gwaslab 3.4.36__py3-none-any.whl → 3.4.37__py3-none-any.whl

gwaslab/util_in_fill_data.py

@@ -4,7 +4,7 @@ import scipy.stats as ss
 from scipy import stats
 from gwaslab.g_Log import Log
 import gc
-from gwaslab.qc_fix_sumstats import sortcolumn
+#from gwaslab.qc_fix_sumstats import sortcolumn
 from gwaslab.g_version import _get_version
 from gwaslab.qc_check_datatype import check_datatype
 
@@ -46,7 +46,7 @@ def filldata(
     fill_iteratively(sumstats,to_fill,log,only_sig,df,extreme,verbose,sig_level)
        
 # ###################################################################################
-    sumstats = sortcolumn(sumstats, verbose=verbose, log=log)
+    #sumstats = sortcolumn(sumstats, verbose=verbose, log=log)
     gc.collect()
     if verbose: log.write("Finished filling data using existing columns.")
     return sumstats
@@ -273,4 +273,43 @@ def fill_iteratively(sumstats,raw_to_fill,log,only_sig,df,extreme,verbose,sig_le
         if filled_count == 0:
             break
          
-        
+###Base functions########################################################################################
+
+def _convert_betase_to_z(beta, se):
+    return beta/se 
+
+def _convert_betase_to_p(beta, se):
+    z = _convert_betase_to_z(beta, se)
+    p = _convert_z_to_p(z)
+    return p
+
+def _convert_betase_to_mlog10p(beta, se):
+    z = _convert_betase_to_z(beta, se)
+    mlog10p = _convert_z_to_mlog10p(z)
+    return mlog10p
+
+def _convert_p_to_chisq(p):
+    return ss.chi2.isf(p, 1)
+
+def _convert_z_to_chisq(z):
+    return (z)**2
+
+def _convert_z_to_p(z):
+    return ss.chi2.sf(z**2,1) 
+
+def _convert_z_to_mlog10p(z):
+    log_pvalue = np.log(2) + ss.norm.logsf(np.abs(z)) #two-sided
+    mlog10p = log_pvalue/np.log(10)
+    return -mlog10p 
+
+def _conver_chisq_to_p(chisq):
+    return ss.chi2.sf(chisq,1)
+
+def _convert_mlog10p_to_p(mlog10p):
+    return np.power(10, -mlog10p) 
+
+def _convert_or_to_beta(OR):
+    return np.log(OR)  
+
+def _convert_beta_to_or(beta):
+    return np.exp(beta)   

gwaslab/viz_aux_quickfix.py

@@ -287,9 +287,9 @@ def _cut(series, mode,cutfactor,cut,skip, ylabels, cut_log, verbose,lines_to_plo
     maxy = series.max()
     series = series.copy()
     if "b" not in mode:
-        if verbose: log.write(" -Maximum -log10(P) values is "+str(maxy) +" .")
+        if verbose: log.write(" -Maximum -log10(P) value is "+str(maxy) +" .")
     elif "b" in mode:
-        if verbose: log.write(" -Maximum DENSITY values is "+str(maxy) +" .")
+        if verbose: log.write(" -Maximum DENSITY value is "+str(maxy) +" .")
     
     maxticker=int(np.round(series.max(skipna=True)))
     

gwaslab/viz_plot_compare_effect.py

@@ -36,6 +36,7 @@ def compare_effect(path1,
                    wc_correction=False, 
                    null_beta=0,
                    is_q=False,
+                   is_q_mc = False,
                    include_all=True,
                    q_level=0.05,
                    sig_level=5e-8,
@@ -530,9 +531,10 @@ def compare_effect(path1,
     if (is_q is True):
         if verbose: log.write(" -Calculating Cochran's Q statistics and peform chisq test...")
         if mode=="beta" or mode=="BETA" or mode=="Beta":
-            sig_list_merged = test_q(sig_list_merged,"EFFECT_1","SE_1","EFFECT_2_aligned","SE_2",q_level=q_level)
+            sig_list_merged = test_q(sig_list_merged,"EFFECT_1","SE_1","EFFECT_2_aligned","SE_2",q_level=q_level,is_q_mc=is_q_mc, log=log, verbose=verbose)
         else:
-            sig_list_merged = test_q(sig_list_merged,"BETA_1","SE_1","BETA_2_aligned","SE_2",q_level=q_level)
+            sig_list_merged = test_q(sig_list_merged,"BETA_1","SE_1","BETA_2_aligned","SE_2",q_level=q_level,is_q_mc=is_q_mc, log=log, verbose=verbose)
+
     ######################### save ###############################################################
     ## save the merged data
     save_path = label[0]+"_"+label[1]+"_beta_sig_list_merged.tsv"
@@ -806,8 +808,15 @@ def compare_effect(path1,
     if legend_mode == "full" and is_q==True :
         title_proxy = Rectangle((0,0), 0, 0, color='w',label=legend_title)
         title_proxy2 = Rectangle((0,0), 0, 0, color='w',label=legend_title2)
-        het_label_sig = r"$P_{het} < $" + "${}$".format(q_level)
-        het_label_sig2 = r"$P_{het} > $" + "${}$".format(q_level)
+        if is_q_mc=="fdr":
+            het_label_sig = r"$FDR_{het} < $" + "${}$".format(q_level)
+            het_label_sig2 = r"$FDR_{het} > $" + "${}$".format(q_level)
+        elif is_q_mc=="bon":
+            het_label_sig = r"$P_{het,bon} < $" + "${}$".format(q_level)
+            het_label_sig2 = r"$P_{het,bon} > $" + "${}$".format(q_level)
+        else:
+            het_label_sig = r"$P_{het} < $" + "${}$".format(q_level)
+            het_label_sig2 = r"$P_{het} > $" + "${}$".format(q_level)
         het_sig = Rectangle((0,0), 0, 0, facecolor='#cccccc',edgecolor="black", linewidth=1, label=het_label_sig)
         het_nonsig = Rectangle((0,0), 0, 0, facecolor='#cccccc',edgecolor="white",linewidth=1, label=het_label_sig2)
         
@@ -876,7 +885,7 @@ def reorderLegend(ax=None, order=None, add=None):
     new_handles = [info[l] for l in order]
     return new_handles, order
 
-def test_q(df,beta1,se1,beta2,se2,q_level=0.05):
+def test_q(df,beta1,se1,beta2,se2,q_level=0.05,is_q_mc=False, log=Log(), verbose=False):
     w1="Weight_1"
     w2="Weight_2"
     beta="BETA_FE"
@@ -891,6 +900,14 @@ def test_q(df,beta1,se1,beta2,se2,q_level=0.05):
     df[q] = df[w1]*(df[beta1]-df[beta])**2 + df[w2]*(df[beta2]-df[beta])**2
     df[pq] = ss.chi2.sf(df[q], 1)
     df["Edge_color"]="white"
+
+    if is_q_mc=="fdr":
+        if verbose: log.write(" -FDR correction applied...")
+        df[pq] = ss.false_discovery_control(df[pq])
+    elif is_q_mc=="bon":
+        if verbose: log.write(" -Bonferroni correction applied...")
+        df[pq] = df[pq] * len(df[pq])
+
     df.loc[df[pq]<q_level,"Edge_color"]="black"
     df.drop(columns=["Weight_1","Weight_2","BETA_FE"],inplace=True)
     # Huedo-Medina, T. B., Sánchez-Meca, J., Marín-Martínez, F., & Botella, J. (2006). Assessing heterogeneity in meta-analysis: Q statistic or I² index?. Psychological methods, 11(2), 193.

gwaslab/viz_plot_mqqplot.py

@@ -104,6 +104,15 @@ def mqqplot(insumstats,
           region_protein_coding = True,
           region_flank_factor = 0.05,
           region_anno_bbox_args = None,
+          cbar_title='LD $r^{2}$',
+          cbar_fontsize = None,
+          cbar_font_family = None,
+          track_n=4,
+          track_n_offset=0,
+          track_fontsize_ratio=0.95,
+          track_exon_ratio=1,
+          track_text_offset=1,
+          track_font_family = None,
           taf = None,
           # track_n, track_n_offset,font_ratio,exon_ratio,text_offset
           tabix=None,
@@ -243,8 +252,14 @@ def mqqplot(insumstats,
         region_ld_colors2 = ["#E4E4E4","#D8E2F2","#AFCBE3","#86B3D4","#5D98C4","#367EB7","#367EB7"]
     if region_title_args is None:
         region_title_args = {"size":10}
+    if cbar_fontsize is None:
+        cbar_fontsize = fontsize
+    if cbar_font_family is None:
+        cbar_font_family = font_family
+    if track_font_family is None:
+        track_font_family = font_family
     if taf is None:
-        taf = [4,0,0.95,1,1]
+        taf = [track_n,track_n_offset,track_fontsize_ratio,track_exon_ratio,track_text_offset]
     if maf_bins is None:
         maf_bins=[(0, 0.01), (0.01, 0.05), (0.05, 0.25),(0.25,0.5)]
     if maf_bin_colors is None:
@@ -289,13 +304,13 @@ def mqqplot(insumstats,
                     scatter_args["rasterized"]=True
                     qq_scatter_args["rasterized"]=True
 
-    if verbose: log.write("Start to plot manhattan/qq plot with the following basic settings {}:".format(_get_version()))
+    if verbose: log.write("Start to create MQQ plot with the following basic settings {}:".format(_get_version()))
     if verbose: log.write(" -Genomic coordinates version: {}...".format(build))
     if build is None or build=="99":
         if verbose: log.write("   -WARNING: Genomic coordinates version is unknown...")
     if verbose: log.write(" -Genome-wide significance level to plot is set to "+str(sig_level_plot)+" ...")
     if verbose: log.write(" -Raw input contains "+str(len(insumstats))+" variants...")
-    if verbose: log.write(" -Plot layout mode is : "+mode)
+    if verbose: log.write(" -MQQ plot layout mode is : "+mode)
     if len(anno_set)>0 and ("m" in mode):
         if verbose: log.write(" -Variants to annotate : "+",".join(anno_set))    
     if len(highlight)>0 and ("m" in mode):
@@ -340,13 +355,14 @@ def mqqplot(insumstats,
     # ax2 : qq plot 
     # ax3 : gene track
     # ax4 : recombination rate
+    # cbar : color bar
     # ax5 : miami plot lower panel
 
     # "m" : Manhattan plot
     # "qq": QQ plot
     # "r" : regional plot
     
-    fig, ax1, ax2, ax3 = _process_layout(mode=mode, 
+    fig, ax1, ax2, ax3, ax4, cbar = _process_layout(mode=mode, 
                                          figax=figax, 
                                          fig_args=fig_args, 
                                          mqqratio=mqqratio, 
@@ -553,7 +569,7 @@ def mqqplot(insumstats,
         if vcf_path is not None:
             sumstats["chr_hue"]=sumstats["LD"]
 
-        if verbose:log.write("Start to create manhattan plot with "+str(len(sumstats))+" variants:")
+        if verbose:log.write("Start to create MQQ plot with "+str(len(sumstats))+" variants:")
         ## default seetings
         
         palette = sns.color_palette(colors,n_colors=sumstats[chrom].nunique())  
@@ -697,7 +713,7 @@ def mqqplot(insumstats,
         # if regional plot : pinpoint lead , add color bar ##################################################
         if (region is not None) and ("r" in mode):
             
-            ax1, ax3, lead_snp_i, lead_snp_i2 =_plot_regional(
+            ax1, ax3, ax4, cbar, lead_snp_i, lead_snp_i2 =_plot_regional(
                                 sumstats=sumstats,
                                 fig=fig,
                                 ax1=ax1,
@@ -738,6 +754,7 @@ def mqqplot(insumstats,
                                 region_recombination = region_recombination,
                                 region_protein_coding=region_protein_coding,
                                 region_flank_factor =region_flank_factor,
+                                track_font_family=track_font_family,
                                 taf=taf,
                                 tabix=tabix,
                                 chrom=chrom,
@@ -745,44 +762,11 @@ def mqqplot(insumstats,
                                 verbose=verbose,
                                 log=log
                             )
+            
         else:
             lead_snp_i= None
             lead_snp_i2=None
-            
-        if region is None:
-            ax1 = _process_xtick(ax1, chrom_df, xtick_chr_dict, fontsize, font_family)
-        
-        # genomewide significant line
-        ax1 = _process_line(ax1, 
-                            sig_line, 
-                            suggestive_sig_line, 
-                            additional_line, 
-                            lines_to_plot , 
-                            sc_linewidth, 
-                            sig_line_color, 
-                            suggestive_sig_line_color, 
-                            additional_line_color,
-                            mode, 
-                            bmean, 
-                            bmedian )
         
-        ax1 = _set_yticklabels(cut=cut,
-                     cutfactor=cutfactor,
-                     cut_log=cut_log,
-                     ax1=ax1,
-                     skip=skip,
-                     maxy=maxy,
-                     maxticker=maxticker,
-                     ystep=ystep,
-                     sc_linewidth=sc_linewidth,
-                     cut_line_color=cut_line_color,
-                     fontsize=fontsize,
-                     font_family=font_family,
-                     ytick3=ytick3,
-                     ylabels=ylabels,
-                     ylabels_converted=ylabels_converted
-                     )
-
         # Get top variants for annotation #######################################################
         if (anno and anno!=True) or (len(anno_set)>0):
             if len(anno_set)>0:
@@ -826,11 +810,72 @@ def mqqplot(insumstats,
                                    verbose=verbose).rename(columns={"GENE":"Annotation"})
 
         # Configure X, Y axes #######################################################
-        ax1 = _process_ylabel(ylabel, ax1,  mode, bwindowsizekb, fontsize, font_family)
-        ax1, ax3 = _process_xlabel(region, xlabel, ax1, gtf_path, mode, fontsize, font_family,  ax3=ax3 )
-        ax1 = _process_spine(ax1, mode)
+        if region is None:
+            # if Manhattan plot 
+            ax1 = _process_xtick(ax1=ax1, 
+                                 chrom_df=chrom_df, 
+                                 xtick_chr_dict=xtick_chr_dict, 
+                                 fontsize = fontsize, 
+                                 font_family=font_family)
         
-        if verbose: log.write("Finished creating Manhattan plot successfully!")
+        ax1, ax3 = _process_xlabel(region=region, 
+                                   xlabel=xlabel, 
+                                   ax1=ax1, 
+                                   gtf_path=gtf_path, 
+                                   mode=mode, 
+                                   fontsize=fontsize, 
+                                   font_family=font_family,  
+                                   ax3=ax3 )
+        
+        ax1, ax4 = _process_ylabel(ylabel=ylabel, 
+                                   ax1=ax1,  
+                                   mode=mode, 
+                                   bwindowsizekb=bwindowsizekb, 
+                                   fontsize=fontsize, 
+                                   font_family=font_family, 
+                                   ax4=ax4)     
+        
+        ax1 = _set_yticklabels(cut=cut,
+                     cutfactor=cutfactor,
+                     cut_log=cut_log,
+                     ax1=ax1,
+                     skip=skip,
+                     maxy=maxy,
+                     maxticker=maxticker,
+                     ystep=ystep,
+                     sc_linewidth=sc_linewidth,
+                     cut_line_color=cut_line_color,
+                     fontsize=fontsize,
+                     font_family=font_family,
+                     ytick3=ytick3,
+                     ylabels=ylabels,
+                     ylabels_converted=ylabels_converted
+                     )
+        
+        ax1, ax4 = _process_ytick(ax1=ax1,  
+                                   fontsize=fontsize, 
+                                   font_family=font_family, 
+                                   ax4=ax4)  
+        
+        if cbar is not None:
+            # regional plot cbar
+            cbar = _process_cbar(cbar, cbar_fontsize=fontsize, cbar_font_family=font_family, cbar_title=cbar_title)        
+        
+        ax1 = _process_spine(ax1, mode)
+        # genomewide significant line
+        ax1 = _process_line(ax1, 
+                            sig_line, 
+                            suggestive_sig_line, 
+                            additional_line, 
+                            lines_to_plot , 
+                            sc_linewidth, 
+                            sig_line_color, 
+                            suggestive_sig_line_color, 
+                            additional_line_color,
+                            mode, 
+                            bmean, 
+                            bmedian )  
+
         
         if mtitle and anno and len(to_annotate)>0: 
             pad=(ax1.transData.transform((skip, title_pad*maxy))[1]-ax1.transData.transform((skip, maxy)))[1]
@@ -872,7 +917,7 @@ def mqqplot(insumstats,
                                 log=log,
                                _invert=_invert
                             )  
-    # Manhatann plot Finished #####################################################################
+    # Manhatann-like plot Finished #####################################################################
 
     # QQ plot #########################################################################################################
     if "qq" in mode:
@@ -943,6 +988,8 @@ def mqqplot(insumstats,
     # Return matplotlib figure object #######################################################################################
     if _get_region_lead==True:
         return fig, log, lead_snp_i, lead_snp_i2
+    
+    if verbose: log.write("Finished creating MQQ plot successfully!")
     return fig, log
 
 ##############################################################################################################################################################################
@@ -1173,11 +1220,34 @@ def _process_line(ax1, sig_line, suggestive_sig_line, additional_line, lines_to_
         medianline = ax1.axhline(y=bmedian, linewidth = sc_linewidth,linestyle="--",color=sig_line_color,zorder=1000)
     return ax1
 
+def _process_cbar(cbar, cbar_fontsize, cbar_font_family, cbar_title):
+    if str(type(cbar))=="list":
+        for cbar_single in cbar:
+            cbar_yticklabels = cbar_single.ax.get_yticklabels()
+            cbar_single.ax.set_yticklabels(cbar_yticklabels, fontsize=cbar_fontsize, family=cbar_font_family )
+            cbar_single.ax.set_title(cbar_title, fontsize=cbar_fontsize, family=cbar_font_family, loc="center",y=-0.2 )
+    else:
+        cbar_yticklabels = cbar.ax.get_yticklabels()
+        cbar.ax.set_yticklabels(cbar_yticklabels, fontsize=cbar_fontsize, family=cbar_font_family )
+        cbar.ax.set_title(cbar_title, fontsize=cbar_fontsize, family=cbar_font_family, loc="center",y=-0.2 )
+    return cbar
+
 def _process_xtick(ax1, chrom_df, xtick_chr_dict, fontsize, font_family):
     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, fontsize, font_family, ax4):
+    ax1_yticklabels = ax1.get_yticklabels()
+    #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) 
+    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) 
+    return ax1, ax4
+
 def _process_xlabel(region, xlabel, ax1, gtf_path, mode, fontsize, font_family,  ax3=None ):
     if region is not None:
         if xlabel is None:
@@ -1192,7 +1262,7 @@ def _process_xlabel(region, xlabel, ax1, gtf_path, mode, fontsize, font_family,
         ax1.set_xlabel(xlabel,fontsize=fontsize,family=font_family)
     return ax1, ax3
 
-def _process_ylabel(ylabel, ax1,  mode, bwindowsizekb, fontsize, font_family):
+def _process_ylabel(ylabel, ax1,  mode, bwindowsizekb, fontsize, font_family, ax4=None):
     if "b" in mode:
         if ylabel is None:
             ylabel ="Density of GWAS \n SNPs within "+str(bwindowsizekb)+" kb"
@@ -1201,7 +1271,10 @@ def _process_ylabel(ylabel, ax1,  mode, bwindowsizekb, fontsize, font_family):
         if ylabel is None:
             ylabel ="$-log_{10}(P)$"
         ax1.set_ylabel(ylabel,fontsize=fontsize,family=font_family)
-    return ax1
+    if ax4 is not None:
+        ax4_ylabel = ax4.get_ylabel()
+        ax4.set_ylabel(ax4_ylabel, fontsize=fontsize, family=font_family )
+    return ax1, ax4
 
 def _process_spine(ax1, mode):
     ax1.spines["top"].set_visible(False)
@@ -1218,6 +1291,7 @@ def _process_layout(mode, figax, fig_args, mqqratio, region_hspace):
     if  mode=="qqm": 
         fig, (ax2, ax1) = plt.subplots(1, 2,gridspec_kw={'width_ratios': [1, mqqratio]},**fig_args)
         ax3 = None
+
     elif mode=="mqq":
         if figax is not None:
             fig = figax[0]
@@ -1226,6 +1300,7 @@ def _process_layout(mode, figax, fig_args, mqqratio, region_hspace):
         else:
             fig, (ax1, ax2) = plt.subplots(1, 2,gridspec_kw={'width_ratios': [mqqratio, 1]},**fig_args)
         ax3 = None
+
     elif mode=="m":
         if figax is not None:
             fig = figax[0]
@@ -1234,10 +1309,12 @@ def _process_layout(mode, figax, fig_args, mqqratio, region_hspace):
             fig, ax1 = plt.subplots(1, 1,**fig_args)
         ax2 = None
         ax3 = None
+
     elif mode=="qq": 
         fig, ax2 = plt.subplots(1, 1,**fig_args) 
         ax1=None
         ax3=None
+
     elif mode=="r": 
         if figax is not None:
             fig = figax[0]
@@ -1257,4 +1334,6 @@ def _process_layout(mode, figax, fig_args, mqqratio, region_hspace):
         ax3 = None
     else:
         raise ValueError("Please select one from the 5 modes: mqq/qqm/m/qq/r/b")
-    return fig, ax1, ax2, ax3
+    ax4=None
+    cbar=None
+    return fig, ax1, ax2, ax3, ax4, cbar

gwaslab/viz_plot_regionalplot.py

@@ -64,6 +64,7 @@ def _plot_regional(
     region_recombination = True,
     region_protein_coding=True,
     region_flank_factor = 0.05,
+    track_font_family="Arial",
     taf=[4,0,0.95,1,1],
     # track_n, track_n_offset,font_ratio,exon_ratio,text_offset
     tabix=None,
@@ -104,21 +105,23 @@ def _plot_regional(
 
         if (vcf_path is not None) and region_ld_legend:
             if region_ref_second is None:
-                ax1 = _add_ld_legend(sumstats=sumstats, 
+                ax1, cbar = _add_ld_legend(sumstats=sumstats, 
                                 ax1=ax1, 
                                 region_ld_threshold=region_ld_threshold, 
                                 region_ld_colors=region_ld_colors)
             else:
-                ax1 = _add_ld_legend(sumstats=sumstats, 
+                
+                ax1, cbar1 = _add_ld_legend(sumstats=sumstats, 
                                 ax1=ax1, 
                                 region_ld_threshold=region_ld_threshold, 
                                 region_ld_colors=region_ld_colors1,
                                 position=1)
-                ax1 = _add_ld_legend(sumstats=sumstats, 
+                ax1, cbar2 = _add_ld_legend(sumstats=sumstats, 
                                 ax1=ax1, 
                                 region_ld_threshold=region_ld_threshold, 
                                 region_ld_colors=region_ld_colors2,
                                 position=2)
+                cbar = [cbar1, cbar2]
         if region_title is not None:
                 ax1 = _add_region_title(region_title, ax1=ax1,region_title_args=region_title_args )
     ## recombinnation rate ##################################################       
@@ -176,6 +179,7 @@ def _plot_regional(
                         gene_track_start_i=gene_track_start_i,
                         gtf_chr_dict=gtf_chr_dict,
                         gtf_gene_name=gtf_gene_name, 
+                        track_font_family=track_font_family,
                         taf=taf,
                         build=build, 
                         verbose=verbose, 
@@ -231,7 +235,7 @@ def _plot_regional(
                     avoid_points=False,
                     lim =1000)     
     
-    return ax1, ax3, lead_snp_i, lead_snp_i2
+    return ax1, ax3, ax4, cbar, lead_snp_i, lead_snp_i2
 
 # + ###########################################################################################################################################################################
 def _get_lead_id(sumstats=None, region_ref=None, log=None):
@@ -336,7 +340,7 @@ def _add_ld_legend(sumstats, ax1, region_ld_threshold, region_ld_colors,position
                                 facecolor='white',
                                 zorder=999998)
     ax1.add_patch(rect)
-    return ax1
+    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):
@@ -385,6 +389,7 @@ def _plot_gene_track(
     region_ld_colors2,
     gene_track_start_i,
     gtf_chr_dict,gtf_gene_name, 
+    track_font_family,
     taf,
     build, 
     verbose=True, 
@@ -452,15 +457,15 @@ def _plot_gene_track(
         if row["end"] >= region[2]:
             #right side
             texts_to_adjust_right.append(ax3.text(x=gene_track_start_i+region[2],
-                    y=row["stack"]*2+taf[4],s=gene_anno,ha="right",va="center",color="black",style='italic', size=font_size_in_points))
+                    y=row["stack"]*2+taf[4],s=gene_anno,ha="right",va="center",color="black",style='italic', size=font_size_in_points,family=track_font_family))
             
         elif row["start"] <= region[1] :
             #left side
             texts_to_adjust_left.append(ax3.text(x=gene_track_start_i+region[1],
-                    y=row["stack"]*2+taf[4],s=gene_anno,ha="left",va="center",color="black",style='italic', size=font_size_in_points))
+                    y=row["stack"]*2+taf[4],s=gene_anno,ha="left",va="center",color="black",style='italic', size=font_size_in_points,family=track_font_family))
         else:
             texts_to_adjust_middle.append(ax3.text(x=(gene_track_start_i+row["start"]+gene_track_start_i+row["end"])/2,
-                    y=row["stack"]*2+taf[4],s=gene_anno,ha="center",va="center",color="black",style='italic',size=font_size_in_points))
+                    y=row["stack"]*2+taf[4],s=gene_anno,ha="center",va="center",color="black",style='italic',size=font_size_in_points,family=track_font_family))
     
     # plot exons
     for index,row in exons.iterrows():

{gwaslab-3.4.36.dist-info → gwaslab-3.4.37.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gwaslab
-Version: 3.4.36
+Version: 3.4.37
 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: <=3.10,>=3.8
+Requires-Python: <=3.10,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: pandas !=1.5,>=1.3

{gwaslab-3.4.36.dist-info → gwaslab-3.4.37.dist-info}/RECORD

@@ -1,34 +1,34 @@
-gwaslab/__init__.py,sha256=vD_LWA3kzEkPtrFT5EnmqMiBWN6xTERIMDJbN00p2oE,2382
+gwaslab/__init__.py,sha256=dFnrh4L620F5JirsSF98SmkuligA-fybIGdBF6r9Ims,2386
 gwaslab/bd_common_data.py,sha256=-YlytsRU3YnwI23EV0U_pFWZ0_0yL23_RwTfBajEuPw,11844
 gwaslab/bd_config.py,sha256=TP-r-DPhJD3XnRYZbw9bQHXaDIkiRgK8bG9HCt-UaLc,580
 gwaslab/bd_download.py,sha256=Nh09FP_d5kLsAyEF-WOYd7tty-ypvJv0PSTEO4JB2cc,15636
 gwaslab/bd_get_hapmap3.py,sha256=poqV3Ko56xhRFKdSK0ROwDQ71b27-9bMOQ0XO36To5c,2034
 gwaslab/g_Log.py,sha256=ICCzc2iP-toIRhXSnRufMqJrB6MtstJXk5qmC2yK6pY,821
 gwaslab/g_Phenotypes.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-gwaslab/g_Sumstats.py,sha256=W8XAP6C1nxs4uFQWi8hOx1qPG03hkV4wFVIwfNvKtNc,32004
+gwaslab/g_Sumstats.py,sha256=9Qu5RFKgeZIkhHp-YwYZcECQOLV8dOGHvx2y9YVO3LA,33210
 gwaslab/g_SumstatsPair.py,sha256=eFFcL0foi7KJ2t7yf98WIyUMv-Kl6IrvSdv3FtqZmXs,5971
 gwaslab/g_SumstatsT.py,sha256=r3fAN-LsUIJhi7mhLH_4NBwHCOawVkbWULKY1vbmdZY,2113
 gwaslab/g_Sumstats_summary.py,sha256=Q69702tABxTVk6QIbqQ4k6eSujhXr_MVVQ5saOdEhlk,6367
-gwaslab/g_meta.py,sha256=KT5Es_xeCijxZ35fb6qyJ1LiBQ8WIuo5eEjGy048qVE,2193
+gwaslab/g_meta.py,sha256=htWlgURWclm9R6UqFcX1a93WN27xny7lGUeyJZOtszQ,2583
 gwaslab/g_vchange_status.py,sha256=eX0jdIb6Spa07ZdpWNqUWqdVBWS0fuH2yrt4PDi3Res,1746
-gwaslab/g_version.py,sha256=hr_Dl0fwgypHQHtSjlnr-IyGSYg_cFrq7ftAZbYGMOA,1688
+gwaslab/g_version.py,sha256=nM7GpPDOdGl2i6-JJyZDrSlJfCCWoq9dFIfHrTcQTQg,1688
 gwaslab/hm_casting.py,sha256=w8Qz0IlFwmn4_uUc7aOccWZCfY_e19ZZr-iYgCu-SnQ,10350
-gwaslab/hm_harmonize_sumstats.py,sha256=yPY_CpQzjd_YkwW_jXGePHkqeDcs7Kzl_eMpE5bnxKI,40859
+gwaslab/hm_harmonize_sumstats.py,sha256=l8kHWVJkveRfzeKjvh6Mx5Z_QLy52GSL_9euYnFtH-U,41692
 gwaslab/hm_rsid_to_chrpos.py,sha256=-pKhY654zS4uULW7FP4yGHNy3e9Wc2ujc1VLBaoUO5A,6564
-gwaslab/io_preformat_input.py,sha256=3dkwgo-eyKpML5U8cmphvQEqWKuome8sKcjpF1JBq7w,19486
+gwaslab/io_preformat_input.py,sha256=vusQAi9vR1Bn8K4Zf9KmDwuwqrhSaAZNZ4zHp6yfjxY,19625
 gwaslab/io_read_ldsc.py,sha256=mro3Vc3dQs6dQ2zsUaUYHOqJGIhJaNzxPeE3zsfO7dA,8659
 gwaslab/io_read_tabular.py,sha256=_gI0EA4CDecTPHTDp6hW2PesagYHHbBQvI_tW8U3Tc8,2366
 gwaslab/io_to_formats.py,sha256=tayh5qoxe9tn_g3mHTbfT3Jkz7kTo8BOPjpMtoMlfAY,21111
 gwaslab/io_to_pickle.py,sha256=XmxhV5-38ED8aEyPYzsskv7HrxCyge9tHJ2F21QA8Ms,1824
-gwaslab/qc_check_datatype.py,sha256=mD0_wfgQsDRx8LFRQ_xaJ9zxDm9A6ZaNDxVOFn-SllU,2737
-gwaslab/qc_fix_sumstats.py,sha256=VdMxXd9IXCRxKzhW1lZXJUaPC77F83glXbw_clwoK7o,80794
+gwaslab/qc_check_datatype.py,sha256=ue_C7bjuL7NllOJNv8ReQESxpbXogleKGlw8ntWFi6Y,3440
+gwaslab/qc_fix_sumstats.py,sha256=XME1RzZqdoKc8bO7NLuyMu_t7gudt1tpMsNdiT6BIcU,87581
 gwaslab/run_script.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 gwaslab/util_ex_calculate_ldmatrix.py,sha256=hjFOZqGfQixTjMSxgVbB-JQwP0QcQMKfbhs-dsLT5Qw,12112
 gwaslab/util_ex_calculate_prs.py,sha256=uOcMRWujEYMYGuO-qGe3okQJYizXGvqDcomXlzLvln8,9049
 gwaslab/util_ex_gwascatalog.py,sha256=Y3CiBu03yrJ4SDubl3mOq62fIkbr7bZ1lwbhWEVWKmA,7576
 gwaslab/util_ex_ldproxyfinder.py,sha256=C705kiw673DaijrccJ8ifO2IXR9RHP8B7Jfp0_-7UWo,9398
 gwaslab/util_ex_plink_filter.py,sha256=Ak09-tEIS_uq1OtiCmcDCXcEjzQHCEfp44AKkhgoOzY,1669
-gwaslab/util_ex_process_h5.py,sha256=Xcdr3sqZ1RpVUdjUKp0nCp50lIuIFL4cojQYhYI6D5w,2267
+gwaslab/util_ex_process_h5.py,sha256=1QzcQurnwedYFiF4ZaEOv0Wl41rBEUjS7yVcMWNIslE,2741
 gwaslab/util_ex_process_ref.py,sha256=vB5tDnlpnStLJq1QgxwhJQ1wRlQ8hy-yI5smm2wUjaA,16445
 gwaslab/util_ex_run_2samplemr.py,sha256=AvhpR_ihR052LBabR1wfEaBqfwCs88VW8Q2ijdKMfUs,9040
 gwaslab/util_ex_run_clumping.py,sha256=fE-PHeYjl8I08ycwCbJrQjF3wixMDYKNe4EASupEMpo,6816
@@ -38,22 +38,22 @@ gwaslab/util_in_calculate_gc.py,sha256=HqyBBDorWoBlmD1i4K2Vr4vTTPqg5YLM8ktdvCpKe
 gwaslab/util_in_calculate_power.py,sha256=Kk46GHKDcub6l1XTT-ZT5hrPmR8EUa_tS_LIPbLRvbU,10112
 gwaslab/util_in_convert_h2.py,sha256=azqGs9whhhukVDFruAwTobor4-LnGHWIOrhK_avRnWs,6468
 gwaslab/util_in_correct_winnerscurse.py,sha256=o7CjUwLp4B_60yrntV76ESNaoPcl-HPOzSw9cYWzpW4,2050
-gwaslab/util_in_fill_data.py,sha256=5J8zt2-wuzL_ehC2JKg2IO-RcQ2eE8yS9X3R6tjsRf4,12873
+gwaslab/util_in_fill_data.py,sha256=vVtxWN-BRDPsGCIEIGJ9cWCayiWBYuOdV3kZyakhpFA,13847
 gwaslab/util_in_filter_value.py,sha256=rF2Nv1H-dxJZIIvw0r1tCB2xAFXt75qbpNJOpnEVffw,14647
 gwaslab/util_in_get_density.py,sha256=n4GFhuqyJ4HBepHJeMXVsddGRweFBaBQNueMg3hs4D8,3905
 gwaslab/util_in_get_sig.py,sha256=hrZrLb50h2V-PtPXkwJ2F_jc1piMJ2wJqWTqSq9cnEg,19805
 gwaslab/viz_aux_annotate_plot.py,sha256=BKwvyXydKjgFo2w2ZCwxtxRLGT-g5e6eayhkSje3Lfc,32124
-gwaslab/viz_aux_quickfix.py,sha256=hrrLADC9h1J7SCL1KDUYf-8zGrhXRHMvrwARSYpNExw,17906
+gwaslab/viz_aux_quickfix.py,sha256=AP7Yg1TQ0q810BKRCM5jLXAjPSFehs2vxY2ocIFr7Ag,17904
 gwaslab/viz_aux_reposition_text.py,sha256=N0jMQSAnFPFWwx9mUFTcVtntdA56I_3vB332jtpezU4,4233
 gwaslab/viz_aux_save_figure.py,sha256=KfpYuSNxYv0EvcoR5n2AWjnGnJzFrYfyoGfJd71NYMQ,2083
 gwaslab/viz_plot_compare_af.py,sha256=vVypmnF-l6JzXyi5HPYFr-GM-OmNQGvip8oTCBvvHsk,5532
-gwaslab/viz_plot_compare_effect.py,sha256=LVRPRpbwrlxEvJPDauKTgPy4zZss3RylnLBOoqdTzEM,49019
+gwaslab/viz_plot_compare_effect.py,sha256=iUlp6tUS7OSlffgGyUIH4tPXQB_BK19OQZSo7xhToRA,49817
 gwaslab/viz_plot_forestplot.py,sha256=xgOnefh737CgdQxu5naVyRNBX1NQXPFKzf51fbh6afs,6771
 gwaslab/viz_plot_miamiplot.py,sha256=rCFEp7VNuVqeBBG3WRkmFAtFklbF79BvIQQYiSY70VY,31238
 gwaslab/viz_plot_miamiplot2.py,sha256=aJcA5eEY44VuGMZMBKM6aPE1D_D6w2O2Jmw5QwUoyik,15371
-gwaslab/viz_plot_mqqplot.py,sha256=PHZ_f1MPg5aqwTyBDcaT6xpNLzkWqUaNb9efqLx0tiE,55775
+gwaslab/viz_plot_mqqplot.py,sha256=nMorIAlepN2IpeWtCfinIzsEfLdjIBCvRSE12b-Rk2U,59112
 gwaslab/viz_plot_qqplot.py,sha256=XVnNbX5oXk2yvXT4uSuGtWW1fbr_FzAlWNjRW_bWmyU,7012
-gwaslab/viz_plot_regionalplot.py,sha256=rIaX99Drq3kCTyahthbkpek3Tf0UpFXLfpIGX_iAh70,37122
+gwaslab/viz_plot_regionalplot.py,sha256=oTY-5eAnPpKyiKBbgXMer2nJHwWT3HBQokxWMit_0Gs,37404
 gwaslab/viz_plot_rg_heatmap.py,sha256=nibSCUnY_ZskCpJx7ppOgyqOuXBaWy6r7c_1McrQmZ0,13877
 gwaslab/viz_plot_stackedregional.py,sha256=Ne7ncUN4iwmYKaDR8ZXeAFYPw29o_M2JzAnZRkyeMA0,9894
 gwaslab/viz_plot_trumpetplot.py,sha256=YAcLDgqPr9JK0vKo_ZDtfKgkhHpQVOxeg2UnbQ2HsA8,37002
@@ -65,8 +65,8 @@ 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-3.4.36.dist-info/LICENSE,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
-gwaslab-3.4.36.dist-info/METADATA,sha256=j5hCOz5Mas0ZHjMla_nMOJJxysnkkqiv3FSclqR0Z34,6806
-gwaslab-3.4.36.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-gwaslab-3.4.36.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
-gwaslab-3.4.36.dist-info/RECORD,,
+gwaslab-3.4.37.dist-info/LICENSE,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
+gwaslab-3.4.37.dist-info/METADATA,sha256=f_nK22RXPBbzF69Zhhx4eIQVIYhsHxZMmZnh5Jkb-wM,6806
+gwaslab-3.4.37.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+gwaslab-3.4.37.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
+gwaslab-3.4.37.dist-info/RECORD,,