-uFXNDBWUEa4,8333
-gwaslab/viz_plot_stackedregional.py,sha256=WckcESSIHQuRCN37cnjzWLWiHCrQT3kUVkRCFiq2bk8,18614
+gwaslab/viz_plot_stackedregional.py,sha256=gt-pj4c4AMgmlNgOCKlpCWJN1iU_Z5NYljITRc-OyI4,19032
 gwaslab/viz_plot_trumpetplot.py,sha256=y4sAFjzMaSLuWrdr9_ao-wPYCK5DlP2ykiqulWsoN_k,42680
 gwaslab/data/formatbook.json,sha256=N2nJs80HH98Rsu9FxaSvIQO9J5yIV97WEtAKjRqYwiY,38207
 gwaslab/data/reference.json,sha256=IrjwFnXjrpVUp3zYfcYClpibJE9Y-94gtrC1Aw8sXxg,12332
@@ -85,9 +88,9 @@ 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-3.5.5.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-gwaslab-3.5.5.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
-gwaslab-3.5.5.dist-info/METADATA,sha256=BAkr3vpGpZJqHRecRn_q4guTT8PeykLZssU02mL1T7Q,7750
-gwaslab-3.5.5.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-gwaslab-3.5.5.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
-gwaslab-3.5.5.dist-info/RECORD,,
+gwaslab-3.5.7.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+gwaslab-3.5.7.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
+gwaslab-3.5.7.dist-info/METADATA,sha256=QKvLYkpRCauJ2uiVpd7xfO_w9DEKg4qsM_CiSRfcUkQ,7750
+gwaslab-3.5.7.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
+gwaslab-3.5.7.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
+gwaslab-3.5.7.dist-info/RECORD,,

{gwaslab-3.5.5.dist-info → gwaslab-3.5.7.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (75.8.2)
 Root-Is-Purelib: true
 Tag: py3-none-any