gwaslab 3.4.36__py3-none-any.whl → 3.4.38__py3-none-any.whl

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,
@@ -204,7 +213,6 @@ def mqqplot(insumstats,
         chr_dict = get_chr_to_number()
     if xtick_chr_dict is None:         
         xtick_chr_dict = get_number_to_chr()
-
     if gtf_chr_dict is None:   
         gtf_chr_dict = get_number_to_chr()
     if rr_chr_dict is None:   
@@ -243,8 +251,14 @@ 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:
@@ -289,40 +303,42 @@ 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(" -Genomic coordinates version: {}...".format(build))
+    log.write("Start to create MQQ plot...{}:".format(_get_version()),verbose=verbose)
+    log.write(" -Genomic coordinates version: {}...".format(build),verbose=verbose)
     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)
+        log.warning("Genomic coordinates version is unknown.")
+    log.write(" -Genome-wide significance level to plot is set to "+str(sig_level_plot)+" ...",verbose=verbose)
+    log.write(" -Raw input contains "+str(len(insumstats))+" variants...",verbose=verbose)
+    log.write(" -MQQ plot layout mode is : "+mode,verbose=verbose)
+    
     if len(anno_set)>0 and ("m" in mode):
-        if verbose: log.write(" -Variants to annotate : "+",".join(anno_set))    
+        log.write(" -Variants to annotate : "+",".join(anno_set),verbose=verbose)    
+    
     if len(highlight)>0 and ("m" in mode):
         if pd.api.types.is_list_like(highlight[0]):
             if highlight_chrpos==False:
-                if len(highlight[0]) == len(highlight_color):
-                    log.write(" -WARNING: number of locus list does not match number of colors !!!")
+                if len(highlight) != len(highlight_color):
+                    log.warning("Number of locus groups in the list does not match number of provided colors.")
                 for i, highlight_set in enumerate(highlight):
-                    if verbose: log.write(" -Set {} loci to highlight ({}) : ".format(i+1, highlight_color[i%len(highlight_color)])+",".join(highlight_set))
+                    log.write(" -Set {} loci to highlight ({}) : ".format(i+1, highlight_color[i%len(highlight_color)])+",".join(highlight_set),verbose=verbose)
             else:
-                if verbose: log.write(" -Loci to highlight ({}): {}".format(highlight_color,highlight))
-            if verbose: log.write("  -Highlight_window is set to: ", highlight_windowkb, " kb") 
+                log.write(" -Loci to highlight ({}): {}".format(highlight_color,highlight),verbose=verbose)
+            log.write("  -highlight_windowkb is set to: ", highlight_windowkb, " kb",verbose=verbose) 
         else:
-            if verbose: log.write(" -Loci to highlight ({}): ".format(highlight_color)+",".join(highlight))    
-            if verbose: log.write("  -Highlight_window is set to: ", highlight_windowkb, " kb") 
+            log.write(" -Loci to highlight ({}): ".format(highlight_color)+",".join(highlight),verbose=verbose)    
+            log.write("  -highlight_windowkb is set to: ", highlight_windowkb, " kb",verbose=verbose) 
     
     if len(pinpoint)>0 :
         if pd.api.types.is_list_like(pinpoint[0]):
-            if len(pinpoint[0]) == len(pinpoint_color):
-                log.write(" -WARNING: number of variant list does not match number of colors !!!")
+            if len(pinpoint) != len(pinpoint_color):
+                log.warning("Number of variant groups in the list does not match number of provided colors.")
             for i, pinpoint_set in enumerate(pinpoint):
-                  if verbose: log.write(" -Set {} variants to pinpoint ({}) : ".format(i+1,pinpoint_color[i%len(pinpoint_color)])+",".join(pinpoint_set))      
+                  log.write(" -Set {} variants to pinpoint ({}) : ".format(i+1,pinpoint_color[i%len(pinpoint_color)])+",".join(pinpoint_set),verbose=verbose)      
         else:
-            if verbose: log.write(" -Variants to pinpoint ({}) : ".format(pinpoint_color)+",".join(pinpoint))   
+            log.write(" -Variants to pinpoint ({}) : ".format(pinpoint_color)+",".join(pinpoint),verbose=verbose)   
     
     if region is not None:
-        if verbose: log.write(" -Region to plot : chr"+str(region[0])+":"+str(region[1])+"-"+str(region[2])+".")  
+        log.write(" -Region to plot : chr"+str(region[0])+":"+str(region[1])+"-"+str(region[2])+".",verbose=verbose)  
     
     # construct line series for coversion
     if additional_line is None:
@@ -340,13 +356,14 @@ 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, 
@@ -383,7 +400,7 @@ def mqqplot(insumstats,
                                      pinpoint=pinpoint,
                                      density_color=density_color)
     
-    sumstats = insumstats.loc[:,usecols].copy()
+    sumstats = insumstats[usecols].copy()
     
     #################################################################################################
     
@@ -392,7 +409,7 @@ def mqqplot(insumstats,
     if (anno == "GENENAME"):
         anno_sig=True
     elif (anno is not None) and (anno is not True):
-        sumstats["Annotation"]=sumstats.loc[:,anno].astype("string")   
+        sumstats["Annotation"]=sumstats[anno].astype("string")   
       
     ## P value
     ## m, qq, r
@@ -416,15 +433,15 @@ def mqqplot(insumstats,
         region_start = region[1]
         region_end = region[2]
         marker_size=(25,45)
-        if verbose:log.write(" -Extract SNPs in region : chr{}:{}-{}...".format(region_chr, region[1], region[2]))
+        log.write(" -Extract SNPs in region : chr{}:{}-{}...".format(region_chr, region[1], region[2]),verbose=verbose)
         
-        in_region_snp = (sumstats[chrom]==region_chr) &(sumstats[pos]<region_end) &(sumstats[pos]>region_start)
+        in_region_snp = (sumstats[chrom]==region_chr) & (sumstats[pos]<region_end) & (sumstats[pos]>region_start)
         
-        if verbose:log.write(" -Extract SNPs in specified regions: "+str(sum(in_region_snp)))
+        log.write(" -Extract SNPs in specified regions: "+str(sum(in_region_snp)),verbose=verbose)
         sumstats = sumstats.loc[in_region_snp,:]
         
         if len(sumstats)==0:
-            log.write(" -Warning : No valid data! Please check the input.")
+            log.warning("No valid data! Please check the input.")
             return None
     
     ## EAF
@@ -438,11 +455,11 @@ def mqqplot(insumstats,
         sumstats["HUE"] = pd.NA
         sumstats["HUE"] = sumstats["HUE"].astype("Int64")
 
-    if verbose: log.write("Finished loading specified columns from the sumstats.")
+    log.write("Finished loading specified columns from the sumstats.",verbose=verbose)
 
 
 #sanity check############################################################################################################
-    log.write("Start conversion and sanity check:",verbose=verbose)
+    log.write("Start data conversion and sanity check:",verbose=verbose)
     
     if _if_quick_qc == False:
         log.write(" -Sanity check will be skipped.", verbose=verbose)
@@ -511,15 +528,19 @@ def mqqplot(insumstats,
                                                                         lines_to_plot=lines_to_plot,
                                                                         log = log)
     except:
-        log.write(" -Warning : No valid data! Please check the input.")
+        log.warning("No valid data! Please check the input.")
         return None
     
+    log.write("Finished data conversion and sanity check.",verbose=verbose)
+    
     # Manhattan plot ##########################################################################################################
+    log.write("Start to create MQQ plot with "+str(len(sumstats))+" variants...",verbose=verbose)
     ## regional plot ->rsq
         #calculate rsq]
     if vcf_path is not None:
         if tabix is None:
             tabix = which("tabix")
+            log.write(" -tabix will be used: {}".format(tabix),verbose=verbose)
         sumstats = process_vcf(sumstats=sumstats, 
                                vcf_path=vcf_path,
                                region=region, 
@@ -552,8 +573,6 @@ 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:")
         ## default seetings
         
         palette = sns.color_palette(colors,n_colors=sumstats[chrom].nunique())  
@@ -585,6 +604,7 @@ def mqqplot(insumstats,
         ## if highlight 
         highlight_i = pd.DataFrame()
         if len(highlight) >0:
+            log.write(" -Creating background plot...",verbose=verbose)
             plot = sns.scatterplot(data=sumstats, x='i', y='scaled_P',
                                hue='chr_hue',
                                palette=palette,
@@ -596,8 +616,7 @@ def mqqplot(insumstats,
                                zorder=2,ax=ax1,edgecolor=edgecolor, **scatter_args)   
             if pd.api.types.is_list_like(highlight[0]) and highlight_chrpos==False:
                 for i, highlight_set in enumerate(highlight):
-                    if verbose: log.write(" -Highlighting set {} target loci...".format(i+1))
-                    print(sumstats["HUE"].dtype)
+                    log.write(" -Highlighting set {} target loci...".format(i+1),verbose=verbose)
                     sns.scatterplot(data=sumstats.loc[sumstats["HUE"]==i], x='i', y='scaled_P',
                         hue="HUE",
                         palette={i:highlight_color[i%len(highlight_color)]},
@@ -609,7 +628,7 @@ def mqqplot(insumstats,
                         zorder=3+i,ax=ax1,edgecolor=edgecolor,**scatter_args)  
                 highlight_i = sumstats.loc[~sumstats["HUE"].isna(),"i"].values
             else:
-                if verbose: log.write(" -Highlighting target loci...")
+                log.write(" -Highlighting target loci...",verbose=verbose)
                 sns.scatterplot(data=sumstats.loc[sumstats["HUE"]==0], x='i', y='scaled_P',
                     hue="HUE",
                     palette={0:highlight_color},
@@ -658,6 +677,7 @@ def mqqplot(insumstats,
                 hue = 'chr_hue'
                 hue_norm=None
                 to_plot = sumstats
+                log.write(" -Creating background plot...",verbose=verbose)
                 plot = sns.scatterplot(data=to_plot, x='i', y='scaled_P',
                        hue=hue,
                        palette= palette,
@@ -677,17 +697,17 @@ def mqqplot(insumstats,
                 for i, pinpoint_set in enumerate(pinpoint):
                     if sum(sumstats[snpid].isin(pinpoint_set))>0:
                         to_pinpoint = sumstats.loc[sumstats[snpid].isin(pinpoint_set),:]
-                        if verbose: log.write(" -Pinpointing set {} target vairants...".format(i+1))
+                        log.write(" -Pinpointing set {} target vairants...".format(i+1),verbose=verbose)
                         ax1.scatter(to_pinpoint["i"],to_pinpoint["scaled_P"],color=pinpoint_color[i%len(pinpoint_color)],zorder=100,s=marker_size[1]+1)
                     else:
-                        if verbose: log.write(" -Target vairants to pinpoint were not found. Skip pinpointing process...")
+                        log.write(" -Target vairants to pinpoint were not found. Skip pinpointing process...",verbose=verbose)
             else:
                 if sum(sumstats[snpid].isin(pinpoint))>0:
                     to_pinpoint = sumstats.loc[sumstats[snpid].isin(pinpoint),:]
-                    if verbose: log.write(" -Pinpointing target vairants...")
+                    log.write(" -Pinpointing target vairants...",verbose=verbose)
                     ax1.scatter(to_pinpoint["i"],to_pinpoint["scaled_P"],color=pinpoint_color,zorder=100,s=marker_size[1]+1)
                 else:
-                    if verbose: log.write(" -Target vairants to pinpoint were not found. Skip pinpointing process...")
+                    log.write(" -Target vairants to pinpoint were not found. Skip pinpointing process...",verbose=verbose)
             
 
         
@@ -697,7 +717,7 @@ 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 +758,7 @@ 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,
@@ -745,50 +766,20 @@ 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
-                     )
+        log.write("Finished creating MQQ plot successfully!",verbose=verbose)
 
         # Get top variants for annotation #######################################################
+        log.write("Start to extract variants for annotation...",verbose=verbose)
         if (anno and anno!=True) or (len(anno_set)>0):
             if len(anno_set)>0:
                 to_annotate=sumstats.loc[sumstats[snpid].isin(anno_set),:]
                 if to_annotate.empty is not True:
-                    if verbose: log.write(" -Found "+str(len(to_annotate))+" specified variants to annotate...")
+                    log.write(" -Found "+str(len(to_annotate))+" specified variants to annotate...",verbose=verbose)
             else:
                 to_annotate=getsig(sumstats.loc[sumstats["scaled_P"]> float(-np.log10(sig_level_lead)),:],
                                snpid,
@@ -801,7 +792,7 @@ def mqqplot(insumstats,
                                mlog10p="scaled_P",
                                verbose=False)
                 if (to_annotate.empty is not True) and ("b" not in mode):
-                    if verbose: log.write(" -Found "+str(len(to_annotate))+" significant variants with a sliding window size of "+str(windowsizekb)+" kb...")
+                    log.write(" -Found "+str(len(to_annotate))+" significant variants with a sliding window size of "+str(windowsizekb)+" kb...",verbose=verbose)
         else:
             to_annotate=getsig(sumstats.loc[sumstats["scaled_P"]> float(-np.log10(sig_level_lead)),:],
                                "i",
@@ -814,7 +805,7 @@ def mqqplot(insumstats,
                                mlog10p="scaled_P",
                                sig_level=sig_level_lead)
             if (to_annotate.empty is not True) and ("b" not in mode):
-                if verbose: log.write(" -Found "+str(len(to_annotate))+" significant variants with a sliding window size of "+str(windowsizekb)+" kb...")
+                log.write(" -Found "+str(len(to_annotate))+" significant variants with a sliding window size of "+str(windowsizekb)+" kb...",verbose=verbose)
         if (to_annotate.empty is not True) and anno=="GENENAME":
             to_annotate = annogene(to_annotate,
                                    id=snpid,
@@ -824,21 +815,105 @@ def mqqplot(insumstats,
                                    build=build,
                                    source=anno_source,
                                    verbose=verbose).rename(columns={"GENE":"Annotation"})
+        log.write("Finished extracting variants for annotation...",verbose=verbose)
 
         # 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 )
+        log.write("Start to process figure arts.",verbose=verbose)
+        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,
+                                 log=log, 
+                                 verbose=verbose)   
+
+        ax1, ax3 = _process_xlabel(region=region, 
+                                   xlabel=xlabel, 
+                                   ax1=ax1, 
+                                   gtf_path=gtf_path, 
+                                   mode=mode, 
+                                   fontsize=fontsize, 
+                                   font_family=font_family,  
+                                   ax3=ax3,
+                                   log=log, 
+                                   verbose=verbose)      
+        
+        ax1, ax4 = _process_ylabel(ylabel=ylabel, 
+                                   ax1=ax1,  
+                                   mode=mode, 
+                                   bwindowsizekb=bwindowsizekb, 
+                                   fontsize=fontsize, 
+                                   font_family=font_family, 
+                                   ax4=ax4,
+                                   log=log, 
+                                   verbose=verbose)      
+        
+
+        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,
+                     log=log, 
+                     verbose=verbose)  
+        
+        ax1, ax4 = _process_ytick(ax1=ax1,  
+                                   fontsize=fontsize, 
+                                   font_family=font_family, 
+                                   ax4=ax4, 
+                                   log=log, 
+                                   verbose=verbose)  
+        
+        # regional plot cbar
+        if cbar is not None:    
+            cbar = _process_cbar(cbar, 
+                                 cbar_fontsize=fontsize, 
+                                 cbar_font_family=font_family, 
+                                 cbar_title=cbar_title, 
+                                 log=log, 
+                                 verbose=verbose)         
+        
         ax1 = _process_spine(ax1, mode)
         
-        if verbose: log.write("Finished creating Manhattan plot successfully!")
+        # 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,
+                            log=log,
+                            verbose=verbose )  
+
         
         if mtitle and anno and len(to_annotate)>0: 
             pad=(ax1.transData.transform((skip, title_pad*maxy))[1]-ax1.transData.transform((skip, maxy)))[1]
             ax1.set_title(mtitle,pad=pad,fontsize=title_fontsize,family=font_family)
         elif mtitle:
             ax1.set_title(mtitle,fontsize=title_fontsize,family=font_family)
-            
+        log.write("Finished processing figure arts.",verbose=verbose)
+
         # Add annotation arrows and texts
+        log.write("Start to annotate variants...",verbose=verbose)
         ax1 = annotate_single(
                                 sumstats=sumstats,
                                 anno=anno,
@@ -872,7 +947,8 @@ def mqqplot(insumstats,
                                 log=log,
                                _invert=_invert
                             )  
-    # Manhatann plot Finished #####################################################################
+        log.write("Finished annotating variants.",verbose=verbose)
+    # Manhatann-like plot Finished #####################################################################
 
     # QQ plot #########################################################################################################
     if "qq" in mode:
@@ -916,9 +992,9 @@ def mqqplot(insumstats,
 
     # Y axis jagged
     if jagged==True:
-        ax1 = _jagged_y(cut=cut,skip=skip,ax1=ax1,mode=1,mqqratio=mqqratio,jagged_len=jagged_len,jagged_wid=jagged_wid)
+        ax1 = _jagged_y(cut=cut,skip=skip,ax1=ax1,mode=1,mqqratio=mqqratio,jagged_len=jagged_len,jagged_wid=jagged_wid,log=log, verbose=verbose)
         if "qq" in mode:
-            ax2 = _jagged_y(cut=cut,skip=skip,ax1=ax2,mode=2,mqqratio=mqqratio,jagged_len=jagged_len,jagged_wid=jagged_wid)
+            ax2 = _jagged_y(cut=cut,skip=skip,ax1=ax2,mode=2,mqqratio=mqqratio,jagged_len=jagged_len,jagged_wid=jagged_wid,log=log, verbose=verbose)
     
     # XY lim
     if ylim is not None:
@@ -943,6 +1019,8 @@ def mqqplot(insumstats,
     # Return matplotlib figure object #######################################################################################
     if _get_region_lead==True:
         return fig, log, lead_snp_i, lead_snp_i2
+    
+    log.write("Finished creating plot successfully!",verbose=verbose)
     return fig, log
 
 ##############################################################################################################################################################################
@@ -1037,22 +1115,22 @@ def _sanity_check(sumstats, mode, chrom, pos, stratified, _if_quick_qc, log, ver
         #sanity check : drop variants with na values in chr and pos df
         sumstats = sumstats.dropna(subset=[chrom,pos])
         after_number=len(sumstats)
-        if verbose:log.write(" -Removed "+ str(pre_number-after_number) +" variants with nan in CHR or POS column ...")
+        log.write(" -Removed "+ str(pre_number-after_number) +" variants with nan in CHR or POS column ...",verbose=verbose)
         out_of_range_chr = sumstats[chrom]<=0
-        if verbose:log.write(" -Removed {} variants with CHR <=0...".format(sum(out_of_range_chr)))
+        log.write(" -Removed {} variants with CHR <=0...".format(sum(out_of_range_chr)),verbose=verbose)
         sumstats = sumstats.loc[~out_of_range_chr,:]
     
     if stratified is True and _if_quick_qc: 
         pre_number=len(sumstats)
         sumstats = sumstats.dropna(subset=["MAF"])
         after_number=len(sumstats)
-        if verbose:log.write(" -Removed "+ str(pre_number-after_number) +" variants with nan in EAF column ...")
+        log.write(" -Removed "+ str(pre_number-after_number) +" variants with nan in EAF column ...",verbose=verbose)
     
     if "b" not in mode and _if_quick_qc:
         pre_number=len(sumstats)
         sumstats = sumstats.dropna(subset=["raw_P"])
         after_number=len(sumstats)
-        if verbose:log.write(" -Removed "+ str(pre_number-after_number) +" variants with nan in P column ...")
+        log.write(" -Removed "+ str(pre_number-after_number) +" variants with nan in P column ...",verbose=verbose)
     return sumstats
 
 def _process_p_value(sumstats, mode,p, mlog10p, scaled, log, verbose ):
@@ -1061,7 +1139,7 @@ def _process_p_value(sumstats, mode,p, mlog10p, scaled, log, verbose ):
         sumstats["scaled_P"] = sumstats["DENSITY"].copy()
         sumstats["raw_P"] = -np.log10(sumstats["DENSITY"].copy()+2)
     elif scaled is True:
-        if verbose:log.write(" -P values are already converted to -log10(P)!")
+        log.write(" -P values are already converted to -log10(P)!",verbose=verbose)
         sumstats["scaled_P"] = sumstats["raw_P"].copy()
         sumstats["raw_P"] = np.power(10,-sumstats["scaled_P"].astype("float64"))
     else:
@@ -1109,7 +1187,7 @@ def _process_highlight(sumstats, highlight, highlight_chrpos, highlight_windowkb
                         sumstats.loc[right_chr&up_pos&low_pos,"HUE"]=0                        
         else:
             # highlight for one set
-            # to_highlight = sumstats.loc[sumstats[snpid].isin(highlight),:]
+            to_highlight = sumstats.loc[sumstats[snpid].isin(highlight),:]
             #assign colors: 0 is hightlight color
             for index,row in to_highlight.iterrows():
                 target_chr = int(row[chrom])
@@ -1122,7 +1200,7 @@ def _process_highlight(sumstats, highlight, highlight_chrpos, highlight_windowkb
 
 def _process_density(sumstats, mode, bwindowsizekb, chrom, pos, verbose, log):
     if "b" in mode and "DENSITY" not in sumstats.columns:
-        if verbose:log.write(" -Calculating DENSITY with windowsize of ",bwindowsizekb ," kb")
+        log.write(" -Calculating DENSITY with windowsize of ",bwindowsizekb ," kb",verbose=verbose)
         large_number = _get_largenumber(sumstats[pos].max(),log=log)
 
         stack=[]
@@ -1143,11 +1221,12 @@ def _process_density(sumstats, mode, bwindowsizekb, chrom, pos, verbose, log):
     elif "b" in mode and "DENSITY" in sumstats.columns:
         bmean=sumstats["DENSITY"].mean()
         bmedian=sumstats["DENSITY"].median()
-        if verbose:log.write(" -DENSITY column exists. Skipping calculation...") 
+        log.write(" -DENSITY column exists. Skipping calculation...",verbose=verbose) 
     return   sumstats, bmean, bmedian
 
-def _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 ):
+def _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 , log=Log(),verbose=True):
     # genomewide significant line
+    log.write(" -Processing lines...",verbose=verbose)
     if sig_line is True:
         sigline = ax1.axhline(y=lines_to_plot[0], 
                                 linewidth = sc_linewidth,
@@ -1173,12 +1252,39 @@ 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_xtick(ax1, chrom_df, xtick_chr_dict, fontsize, font_family):
+def _process_cbar(cbar, cbar_fontsize, cbar_font_family, cbar_title, log=Log(),verbose=True):
+    log.write(" -Processing color bar...",verbose=verbose)
+    if 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, 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_xlabel(region, xlabel, ax1, gtf_path, mode, fontsize, font_family,  ax3=None ):
+def _process_ytick(ax1, fontsize, font_family, ax4, log=Log(),verbose=True):
+    log.write(" -Processing Y labels...",verbose=verbose)
+    ax1_yticklabels = ax1.get_yticklabels()
+    #ax1.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 , log=Log(),verbose=True):
+    log.write(" -Processing X labels...",verbose=verbose)
     if region is not None:
         if xlabel is None:
             xlabel = "Chromosome "+str(region[0])+" (MB)"
@@ -1192,7 +1298,8 @@ 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, log=Log(),verbose=True):
+    log.write(" -Processing Y labels...",verbose=verbose)
     if "b" in mode:
         if ylabel is None:
             ylabel ="Density of GWAS \n SNPs within "+str(bwindowsizekb)+" kb"
@@ -1201,7 +1308,10 @@ 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 +1328,7 @@ 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 +1337,7 @@ 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 +1346,12 @@ 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 +1371,6 @@ 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