gwaslab 3.4.49__py3-none-any.whl → 3.5.1__py3-none-any.whl

gwaslab/viz_plot_mqqplot.py

@@ -139,7 +139,8 @@ def mqqplot(insumstats,
           anno_gtf_path=None,
           anno_adjust=False,
           anno_max_iter=100,
-          arm_offset=50,
+          arrow_kwargs=None,
+          arm_offset=None,
           arm_scale=1,
           anno_height=1,
           arm_scale_d=None,
@@ -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)
@@ -291,7 +293,7 @@ def mqqplot(insumstats,
     if maf_bin_colors is None:
         maf_bin_colors = ["#f0ad4e","#5cb85c", "#5bc0de","#000042"]
     if save_args is None:
-        save_args = {"dpi":300,"facecolor":"white"}
+        save_args = {"dpi":400,"facecolor":"white"}
     if highlight is None:
         highlight = list()
     if highlight_anno_args is None:
@@ -329,6 +331,20 @@ def mqqplot(insumstats,
                     fig_args["dpi"]=72
                     scatter_args["rasterized"]=True
                     qq_scatter_args["rasterized"]=True
+                else:
+                    fig_args["dpi"] = save_args["dpi"]
+    
+    # configure dpi if saving the plot
+    fig_args, scatter_args, qq_scatter_args, save_args = _configure_fig_save_kwargs(save = save, 
+                                                                                    fig_args = fig_args, 
+                                                                                    scatter_args = scatter_args, 
+                                                                                    qq_scatter_args = qq_scatter_args, 
+                                                                                    save_args = save_args)
+
+
+    if len(anno_d) > 0 and arm_offset is None:
+        # in pixels
+        arm_offset = fig_args["dpi"] * repel_force * fig_args["figsize"][0]*0.5
 
     log.write("Start to create MQQ plot...{}:".format(_get_version()),verbose=verbose)
     log.write(" -Genomic coordinates version: {}...".format(build),verbose=verbose)
@@ -401,7 +417,7 @@ def mqqplot(insumstats,
     if mode=="b":
         sig_level=1,
         sig_line=False,
-        windowsizekb = 100000000   
+        #windowsizekb = 100000000   
         mode="mb"
         scatter_args={"marker":"s"}
         marker_size= (marker_size[1],marker_size[1])
@@ -522,8 +538,12 @@ def mqqplot(insumstats,
                                                     pos=pos, 
                                                     verbose=verbose, 
                                                     log=log)
+        
+        lines_to_plot = pd.Series(lines_to_plot.to_list() + [bmean, bmedian])
+    
     else:
         bmean, bmedian=0,0 
+    
 # P value conversion #####################################################################################################  
     
     # add raw_P and scaled_P
@@ -956,7 +976,7 @@ def mqqplot(insumstats,
             ax1.set_title(mtitle,fontsize=title_fontsize,family=font_family)
         log.write("Finished processing figure arts.",verbose=verbose)
 
-        # Add annotation arrows and texts
+        ## Add annotation arrows and texts
         log.write("Start to annotate variants...",verbose=verbose)
         ax1 = annotate_single(
                                 sumstats=sumstats,
@@ -984,6 +1004,7 @@ 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,
@@ -1055,7 +1076,8 @@ def mqqplot(insumstats,
         fig.suptitle(title , fontsize = title_fontsize ,x=0.5, y=1.05)
     else:
         fig.suptitle(title , fontsize = title_fontsize, x=0.5,y=1)
-
+        ## Add annotation arrows and texts
+    
     # Saving figure
     save_figure(fig = fig, save = save, keyword=mode, save_args=save_args, log = log, verbose=verbose)
 
@@ -1069,7 +1091,31 @@ def mqqplot(insumstats,
 
 ##############################################################################################################################################################################
 
+def _configure_fig_save_kwargs(save=None, 
+                               fig_args=None, 
+                               scatter_args=None, 
+                               qq_scatter_args=None, 
+                               save_args=None):
+    if fig_args is None:
+        fig_args = dict()
+    if scatter_args is None:
+        scatter_args = dict()
+    if qq_scatter_args is None:
+        qq_scatter_args = dict()
+    if save_args is None:
+        save_args = dict()
 
+    if save is not None:
+        if type(save) is not bool:
+            if len(save)>3:
+                if save[-3:]=="pdf" or save[-3:]=="svg":
+                    # to save as vectorized plot
+                    fig_args["dpi"]=72
+                    scatter_args["rasterized"]=True
+                    qq_scatter_args["rasterized"]=True
+                else:
+                    fig_args["dpi"] = save_args["dpi"]
+    return fig_args, scatter_args, qq_scatter_args, save_args
 
 
 def _add_pad_to_x_axis(ax1, xpad, xpadl, xpadr, sumstats, pos, chrpad, xtight, log, verbose):
@@ -1104,12 +1150,6 @@ def _add_pad_to_x_axis(ax1, xpad, xpadl, xpadr, sumstats, pos, chrpad, xtight, l
     return ax1
 
 
-
-
-
-
-
-
 ##############################################################################################################################################################################
 def _configure_cols_to_use(insumstats, snpid,  chrom, pos, ea, nea, eaf, p, mlog10p,scaled, mode,stratified,anno, anno_set, anno_alias,_chrom_df_for_i,highlight ,pinpoint,density_color):
     usecols=[]
@@ -1287,9 +1327,10 @@ def _process_density(sumstats, mode, bwindowsizekb, chrom, pos, verbose, log):
                 else:
                     break
         df = pd.DataFrame(stack,columns=["SNPID","TCHR+POS","DENSITY"])
-        sumstats["DENSITY"] = df["DENSITY"].values
-        bmean=sumstats["DENSITY"].mean()
-        bmedian=sumstats["DENSITY"].median()
+        sumstats["DENSITY"] = df["DENSITY"].astype("Float64").values
+
+        bmean=sumstats.drop_duplicates(subset="SNPID")["DENSITY"].mean()
+        bmedian=sumstats.drop_duplicates(subset="SNPID")["DENSITY"].median()
     elif "b" in mode and "DENSITY" in sumstats.columns:
         bmean=sumstats["DENSITY"].mean()
         bmedian=sumstats["DENSITY"].median()
@@ -1305,6 +1346,7 @@ def _process_line(ax1, sig_line, suggestive_sig_line, additional_line, lines_to_
                                 linestyle="--",
                                 color=sig_line_color,
                                 zorder=1)
+        
     if suggestive_sig_line is True:
         suggestive_sig_line = ax1.axhline(y=lines_to_plot[1], 
                                             linewidth = sc_linewidth, 
@@ -1312,15 +1354,20 @@ def _process_line(ax1, sig_line, suggestive_sig_line, additional_line, lines_to_
                                             color=suggestive_sig_line_color,
                                             zorder=1)
     if additional_line is not None:
-        for index, level in enumerate(lines_to_plot[2:].values):
+        for index, level in enumerate(lines_to_plot[2:2+len(additional_line)].values):
             ax1.axhline(y=level, 
                         linewidth = sc_linewidth, 
                         linestyle="--", 
                         color=additional_line_color[index%len(additional_line_color)],
                         zorder=1)
-    if "b" in mode:   
+    if "b" in mode: 
+        bmean = lines_to_plot.iat[-2]
+        bmedian = lines_to_plot.iat[-1]
         # for brisbane plot, add median and mean line 
+        log.write(" -Plotting horizontal line (  mean DENISTY): y = {}".format(bmean),verbose=verbose) 
         meanline = ax1.axhline(y=bmean, linewidth = sc_linewidth,linestyle="-",color=sig_line_color,zorder=1000)
+
+        log.write(" -Plotting horizontal line ( median DENISTY): y = {}".format(bmedian),verbose=verbose) 
         medianline = ax1.axhline(y=bmedian, linewidth = sc_linewidth,linestyle="--",color=sig_line_color,zorder=1000)
     return ax1
 
@@ -1441,10 +1488,16 @@ def _process_layout(mode, figax, fig_args, mqqratio, region_hspace):
             ax2 = None
             plt.subplots_adjust(hspace=region_hspace)
     elif mode =="b" :
-        fig_args["figsize"] = (15,5)
-        fig, ax1 = plt.subplots(1, 1,**fig_args)
-        ax2 = None
-        ax3 = None
+        if figax is not None:
+            fig = figax[0]
+            ax1 = figax[1]
+            ax3 = None
+            ax2 = None
+        else:
+            fig_args["figsize"] = (15,5)
+            fig, ax1 = plt.subplots(1, 1,**fig_args)
+            ax2 = None
+            ax3 = None
     else:
         raise ValueError("Please select one from the 5 modes: mqq/qqm/m/qq/r/b")
     ax4=None

gwaslab/viz_plot_phe_heatmap.py

@@ -0,0 +1,260 @@
+import pandas as pd
+import matplotlib.pyplot as plt
+import seaborn as sns
+import numpy as np
+import scipy as sp
+from gwaslab.viz_aux_quickfix import _quick_assign_i_with_rank
+from gwaslab.viz_aux_quickfix import _get_largenumber
+from gwaslab.viz_aux_quickfix import _quick_fix_p_value
+from gwaslab.viz_aux_quickfix import _quick_fix_pos
+from gwaslab.viz_aux_quickfix import _quick_fix_chr
+from gwaslab.viz_aux_quickfix import _quick_fix_eaf
+from gwaslab.viz_aux_quickfix import _quick_fix_mlog10p
+from gwaslab.viz_aux_quickfix import _dropna_in_cols
+from gwaslab.viz_plot_mqqplot import _process_p_value
+from gwaslab.viz_plot_mqqplot import _configure_fig_save_kwargs
+from gwaslab.viz_plot_mqqplot import mqqplot
+from gwaslab.viz_aux_save_figure import save_figure
+from gwaslab.g_Log import Log
+import copy
+from gwaslab.bd_common_data import get_chr_to_number
+from gwaslab.bd_common_data import get_number_to_chr
+from gwaslab.g_version import _get_version
+
+def _gwheatmap(
+    insumstats,    
+    chrom="CHR",
+    pos="POS",
+    ref_chrom="REF_CHR",
+    ref_pos="REF_START",
+    p="P",
+    scaled=False,
+    sizes = (10,50),
+    alpha=0.5,
+    mlog10p="MLOG10P",
+    snpid="SNPID",
+    eaf=None,
+    group="CIS/TRANS",
+    ea="EA",
+    nea="NEA",
+    colors=None,
+    check = True,
+    chr_dict = None,
+    xchrpad = 0, 
+    ychrpad=0,
+    use_rank = False,
+    xtick_chr_dict=None, 
+    ytick_chr_dict=None, 
+    fontsize=10, 
+    add_b =False,
+    log=Log(),
+    fig_kwargs=None,
+    scatter_kwargs=None,
+    height_ratios=None,
+    hspace = 0.1,
+    font_family="Arial",
+    cis_windowsizekb=100,
+    verbose=True,
+    save=True,
+    save_kwargs=None,
+    grid_linewidth=1,
+    grid_linecolor="grey",
+    **mqq_kwargs
+):
+    log.write("Start to create genome-wide scatter plot...{}:".format(_get_version()),verbose=verbose)
+    if height_ratios is None:
+        height_ratios = [1, 2]
+    if xtick_chr_dict is None:         
+        xtick_chr_dict = get_number_to_chr()
+    if ytick_chr_dict is None:         
+        ytick_chr_dict = get_number_to_chr()
+    if chr_dict is None:          
+        chr_dict = get_chr_to_number()
+    if colors is None:
+        colors=["#CB132D","#597FBD"]
+    if fig_kwargs is None:
+        fig_kwargs= dict(figsize=(15,15))
+    if save_kwargs is None:
+        save_kwargs = {"dpi":300,"facecolor":"white"}
+    if scatter_kwargs is None:
+        scatter_kwargs = {}
+
+    fig_kwargs, scatter_kwargs, qq_scatter_args, save_kwargs = _configure_fig_save_kwargs(save=save, 
+                                                                                    fig_args = fig_kwargs, 
+                                                                                    scatter_args = scatter_kwargs, 
+                                                                                    qq_scatter_args = dict(), 
+                                                                                    save_args = save_kwargs)
+
+    sumstats = insumstats.copy()
+    
+    # Data QC and format
+    if check ==True:
+        sumstats[pos] = _quick_fix_pos(sumstats[pos])
+        sumstats[chrom] = _quick_fix_chr(sumstats[chrom], chr_dict=chr_dict)
+        sumstats[ref_pos] = _quick_fix_pos(sumstats[ref_pos])
+        sumstats[ref_chrom] = _quick_fix_chr(sumstats[ref_chrom], chr_dict=chr_dict)
+        sumstats = _dropna_in_cols(sumstats, [pos, chrom, ref_pos, ref_chrom], log=log, verbose=verbose)
+    
+    # dropna
+    sumstats = sumstats.sort_values(by=group)
+
+    if scaled is True:
+        sumstats["raw_P"] = pd.to_numeric(sumstats[mlog10p], errors='coerce')
+    else:
+        sumstats["raw_P"] = sumstats[p].astype("float64")
+
+    sumstats =  _process_p_value(sumstats=sumstats, 
+                                mode="m",
+                                p=p, 
+                                mlog10p=mlog10p, 
+                                scaled=scaled, 
+                                log=log, 
+                                verbose=verbose )
+    
+    
+    
+    if add_b ==False:
+        fig, ax1 = plt.subplots(**fig_kwargs)
+    else:
+        fig, (ax2, ax1) = plt.subplots( nrows=2 ,sharex=True, gridspec_kw={'height_ratios': height_ratios }, **fig_kwargs)
+        plt.subplots_adjust(hspace=hspace)   
+
+    ## assign i for variants
+    sumstats, chrom_df_x = _quick_assign_i_with_rank(sumstats, 
+                                                chrpad=xchrpad, 
+                                                use_rank=use_rank, 
+                                                chrom=chrom,
+                                                pos=pos,
+                                                verbose=verbose)
+    chrom_df_b = chrom_df_x
+    sumstats = sumstats.rename(columns={"i":"i_x"})
+    add_x_unique = list(sumstats["_ADD"].unique()) 
+    
+    ## determine grouping methods for Y
+    ## assign i for Y group
+    sumstats, chrom_df_y = _quick_assign_i_with_rank(sumstats, 
+                              chrpad=ychrpad, 
+                              use_rank=use_rank, 
+                              chrom=ref_chrom,
+                              pos=ref_pos,
+                              verbose=verbose)
+    
+    sumstats = sumstats.rename(columns={"i":"i_y"})
+    add_y_unique = list(sumstats["_ADD"].unique()) 
+    
+    if add_b == True:
+        sumstats["i"] = sumstats["i_x"]
+        fig,log = mqqplot(sumstats,
+                        chrom=chrom,
+                        pos=pos,
+                        p=p,
+                        mlog10p=mlog10p,
+                        snpid=snpid,
+                        scaled=scaled,
+                        log=log, 
+                        mode="b",
+                        figax=(fig,ax2),
+                        _chrom_df_for_i = chrom_df_b,
+                        _invert=False,
+                        _if_quick_qc=False,
+                        **mqq_kwargs
+                        )
+    ## 
+    #min_xy = min(min(sumstats["i_x"]),min(sumstats["i_y"]))
+    #max_xy = max(max(sumstats["i_x"]),max(sumstats["i_y"]))
+    
+    ## determine color 
+
+    ## determine dot size
+
+    ## plot  
+    legend = True
+    style=None
+    linewidth=0
+    edgecolor="black"
+
+    palette = sns.color_palette(colors,n_colors=sumstats[group].nunique()) 
+    
+    #for index,g in enumerate(sumstats[group].unique()):
+    #    
+    #    palette = sns.color_palette("dark:{}".format(colors[index]), as_cmap=True)
+    #    
+    #    plot = sns.scatterplot(data=sumstats.loc[sumstats[group]==g,:], x='i_x', y='i_y',
+    #            hue="scaled_P",
+    #            palette=palette,
+    #            size="scaled_P",
+    #            alpha=alpha,
+    #            sizes=sizes,
+    #            legend=legend,
+    #            style=style,
+    #            linewidth=linewidth,
+    #            edgecolor = edgecolor,
+    #            zorder=2,
+    #            ax=ax1)   
+    
+    plot = sns.scatterplot(data=sumstats, x='i_x', y='i_y',
+            hue=group,
+            palette=palette,
+            size="scaled_P",
+            alpha=alpha,
+            sizes=sizes,
+            legend=legend,
+            style=style,
+            linewidth=linewidth,
+            edgecolor = edgecolor,
+            zorder=2,
+            ax=ax1, **scatter_kwargs)   
+    
+    handles, labels = ax1.get_legend_handles_labels()
+    new_labels = []
+    ncol = len(labels)
+    for i in labels:
+        if i==group:
+            new_labels.append("Group")
+        elif i=="scaled_P":
+            new_labels.append("$-log_{10}(P)$")
+        else:
+            new_labels.append(i)
+    
+    ax1.legend(labels = new_labels,  handles=handles, loc="lower center", bbox_to_anchor=(.45, -0.17), 
+                    ncol=ncol, scatterpoints=2, title=None, frameon=False)
+
+    ## add vertical line
+    for i in add_x_unique:
+        ax1.axvline(x = i+0.5, linewidth = grid_linewidth,color=grid_linecolor,zorder=1000 )
+    for i in add_y_unique:
+        ax1.axhline(y = i+0.5,  linewidth = grid_linewidth,color=grid_linecolor,zorder=1000 )
+
+    
+    ## add X tick label 
+    ax1 = _process_xtick(ax1, chrom_df_x, xtick_chr_dict, fontsize, font_family, log=log,verbose=True)
+    ## add Y tick label 
+    ax1 = _process_ytick(ax1, chrom_df_y, ytick_chr_dict, fontsize, font_family, log=log,verbose=True)
+    
+    ## set x y lim
+    ax1.set_ylim([0.5,sumstats["i_y"].max()+1])
+    ax1.set_xlim([0.5,sumstats["i_x"].max()+1])
+
+    ## set x y label
+
+    xlabel = "pQTL position"
+    ax1.set_xlabel(xlabel,fontsize=fontsize,family=font_family)
+    ylabel = "location of the gene encoding the target protein"
+    ax1.set_ylabel(ylabel,fontsize=fontsize,family=font_family)
+    
+    save_figure(fig = fig, save = save, keyword="gwheatmap",  save_args=save_kwargs, log = log, verbose=verbose)
+
+    return fig, log
+
+################################################################################################################
+def _process_xtick(ax1, chrom_df, xtick_chr_dict, fontsize, font_family, log=Log(),verbose=True):
+    log.write(" -Processing X ticks...",verbose=verbose)
+    ax1.set_xticks(chrom_df.astype("float64"))
+    ax1.set_xticklabels(chrom_df.index.astype("Int64").map(xtick_chr_dict),fontsize=fontsize,family=font_family)    
+    return ax1
+
+def _process_ytick(ax1, chrom_df, ytick_chr_dict, fontsize, font_family, log=Log(),verbose=True):
+    log.write(" -Processing Y ticks...",verbose=verbose)
+    ax1.set_yticks(chrom_df.astype("float64"))
+    ax1.set_yticklabels(chrom_df.index.astype("Int64").map(ytick_chr_dict),fontsize=fontsize,family=font_family)    
+    return ax1

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-3.4.49.dist-info → gwaslab-3.5.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gwaslab
-Version: 3.4.49
+Version: 3.5.1
 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-3.4.49.dist-info → gwaslab-3.5.1.dist-info}/RECORD

@@ -2,21 +2,22 @@ gwaslab/__init__.py,sha256=7TKJaODdpeuQKibL7gIEa4MtyQ0pmrU-vIHQ-Et27lQ,2433
 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=qWBh14-XheS88KLm2vr0OKRAhU9VmbUvy90T4L52zAo,36265
+gwaslab/g_Sumstats.py,sha256=c_qYY2H-nf-JtGepzafoHuYwnWxmOOBf9CDytPZc60Q,36704
 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=dhN-3rbJKALlFhTZACsxBZL_U8j4PQmcVuCuWx9dapo,1886
+gwaslab/g_version.py,sha256=Wpfo8Y_fjYS4ajalombaHrLezBO7BOr070GnjQHhOGw,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=bF7oHBtMnxJgksIit0O0_U94dZFh8r5YblgDqEEsqoM,806
 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
@@ -50,25 +51,28 @@ gwaslab/util_in_correct_winnerscurse.py,sha256=Gp--yAQ8MMzdkWIvXP9C1BHVjZc-YzqHf
 gwaslab/util_in_fill_data.py,sha256=iVq5WLWwFI03v9HyvBanu5si3j2p-oyPFTl8jsX69xM,14693
 gwaslab/util_in_filter_value.py,sha256=dY4X66N9A4MHCRHjPqLYFufMM91ggLRwUBf_nJYh8Lg,23605
 gwaslab/util_in_get_density.py,sha256=kpKXH69acMkeYVG5vs-VbJC3COhmuLBfYco-wuOxgjc,3934
-gwaslab/util_in_get_sig.py,sha256=9kq1GXacknO2YnVmsTli1GlPA728ASweTZ3UKm3Wszo,38783
+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=UTOx-OpFsM_UVphBHxqQZwCFI8bjwwB6CMsgFbAfheQ,32215
+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=5XM-J9D2yp5FVbK6YQKEhSCqAYBLNWSQms9WjpXxVn8,18313
+gwaslab/viz_aux_property.py,sha256=UIaivghnLXYpTwkKnXRK0F28Jbn9L6OaICk3K73WZaU,33
+gwaslab/viz_aux_quickfix.py,sha256=HnhVvY0GP0EN0gLJ-B11OYiE5PWDcdKGUpQ3QZeu0lE,18592
 gwaslab/viz_aux_reposition_text.py,sha256=iRIP-Rkltlei068HekJcVubiqPrunBqvAoSQ1eHk04M,4304
-gwaslab/viz_aux_save_figure.py,sha256=nL-aoE8Kg06h7FgleGRBIZjhI-6w5gpn3E1HWMwBig8,2664
+gwaslab/viz_aux_save_figure.py,sha256=GdUXNBOelsWqtTXm8pEZzeGGwDxHYnBkyrGwLOK16ew,2723
 gwaslab/viz_plot_compare_af.py,sha256=qtXW45-Sq_ugK8ZfqBYMpmf58SKi3lB3YyHnzn_akcE,5344
-gwaslab/viz_plot_compare_effect.py,sha256=lV-4KSQatTSsYqzEGGTkBu17I2VlVyVh1uJr-kCq630,49585
+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=q_c_ZDRdirEcdHHnb030h7dTUWAFy9OVuzwbdCzZ3gU,64580
+gwaslab/viz_plot_mqqplot.py,sha256=emyEXZZenzm8eh3XFCkTWI8sz0fEnL5QJxohOZMxWZc,67189
+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_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_stackedregional.py,sha256=HfNUhwxevbwSoauE0ysG020U7YFVy4111nkIWdaJ4Q8,16664
 gwaslab/viz_plot_trumpetplot.py,sha256=ZHdc6WcVx0-oKoj88yglRkmB4bS9pOiEMcuwKW35Yvo,42672
 gwaslab/data/formatbook.json,sha256=N2nJs80HH98Rsu9FxaSvIQO9J5yIV97WEtAKjRqYwiY,38207
 gwaslab/data/reference.json,sha256=IrjwFnXjrpVUp3zYfcYClpibJE9Y-94gtrC1Aw8sXxg,12332
@@ -78,9 +82,9 @@ 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-3.4.49.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-gwaslab-3.4.49.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
-gwaslab-3.4.49.dist-info/METADATA,sha256=bA0qeWgxt5mOkt_aL4aW_v4csyNSJCsbY6wrKMLyqY8,7752
-gwaslab-3.4.49.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
-gwaslab-3.4.49.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
-gwaslab-3.4.49.dist-info/RECORD,,
+gwaslab-3.5.1.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+gwaslab-3.5.1.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
+gwaslab-3.5.1.dist-info/METADATA,sha256=Dqj65vurvDR3JCwlyCVnnfUS64cmN1vMJJjUTCm3xLI,7758
+gwaslab-3.5.1.dist-info/WHEEL,sha256=R06PA3UVYHThwHvxuRWMqaGcr-PuniXahwjmQRFMEkY,91
+gwaslab-3.5.1.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
+gwaslab-3.5.1.dist-info/RECORD,,

{gwaslab-3.4.49.dist-info → gwaslab-3.5.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.2.0)
+Generator: setuptools (75.5.0)
 Root-Is-Purelib: true
 Tag: py3-none-any