gwaslab 3.6.8__py3-none-any.whl → 3.6.10__py3-none-any.whl

gwaslab/g_Log.py

@@ -31,4 +31,16 @@ class Log():
             self.log_text = self.log_text + str(time.strftime('%Y/%m/%d %H:%M:%S')) + " " + " ".join(map(str,message)) + end
         else:
             if verbose: print(*message,end=end)
-            self.log_text = self.log_text + " ".join(map(str,message)) + end
+            self.log_text = self.log_text + " ".join(map(str,message)) + end
+
+    def get_log_for_last_operation(self):
+        last_log = []
+        rows = self.log_text.strip().split("\n")
+
+        # Iterate backwards to find the last operation
+        for line in reversed(rows):
+            last_log.append(line)
+            if "Start to" in line:
+                break
+
+        return "".join(reversed(last_log))

gwaslab/g_Sumstats.py

@@ -102,7 +102,7 @@ from gwaslab.viz.viz_plot_mqqplot import mqqplot
 from gwaslab.viz.viz_plot_trumpetplot import plottrumpet
 from gwaslab.viz.viz_plot_compare_af import plotdaf
 from gwaslab.viz.viz_plot_credible_sets import _plot_cs
-
+from gwaslab.viz.viz_plot_associations import _plot_associations
 from gwaslab.io.io_read_pipcs import _read_pipcs
 from gwaslab.io.io_load_ld import tofinemapping_using_ld
 from gwaslab.io.io_preformat_input import preformat
@@ -112,6 +112,7 @@ from gwaslab.io.io_to_pickle import _reload
 
 #20220309
 class Sumstats():
+    
     def __init__(self,
              sumstats=None,
              fmt=None,
@@ -274,6 +275,10 @@ class Sumstats():
         self.id = id(self)
         self.tmp_path = _path(pid=self.id, log = self.log, verbose=verbose)
 
+    def __getitem__(self, index):
+        return self.data[index]
+    def __len__(self):
+        return len(self.data)
 #### healper #################################################################################
     def update_meta(self, **kwargs):
         self.meta = _update_meta(self.meta, self.data,log = self.log, **kwargs)
@@ -695,7 +700,8 @@ class Sumstats():
         return fig, outliers
     
     def infer_ancestry(self, **kwargs):
-        self.meta["gwaslab"]["inferred_ancestry"] = _infer_ancestry(self.data, **kwargs)
+        self.meta["gwaslab"]["inferred_ancestry"] = _infer_ancestry(self.data, log=self.log,
+                                                                    **kwargs)
 
     def plot_gwheatmap(self, **kwargs):
         fig = _gwheatmap(self.data, **kwargs)
@@ -811,6 +817,9 @@ class Sumstats():
         self.associations = associations_full
         
         return associations_summary
+    def plot_associations(self,**kwargs):
+
+        _plot_associations(self.associations, **kwargs)
 
     def check_cis(self, gls=False, **kwargs):
         if "SNPID" in self.data.columns:

gwaslab/g_version.py

@@ -17,8 +17,8 @@ def _get_version():
 def gwaslab_info():
     # version meta information
     dic={
-   "version":"3.6.0",
-   "release_date":"20250902"
+   "version":"3.6.10",
+   "release_date":"20251101"
     }
     return dic   
 

gwaslab/util/util_ex_phewwas.py

@@ -25,15 +25,19 @@ def _extract_associations(sumstats, rsid="rsID", log = Log(), verbose=True):
     assoc_traits_agg = assoc_traits_agg.rename(columns={"trait":"GWASCATALOG_TRAIT",
                                                         "riskFrequency":"RAF",
                                                         "betaNum":"Beta",
-                                                        "pvalue":"P-value"
+                                                        "pvalue":"P-value",
+                                                        "betaUnit":"Unit"
                                                         })
     
     summary_columns=['GWASCATALOG_TRAIT','associationId', 'rsID', "geneName", 
-                     'RA', 'RAF','Beta', 'P-value','cohort','initialSampleSize','publicationInfo.pubmedId',
+                     'RA', 'RAF','Beta',"Unit", 'P-value','cohort','initialSampleSize','publicationInfo.pubmedId',
                      "functionalClass","gene.geneName"]
     
     assoc_traits_agg_summary = assoc_traits_agg[summary_columns]
 
+    assoc_traits_agg_summary = _align_beta(sumstats, assoc_traits_agg_summary, log, verbose)
+    assoc_traits_agg = _align_beta(sumstats, assoc_traits_agg, log, verbose)
+
     return assoc_traits_agg, assoc_traits_agg_summary
 
 def get_associations_from_gwascatalog(sumstats, rsid="rsID", log=Log(), verbose=True):
@@ -125,3 +129,41 @@ def parse_range(x):
     low = np.log(range_list[0])
     beta = (high + low)/2
     return beta
+
+def _align_beta(sumstats, assoc_traits_agg_summary, log, verbose):
+    # merge with sumstats
+    log.write("Merging GWAS Catalog associationms with Sumstats...",)
+    assoc_traits_agg_summary = pd.merge(sumstats[["rsID","CHR","POS","EA","NEA","BETA"]], assoc_traits_agg_summary, on = "rsID", how="inner")
+    # check direction 
+    assoc_traits_agg_summary["GC_Beta_GL_RA"] = np.nan
+    assoc_traits_agg_summary["GC_Beta_GL_EA"] = np.nan
+
+    # get sumstats RA
+    assoc_traits_agg_summary["_GL_RA_BETA"] = assoc_traits_agg_summary["BETA"].abs()
+    assoc_traits_agg_summary["_GL_RA"] = assoc_traits_agg_summary["EA"]
+    assoc_traits_agg_summary["_GL_NRA"] = assoc_traits_agg_summary["NEA"]
+    is_GL_RA_flipped = assoc_traits_agg_summary["BETA"]<0
+    assoc_traits_agg_summary.loc[is_GL_RA_flipped, "_GL_RA"] = assoc_traits_agg_summary.loc[is_GL_RA_flipped, "NEA"]
+    assoc_traits_agg_summary.loc[is_GL_RA_flipped, "_GL_NRA"] = assoc_traits_agg_summary.loc[is_GL_RA_flipped, "EA"]
+    
+    is_matched = assoc_traits_agg_summary["_GL_RA"] == assoc_traits_agg_summary["RA"]
+    log.write(" -GL_RA matched RA for {} variants ".format(sum(is_matched)), verbose=verbose)
+    assoc_traits_agg_summary.loc[is_matched, "GC_Beta_GL_RA"] = assoc_traits_agg_summary.loc[is_matched, "Beta"]
+    
+    is_flipped = assoc_traits_agg_summary["_GL_NRA"] == assoc_traits_agg_summary["RA"]
+    log.write(" -GL_NRA matched RA for {} variants... Aligning with Sumstats Risk allele (BETA>0) in GC_Beta_GL_RA... ".format(sum(is_flipped)), verbose=verbose)
+    assoc_traits_agg_summary.loc[is_flipped, "GC_Beta_GL_RA"] = - assoc_traits_agg_summary.loc[is_flipped, "Beta"]
+
+    is_matched = assoc_traits_agg_summary["EA"] == assoc_traits_agg_summary["RA"]
+    log.write(" -EA matched RA for {} variants ".format(sum(is_matched)), verbose=verbose)
+    assoc_traits_agg_summary.loc[is_matched, "GC_Beta_GL_EA"] = assoc_traits_agg_summary.loc[is_matched, "Beta"]
+    
+    is_flipped = assoc_traits_agg_summary["NEA"] == assoc_traits_agg_summary["RA"]
+    log.write(" -NEA matched RA for {} variants... Aligning with Sumstats Risk allele (BETA>0) in GC_Beta_GL_RA... ".format(sum(is_flipped)), verbose=verbose)
+    assoc_traits_agg_summary.loc[is_flipped, "GC_Beta_GL_EA"] = - assoc_traits_agg_summary.loc[is_flipped, "Beta"]
+
+    not_match = (assoc_traits_agg_summary["_GL_RA"] != assoc_traits_agg_summary["RA"])& (assoc_traits_agg_summary["_GL_NRA"] != assoc_traits_agg_summary["RA"])
+    log.write(" -NEA and EA not matching RA for {} variants... ".format(sum(not_match)), verbose=verbose)
+
+
+    return assoc_traits_agg_summary

gwaslab/util/util_in_calculate_power.py

@@ -27,17 +27,19 @@ def get_power(
         log.write("  -Number of cases:{}".format(ncase), verbose=verbose)
         log.write("  -Number of controls:{}".format(ncontrol), verbose=verbose)
         if genotype_rr is not None:
-            log.write("  -Risk allele RR:{:.3f}".format(genotype_rr), verbose=verbose)
+            log.write("  -Risk allele RR:{}".format(genotype_rr), verbose=verbose)
         elif genotype_or is not None:
-            log.write("  -Risk allele OR:{:.3f}".format(genotype_or), verbose=verbose)
+            log.write("  -Risk allele OR:{}".format(genotype_or), verbose=verbose)
         elif beta is not None:
-            log.write("  -Risk allele beta:{:.3f}".format(beta), verbose=verbose)
+            log.write("  -Risk allele beta:{}".format(beta), verbose=verbose)
         else:
             genotype_rr = 0.1
-            log.write("  -Risk allele RR:{:.3f}".format(genotype_rr), verbose=verbose)
-        log.write("  -Disease prevalence:{:.3f}".format(prevalence), verbose=verbose)
-        log.write("  -Risk allele frequency: {:.3f}".format(daf), verbose=verbose)
-        log.write("  -Significance level: {:.3e}".format(sig_level), verbose=verbose)
+            log.write("  -Risk allele RR:{}".format(genotype_rr), verbose=verbose)
+
+        log.write("  -Disease prevalence:{}".format(prevalence), verbose=verbose)
+        log.write("  -Risk allele frequency: {}".format(daf), verbose=verbose)
+        log.write("  -Significance level: {}".format(sig_level), verbose=verbose)
+        
         # Skol, A. D., Scott, L. J., Abecasis, G. R., & Boehnke, M. (2006). Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nature genetics, 38(2), 209-213.
         aaf = daf**2
         abf = 2 * (daf) * (1 - daf)
@@ -68,9 +70,9 @@ def get_power(
         abp= x[1] * prevalence / (x[0]*aaf + x[1]*abf + x[2]*bbf)
         bbp= x[2] * prevalence / (x[0]*aaf + x[1]*abf + x[2]*bbf)
         log.write("Probability of disease :", verbose=verbose)
-        log.write(" - Individuals with AA genotype: {:.3f}".format(aap), verbose=verbose)
-        log.write(" - Individuals with AB genotype: {:.3f}".format(abp), verbose=verbose)
-        log.write(" - Individuals with BB genotype: {:.3f}".format(bbp), verbose=verbose)
+        log.write(" - Individuals with AA genotype: {}".format(aap), verbose=verbose)
+        log.write(" - Individuals with AB genotype: {}".format(abp), verbose=verbose)
+        log.write(" - Individuals with BB genotype: {}".format(bbp), verbose=verbose)
         
         pcase= (aap * aaf + abp * abf*0.5) / prevalence
         pcontrol=((1-aap )* aaf + (1-abp )* abf*0.5) / (1 - prevalence)
@@ -78,16 +80,19 @@ def get_power(
         vcase = pcase *(1-pcase)
         vcontrol =pcontrol *(1-pcontrol)
         log.write("Expected risk allele frequency:", verbose=verbose)
-        log.write(" - In cases: {:.3f}".format(pcase), verbose=verbose)
-        log.write(" - In controls: {:.3f}".format(pcontrol), verbose=verbose)
+        log.write(" - In cases: {}".format(pcase), verbose=verbose)
+        log.write(" - In controls: {}".format(pcontrol), verbose=verbose)
 
         num= (pcase - pcontrol)
-        den= np.sqrt( (vcase/ncase +  vcontrol/ncontrol)*0.5 )
+        for_sqrt = (vcase/ncase +  vcontrol/ncontrol)*0.5
+        if np.iterable(for_sqrt):
+            for_sqrt[for_sqrt < 0] = np.nan
+        den= np.sqrt( for_sqrt )
         u = num / den
 
         c = ss.norm.isf(sig_level/2)
         power = 1 - ss.norm.cdf(c-u) + ss.norm.cdf(-c-u)
-        log.write("Expected power: {:.3f}".format(power), verbose=verbose)
+        log.write("Expected power: {}".format(power), verbose=verbose)
 
     elif mode=="q":
         if beta is None:

gwaslab/viz/viz_aux_save_figure.py

@@ -53,7 +53,8 @@ def get_default_path(keyword,fmt="png"):
                         "afc":"allele_frequency_comparision",
                         "gwheatmap":"genome_wide_heatmap",
                         "scatter":"scatter",
-                        "forest":"forest"
+                        "forest":"forest",
+                        "gwaslab":"gwaslab"
                         }
     prefix = path_dictionary[keyword]
     count = 1

gwaslab/viz/viz_plot_associations.py

@@ -0,0 +1,61 @@
+import seaborn as sns
+import matplotlib.pyplot as plt
+from gwaslab.io.io_process_args import _update_args
+from gwaslab.io.io_process_args import _update_arg
+from gwaslab.g_Log import Log
+
+def _plot_associations(associations, 
+                       values="Beta",
+                        fig_args=None,
+                        log=Log(),
+                        verbose=True,
+                        sort="P-value",
+                        fontsize=12,
+                        font_family="Arial",
+                        cmap=None,
+                        ylabel="Traits",
+                        xlabel="rsID - Gene Name",
+                        **args               
+                       ):
+    
+    log.write("Start to create heatmap for associations...", verbose=verbose)
+    
+    cmap = _update_arg(cmap, "RdBu")
+
+    log.write(f" -Value to plot: {values}", verbose=verbose)
+    log.write(f" -Total number of associations :{len(associations)} ", verbose=verbose)
+    log.write(f" -Sorting associations by :{sort} ", verbose=verbose)
+
+    associations = associations.sort_values(by=[sort]).drop_duplicates(subset=["rsID","GWASCATALOG_TRAIT"])
+
+    log.write(f" -Keeping unique rsID-traits pairs :{len(associations)} ", verbose=verbose)
+
+    associations = associations.dropna(subset=[values])
+    log.write(f" -Keeping associations without NA in {values} :{len(associations)} ", verbose=verbose)
+
+    log.write(f" -Total number of unique variants for plotting :{associations['rsID'].nunique()} ", verbose=verbose)
+    log.write(f" -Total number of unique traits for plotting:{associations['GWASCATALOG_TRAIT'].nunique()} ", verbose=verbose)
+
+    matrix_beta = associations.pivot_table(index=['rsID','gene.geneName'], 
+                                    columns='GWASCATALOG_TRAIT', 
+                                    values=[values])
+
+    matrix_beta = matrix_beta.astype("float64")
+    
+    matrix_beta.columns = matrix_beta.columns.droplevel(0)
+
+    height = max(2, len(matrix_beta)//2)
+    width = max(2, len(matrix_beta.columns)//2)
+
+    fig_args = _update_args(fig_args, dict(figsize=(width,height)))
+    fig,ax = plt.subplots(**fig_args)
+    
+    sns.heatmap(matrix_beta.T, annot=True, fmt=".2f",cmap="RdBu",ax=ax)
+    
+
+    ax.set_xlabel(xlabel,fontsize=fontsize, fontfamily=font_family)
+    ax.set_ylabel(ylabel,fontsize=fontsize, fontfamily=font_family)
+
+
+    log.write("Finished creating heatmap for associations.", verbose=verbose)
+    return fig, ax

gwaslab/viz/viz_plot_mqqplot.py

@@ -296,7 +296,7 @@ def mqqplot(insumstats,
             region_ref.append(region_ref_second)
     region_ref_index_dic = {value: index for index,value in enumerate(region_ref)}
         
-    taf = _update_args(taf, [track_n,track_n_offset,track_fontsize_ratio,track_exon_ratio,track_text_offset])
+    taf = _update_arg(taf, [track_n,track_n_offset,track_fontsize_ratio,track_exon_ratio,track_text_offset])
     region_marker_shapes = _update_arg(region_marker_shapes, ['o', '^','s','D','*','P','X','h','8'])
     region_grid_line = _update_args(region_grid_line,  {"linewidth": 2,"linestyle":"--"})
     region_lead_grid_line = _update_args(region_lead_grid_line, {"alpha":0.5,"linewidth" : 2,"linestyle":"--","color":"#FF0000"})

gwaslab/viz/viz_plot_template.py

@@ -0,0 +1,98 @@
+import seaborn as sns
+import matplotlib.pyplot as plt
+from gwaslab.io.io_process_args import _update_args
+from gwaslab.io.io_process_args import _update_arg
+from gwaslab.g_Log import Log
+from gwaslab.viz.viz_aux_save_figure import save_figure
+
+def _plot( associations, 
+            values="Beta",
+            sort="P-value",
+            mode="gwaslab",
+            fontsize=12,
+            font_family="Arial",
+            cmap=None,
+            ylabel="Y",
+            xlabel="X",
+            xlim=None,
+            ylim=None,
+            yticks=None,
+            xticks=None,
+            title="Title",
+            title_pad=1.08, 
+            title_fontsize=13,
+            linewidth=None,
+            linestyle=None,
+            linecolor=None,
+            dpi=200,
+            fig_args= None,
+            scatter_args=None,
+            save=None,
+            save_args=None,
+            log=Log(),
+            verbose=True,
+            **args               
+            ):
+    
+    # update args
+    
+    cmap = _update_arg(cmap, "RdBu")
+
+    fig_args = _update_args(fig_args, dict(figsize=(10,10)))
+
+    # create fig and ax    
+    fig,ax = plt.subplots(**fig_args)
+
+    # draw lines
+    horizontal_line = ax.axhline(y=1, linewidth = linewidth,
+                            linestyle="--",
+                            color=linecolor,zorder=1000)
+    vertical_line   = ax.axvline(x=1, linewidth = linewidth,
+                            linestyle="--",
+                            color=linecolor,zorder=1000)
+
+    # ticks
+    if xticks is not None:
+        ax.set_xticks(xticks)
+        ax.set_xticklabels(xticks,
+                            fontsize=fontsize,
+                            family=font_family)    
+    
+    if yticks is not None:
+        ax.set_xticks(yticks)
+        ax.set_xticklabels(yticks,
+                            fontsize=fontsize,
+                            family=font_family)    
+
+    # labels
+    ax.set_xlabel(xlabel,
+                  fontsize=fontsize, 
+                  fontfamily=font_family)
+    ax.set_ylabel(ylabel,
+                  fontsize=fontsize, 
+                  fontfamily=font_family)
+
+    ax.tick_params(axis='x', 
+                    labelsize=fontsize,
+                    labelfontfamily=font_family)
+    ax.tick_params(axis='y', 
+                    labelsize=fontsize,
+                    labelfontfamily=font_family)
+    
+    # title
+    title_pad = title_pad -0.05
+    fig.suptitle(title , 
+                 fontsize = title_fontsize, 
+                 x=0.5,
+                 y=title_pad)
+    
+    # spines
+    ax.spines["top"].set_visible(False)
+    ax.spines["right"].set_visible(False)
+    ax.spines["left"].set_visible(True)
+    ax.spines["bottom"].set_visible(True)
+
+    save_figure(fig = fig, save = save, keyword=mode, save_args=save_args, log = log, verbose=verbose)
+
+    log.write("Finished creating plots.", verbose=verbose)
+    return fig, ax

gwaslab/viz/viz_plot_trumpetplot.py

@@ -170,10 +170,11 @@ def plottrumpet(mysumstats,
             cols_to_use.append(chrom) if chrom not in cols_to_use else cols_to_use
 
     if size != "ABS_BETA":
-        if size not in cols_to_use:
+        if size is not None and size not in cols_to_use:
             cols_to_use.append(size)
     if "hue" in scatter_args.keys():
-        cols_to_use.append(scatter_args["hue"]) 
+        if scatter_args["hue"] not in cols_to_use:
+            cols_to_use.append(scatter_args["hue"]) 
     #filter by p #################################################################################################################
     if p in mysumstats.columns:
         sumstats = mysumstats.loc[mysumstats[p]< p_level,cols_to_use ].copy()
@@ -287,7 +288,10 @@ def plottrumpet(mysumstats,
     sumstats["ABS_BETA"] = sumstats[beta].abs()
 
     ##################################################################################################
-    size_norm = (sumstats[size].min(), sumstats[size].max())
+    if size is None:
+        size_norm = None
+    else:
+        size_norm = (sumstats[size].min(), sumstats[size].max())
     ## if highlight  ##################################################################################################
 
     log.write(" -Creating scatter plot...", verbose=verbose)
@@ -389,15 +393,30 @@ def plottrumpet(mysumstats,
     
     #second_legend = ax.legend(title="Power", loc="upper right",fontsize =fontsize,title_fontsize=fontsize)
     log.write(" -Creating legends...")
+    # curve, size,  hue
     h,l = ax.get_legend_handles_labels()
+    
     if len(ts)>0:
+        # power curves
         l1 = ax.legend(h[:int(len(ts))],l[:int(len(ts))], title="Power", loc="upper right",fontsize =fontsize,title_fontsize=fontsize)
         for line in l1.get_lines():
             line.set_linewidth(5.0)
-    if hue is None:
-        l2 = ax.legend(h[int(len(ts)):],l[int(len(ts)):], title=None, loc="lower right",fontsize =fontsize,title_fontsize=fontsize)
+    ## hue
+    if hue is not None or size is not None:
+    #    # sizes
+        if hue is None and size is not None:
+            hue_size_legend_title = size
+        elif hue is not None and size is None:
+            hue_size_legend_title = hue
+        else:
+            hue_size_legend_title = None
+        l2 = ax.legend(h[int(len(ts)):],l[int(len(ts)):], title=hue_size_legend_title, loc="lower right",fontsize =fontsize,title_fontsize=fontsize)
+    
+    ## hue
     if len(ts)>0:
         ax.add_artist(l1)
+    if hue is not None or size is not None:
+        ax.add_artist(l2)
     #first_legend = ax.legend(handles=dots, loc="lower right" ,title=size,fontsize =fontsize,title_fontsize=fontsize)
     #ax.add_artist(first_legend)
     ##################################################################################################
@@ -780,17 +799,31 @@ def plot_power_x(
                 log=Log()):
     
     #Checking columns#################################################################################################################
+    """
+    Create power cure with user-specified x axis
+    q mode:
+        N
+        MAF
+    b mode:
+        N_CASE
+        N_CONTROL
+        PREVALENCE
+    BETA
+    """
+
     log.write("Start to create power plot...", verbose=verbose)
     matplotlib.rc('font', family=font_family)
 
     log.write(" -Settings:", verbose=verbose)
     log.write("  -Mode: {}".format(mode), verbose=verbose)
+    
     if mode == "q" :
         log.write("  -X axis: {}".format(x), verbose=verbose)
         if x!="N":
             log.write("  -N: {}".format(ns), verbose=verbose)
         if x!="MAF":
             log.write("  -MAF: {}".format(mafs), verbose=verbose)
+
     if mode == "b" :
         log.write("  -X axis: {}".format(x), verbose=verbose)
         if x!="N_CASE":
@@ -846,8 +879,11 @@ def plot_power_x(
         prevalence_range = np.linspace(0.01,0.99,n_matrix)
     else:
         prevalence_range = np.linspace(prevalence_range[0],prevalence_range[1],n_matrix)
-    #configure power threshold###################################################################################################
     
+    
+    #configure power threshold###################################################################################################
+    # for hue
+    # which is the variable
     if type(ns) is list:
         var_to_change = ns
         legend_title = "N"
@@ -895,12 +931,13 @@ def plot_power_x(
     ##creating power line############################################################################################
     if mode=="q":
         for i,value in enumerate(var_to_change):
-            
+            # iterate through variables
             n = ns
             beta = betas
             maf = mafs
             sig_level = sig_levels
             
+            # update the variable
             if legend_title == "BETA":
                 beta = value
             elif legend_title == "MAF":
@@ -910,7 +947,7 @@ def plot_power_x(
             elif legend_title == "Significance level":
                 sig_level = value
 
-
+            # update X
             if x == "N":
                 x_values = n_range
                 n = x_values

{gwaslab-3.6.8.dist-info → gwaslab-3.6.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gwaslab
-Version: 3.6.8
+Version: 3.6.10
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <gwaslab@gmail.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/

{gwaslab-3.6.8.dist-info → gwaslab-3.6.10.dist-info}/RECORD

@@ -1,8 +1,8 @@
 gwaslab/__init__.py,sha256=tr8AGz-BqvOc5V0aUHNC-xW--LIAiUXrFo8HTR4SI9k,2861
 gwaslab/cache_manager.py,sha256=HOTnSkCOyGEPLRl90WT8D_6pAdI8d8AzenMIDGuCeWc,28113
-gwaslab/g_Log.py,sha256=C3Zv-_6c3C9ms8bgQ-ytplz22sjk7euqXYkWr9zNeAs,1573
+gwaslab/g_Log.py,sha256=gIZm2TG5ktW6Vpbg0daCrZevk6u_pmbZa_5jg-GhWSc,1914
 gwaslab/g_Phenotypes.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-gwaslab/g_Sumstats.py,sha256=7gRp2DIBxcBVYC6H5_4_3lde-VkGSKCiFCHOM3vLE1Q,45366
+gwaslab/g_Sumstats.py,sha256=w01312c5_fHMhs6cCFpQ78yXw5Rh6sRAQdvOnInuHg4,45735
 gwaslab/g_SumstatsMulti.py,sha256=CDnYMK0L8bV-LNOwO4h9yJahOVHR-sPAxZMNaeKFb3U,15098
 gwaslab/g_SumstatsPair.py,sha256=3-4aFh6pMZ4phcqHCCfyFPC3ySuck43wuTsfLG-ZAyY,13470
 gwaslab/g_SumstatsSet.py,sha256=xuGLpsHyhY2SjMVsFHGdL3iCa-Leb_3bu_R8totkzBY,30180
@@ -14,8 +14,7 @@ gwaslab/g_meta.py,sha256=pXtSsQfFPv2UJmOxKMmLtcsp_Ku_H73YP7PnlfMd0sg,6472
 gwaslab/g_meta_update.py,sha256=W1m6mh5jNUeZAW4T6F6kKZ10gE4l8YieoEC2mAfkzGg,2495
 gwaslab/g_vchange_status.py,sha256=lc3G65-QBV5k5yK-ySGIxiUT0hMBmESLhMKYncwjSwU,1986
 gwaslab/g_vchange_status_polars.py,sha256=kxyGQCur0ibVFBCyZghA-XNf_kLDXKK-l7VC-Om2IdA,1839
-gwaslab/g_version.py,sha256=pW2dwSPMZRQYVnUfhCRZJgqUZrsdoO-wzycgeKdD8L8,1964
-gwaslab/hm_harmonize_sumstats.py,sha256=WkUGNxftEGF5NAJktbEqQfniwcoD6zWHd-4bGrBxOtM,84472
+gwaslab/g_version.py,sha256=5CD7sWiCBN8MbBjnZvVpzZgVcUwOWQF64aXsu0VEgFU,1965
 gwaslab/run_script.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 gwaslab/bd/bd_common_data.py,sha256=mlw977K-ihKf7TQEn6FwUCyJ2vcnq6KIhrX6J3bRMVA,14226
 gwaslab/bd/bd_config.py,sha256=t3YeDMGRSP8k3lw4rHHilIM4jAXSzFOF9DtuuIbpDS8,924
@@ -65,7 +64,7 @@ gwaslab/util/util_ex_infer_ancestry.py,sha256=AXLEhuJUBT6XIYjADB-envFRGIZ-misneg
 gwaslab/util/util_ex_ldproxyfinder.py,sha256=8E4g82gCmolAvrg52urNMJX11MZMwOAPGQaZ4cfggiU,16918
 gwaslab/util/util_ex_ldsc.py,sha256=ss1QlwH7duLuVx_Ckb9mDbyz2neK8tv0WefUGCqzZUc,21685
 gwaslab/util/util_ex_match_ldmatrix.py,sha256=uVfHKxWQRtUQ0lUkt1o2LtZPSd3fh1yQ1rElFa4FDao,17525
-gwaslab/util/util_ex_phewwas.py,sha256=Reg3TUMDpLuUCNGHxpVa_fxrlzpeXFOUShTDXUcxiLk,5887
+gwaslab/util/util_ex_phewwas.py,sha256=oLbAgh_ULLWNP0m6bmD9xtx3EdDcH3HSIeTjxHX_0HU,8745
 gwaslab/util/util_ex_plink_filter.py,sha256=pK1Yxtv9-J4rMOdVAG7VU9PktvI6-y4FxBiVEH0QuRs,1673
 gwaslab/util/util_ex_process_h5.py,sha256=LqfQKBjXnbPSRUVJy9hhRhuoS5wG93yoIguiFDZN1A4,2837
 gwaslab/util/util_ex_process_ref.py,sha256=qtDRxJT0O2NgW4fd6VkRMxIHhSdzhSwz6bfa4iLQvcc,17132
@@ -81,7 +80,7 @@ gwaslab/util/util_ex_run_prscs.py,sha256=DJu-tIX6gQcdsZFcqESNM2NN0gO5vfhGBzwOgHO
 gwaslab/util/util_ex_run_scdrs.py,sha256=Oxjx5eTyfAXqv0-V2GrYJrm-loYaHJ_zY0U4Ictb3tk,3135
 gwaslab/util/util_ex_run_susie.py,sha256=Wp7aH8xSQb4mWmvMSYIEsBUInNwZhkxoxEbjY51PEl4,6847
 gwaslab/util/util_in_calculate_gc.py,sha256=MWOXVzJv7SZx4i2_ncRiqsiEOADc7EfghaUzgGy4jaE,2219
-gwaslab/util/util_in_calculate_power.py,sha256=JfHJFg3tNF0f4NHgWlzVW2mSxCiP07mAHIyEfVfxTak,10360
+gwaslab/util/util_in_calculate_power.py,sha256=iF7VPKhOyS-fCvO9kf94voqOUMvoIEFUYOTC49x4SZU,10424
 gwaslab/util/util_in_convert_h2.py,sha256=a8Cbudt3xn9WP2bPc-7ysuowB-LYub8j8GeDXl7Lk7Q,6483
 gwaslab/util/util_in_correct_winnerscurse.py,sha256=Gp--yAQ8MMzdkWIvXP9C1BHVjZc-YzqHfYWhAj19w9w,2110
 gwaslab/util/util_in_estimate_ess.py,sha256=QDOQ5vXfHtVkUEqX-TscsC831-FMTtGXXiHo1YxSFzU,1009
@@ -98,7 +97,8 @@ gwaslab/viz/viz_aux_chromatin.py,sha256=aWZaXOSvGyZY7wQcoFDaqHRYCSHZbi_K4Q70HruN
 gwaslab/viz/viz_aux_property.py,sha256=UIaivghnLXYpTwkKnXRK0F28Jbn9L6OaICk3K73WZaU,33
 gwaslab/viz/viz_aux_quickfix.py,sha256=6xgJYHBEz6iTRkuIAS1e28PQJH1eIViBCOMvczxI-BQ,18698
 gwaslab/viz/viz_aux_reposition_text.py,sha256=iRIP-Rkltlei068HekJcVubiqPrunBqvAoSQ1eHk04M,4304
-gwaslab/viz/viz_aux_save_figure.py,sha256=HwIRDMYpeXfkBgb7mqzLN7OVPMz163U-ZVOlQJABzeg,2811
+gwaslab/viz/viz_aux_save_figure.py,sha256=IOhojOCPPUDjZZYw7i4BgzCpAeasNpnzBTyrpiSoH_4,2856
+gwaslab/viz/viz_plot_associations.py,sha256=0hdepohuQOLft5nI2GVFLz-2Q0jUsLiJPTemkH7bNJI,2472
 gwaslab/viz/viz_plot_compare_af.py,sha256=pnL6pEQOSXZ1Zm2UTX-TdvTYSFD9zSY2vaJZSo4Ry_w,5348
 gwaslab/viz/viz_plot_compare_effect.py,sha256=KF0Ug4OwVwfl205Z5nRqGwXBLceuwJXYXj6378sT1Sg,69629
 gwaslab/viz/viz_plot_credible_sets.py,sha256=CjTtO5Dk2R-_GpZ0KN2NW0bN-EDga1OCjt9U8zDiTcw,5864
@@ -106,7 +106,7 @@ gwaslab/viz/viz_plot_effect.py,sha256=quWnT_WwERt61s0iVpnznQWgw8a5S3LeVkMuWNi6iE
 gwaslab/viz/viz_plot_forestplot.py,sha256=xgOnefh737CgdQxu5naVyRNBX1NQXPFKzf51fbh6afs,6771
 gwaslab/viz/viz_plot_miamiplot.py,sha256=nzPqP8HD2RElrFFP0OtnsYoAEjVpkfcvkRZNul6pJPg,31318
 gwaslab/viz/viz_plot_miamiplot2.py,sha256=7Ixar822FLGEe8Jo2y54cOfcBC_AxQnwvbM7qth_Juw,18100
-gwaslab/viz/viz_plot_mqqplot.py,sha256=n7PZ1ffPye1JMhjdCtL7wKuwWCWRHxuLCyNFCCtmTqw,74161
+gwaslab/viz/viz_plot_mqqplot.py,sha256=qAi7eVAHTqkZk6AQAEW1yPBrSpIsEkD9mQ-O4zhwzzU,74160
 gwaslab/viz/viz_plot_phe_heatmap.py,sha256=wUv3x7x2kyQWUfIrRiyxlAwILHbg3L4V-tMMvji8VQI,9589
 gwaslab/viz/viz_plot_qqplot.py,sha256=XVRabkCKrAV83I-bbdMt5Hh0wkZEyZPiq-Wxtiq7azs,6619
 gwaslab/viz/viz_plot_regional2.py,sha256=p-A1N-18ENo0FSwTW6rJlCacEeHJFW7dVwuQ91Ozv-8,43160
@@ -114,10 +114,11 @@ gwaslab/viz/viz_plot_regionalplot.py,sha256=UZSeXHfQlGWAYW_tMt00lZt8_vhiB6QcVLvM
 gwaslab/viz/viz_plot_rg_heatmap.py,sha256=AvVAlOOAwhqGWCses7MfdIXLVQSIA2SFE6bd7K1NaLw,13865
 gwaslab/viz/viz_plot_scatter_with_reg.py,sha256=0cpE6ui7yuJ1lhoLu_klac2OSzd5QDx6V51fyplB3GI,8366
 gwaslab/viz/viz_plot_stackedregional.py,sha256=bgVQir_Wj3TxB3o7NJFf7b8HETlWjppgfwLsbUyr3oo,20668
-gwaslab/viz/viz_plot_trumpetplot.py,sha256=_FKVkxckEFE11jZDwcHhF_bLuYbzxTWDaRTs6ylNEGg,42982
-gwaslab-3.6.8.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-gwaslab-3.6.8.dist-info/licenses/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
-gwaslab-3.6.8.dist-info/METADATA,sha256=wH3szvvkbal87X3T_iWS3KFB-vKDcy0OtCqqh7M2Gh4,7073
-gwaslab-3.6.8.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-gwaslab-3.6.8.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
-gwaslab-3.6.8.dist-info/RECORD,,
+gwaslab/viz/viz_plot_template.py,sha256=3tOT4pWcxN8je6XEcqPTQ7PJXEG25cwXUnDnoIhqjMA,2917
+gwaslab/viz/viz_plot_trumpetplot.py,sha256=BwQ22RdBEefLBdQU6H9eoYioZicjhFCvCARncXa_Jww,43862
+gwaslab-3.6.10.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+gwaslab-3.6.10.dist-info/licenses/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
+gwaslab-3.6.10.dist-info/METADATA,sha256=-3PRSVGLmsptQANloRqgg0zQESyteNHkhibxqRvudlI,7074
+gwaslab-3.6.10.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+gwaslab-3.6.10.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
+gwaslab-3.6.10.dist-info/RECORD,,