gwaslab 3.4.46__py3-none-any.whl → 3.4.47__py3-none-any.whl

gwaslab/g_version.py

@@ -15,16 +15,16 @@ def _get_version():
 def gwaslab_info():
     # version meta information
     dic={
-   "version":"3.4.46",
-   "release_date":"20240624"
+   "version":"3.4.47",
+   "release_date":"20240703"
     }
     return dic   
 
-def _checking_plink_version(v=2,log=Log(), verbose=True):
-    if v==1:
-        which_plink_script = "plink --version"
-    elif v==2:
-        which_plink_script = "plink2 --version" 
+def _checking_plink_version(plink=None,plink2=None,log=Log(), verbose=True):
+    if plink is not None:
+        which_plink_script = "{} --version".format(plink)
+    elif plink2 is not None:
+        which_plink_script = "{}  --version".format(plink2)
     output = subprocess.check_output(which_plink_script, stderr=subprocess.STDOUT, shell=True,text=True)
     log.write(" -PLINK version: {}".format(output.strip()))
     return log

gwaslab/io_to_formats.py

@@ -212,8 +212,10 @@ def tofmt(sumstats,
     log.write(" -Start outputting sumstats in "+fmt+" format...")
     
     if "CHR" in sumstats.columns:
+        # output X,Y,MT instead of 23,24,25
         if xymt_number is False and pd.api.types.is_integer_dtype(sumstats["CHR"]):
             sumstats["CHR"]= sumstats["CHR"].map(get_number_to_chr(xymt=xymt,prefix=chr_prefix))
+        # add prefix to CHR
         elif chr_prefix is not None:
             sumstats["CHR"]= chr_prefix + sumstats["CHR"].astype("string")
 
@@ -437,17 +439,20 @@ def _configure_output_cols_and_args(sumstats, rename_dictionary, cols, no_status
             ouput_cols.append(i)  
     
     # + additional cols and remove duplicated
-    ouput_cols = list(set(ouput_cols + cols)) 
+    ouput_cols_final = []
+    for i in ouput_cols + cols:
+        if i not in ouput_cols_final:
+            ouput_cols_final.append(i)
     
     # remove STATUS
     try:
         if no_status == True:
-            ouput_cols.remove("STATUS")
+            ouput_cols_final.remove("STATUS")
     except:
         pass
     
     #filter and rename to target fromat headers
-    sumstats = sumstats[ouput_cols]
+    sumstats = sumstats[ouput_cols_final]
     sumstats = sumstats.rename(columns=rename_dictionary) 
 
     # configure target format args and reorder columns

gwaslab/util_ex_calculate_ldmatrix.py

@@ -17,6 +17,8 @@ def tofinemapping(sumstats,
                   vcf=None, 
                   loci=None,
                   out="./",
+                  plink="plink",
+                  plink2="plink2",
                   windowsizekb=1000,
                   n_cores=1, 
                   mode="r",
@@ -56,6 +58,9 @@ def tofinemapping(sumstats,
     else:
         sig_df = sumstats.loc[sumstats["SNPID"].isin(loci),:]
     
+    log.write(" -plink1.9 path: {}".format(plink),verbose=verbose)
+    log.write(" -plink2 path: {}".format(plink2),verbose=verbose)
+
     # Drop duplicate!!!!
     log.write(" -Dropping duplicated SNPIDs...",verbose=verbose)
     sumstats = sumstats.drop_duplicates(subset=["SNPID"]).copy()
@@ -68,11 +73,13 @@ def tofinemapping(sumstats,
     if exclude_hla==True:
         sig_df = _exclude_hla(sig_df, log=log, verbose=verbose)
     
+    sig_df = sig_df.reset_index()
+    
     ## for each lead variant 
     for index, row in sig_df.iterrows():
         # extract snplist in each locus
         gc.collect()
-
+        log.write(" -Locus #{}---------------------------------------------------------------".format(index+1))
         log.write(" -Processing locus with lead variant {} at CHR {} POS {} ...".format(row["SNPID"],row["CHR"],row["POS"]))
         locus_sumstats = _extract_variants_in_locus(sumstats, windowsizekb, locus = (row["CHR"],row["POS"]))
         
@@ -84,7 +91,10 @@ def tofinemapping(sumstats,
                                                                     n_cores=n_cores, 
                                                                     log=log,
                                                                     load_bim=True,
-                                                                    overwrite=overwrite,**kwargs)
+                                                                    overwrite=overwrite,
+                                                                    plink=plink,
+                                                                    plink2=plink2,
+                                                                    **kwargs)
 
         ## check available snps with reference file
         matched_sumstats = _align_sumstats_with_bim(row=row, 
@@ -114,7 +124,10 @@ def tofinemapping(sumstats,
                                                             windowsizekb=windowsizekb,
                                                             out=out,
                                                             plink_log=plink_log,
-                                                            log=log,filetype=filetype,
+                                                            log=log,
+                                                            filetype=filetype,
+                                                            plink=plink,
+                                                            plink2=plink2,
                                                             verbose=verbose)
     
     
@@ -143,12 +156,12 @@ def tofinemapping(sumstats,
 
 
 
-def _calculate_ld_r(study, matched_sumstats_snpid, row, bfile_prefix, n_cores, windowsizekb,out,plink_log,log,memory,mode,filetype,verbose=True):
+def _calculate_ld_r(study, matched_sumstats_snpid, row, bfile_prefix, n_cores, windowsizekb,out,plink_log,log,memory,mode,filetype,plink,plink2,verbose=True):
     '''
     Calculate LD r matrix by calling PLINK; return file name and log
     '''
     log.write(" -Start to calculate LD r matrix...",verbose=verbose)
-    log = _checking_plink_version(v=1, log=log)
+    log = _checking_plink_version(plink=plink, log=log)
     if "@" in bfile_prefix:
         bfile_to_use = bfile_prefix.replace("@",str(row["CHR"]))
     else:
@@ -165,7 +178,7 @@ def _calculate_ld_r(study, matched_sumstats_snpid, row, bfile_prefix, n_cores, w
             raise ValueError("Please use bfile instead of pfile for PLINK1.")
         
         script_vcf_to_bfile = """
-        plink \
+        {} \
             --bfile {} \
             --keep-allele-order \
             --extract {} \
@@ -175,7 +188,7 @@ def _calculate_ld_r(study, matched_sumstats_snpid, row, bfile_prefix, n_cores, w
             --threads {} {}\
             --write-snplist \
             --out {}
-        """.format(bfile_to_use, snplist_path , row["CHR"], mode, n_cores, memory_flag if memory is not None else "", output_prefix)
+        """.format(plink, bfile_to_use, snplist_path , row["CHR"], mode, n_cores, memory_flag if memory is not None else "", output_prefix)
 
         try:
             output = subprocess.check_output(script_vcf_to_bfile, stderr=subprocess.STDOUT, shell=True,text=True)

gwaslab/util_ex_calculate_prs.py

@@ -18,6 +18,8 @@ def _calculate_prs(sumstats,
           memory=None, 
           overwrite=False,
           mode=None,delete=True,
+          plink="plink",
+          plink2="plink2",
           log=Log(),**kwargs):
     
     #matching_alleles
@@ -30,14 +32,18 @@ def _calculate_prs(sumstats,
         chrlist.sort()
         plink_log = ""
         #process reference fileWWW
-        bfile_prefix, plink_log, ref_bim, filetype = _process_plink_input_files(  chrlist=chrlist,
+        bfile_prefix, plink_log, ref_bim, filetype = _process_plink_input_files(  
+                                                                    chrlist=chrlist,
                                                                     bfile=bfile, 
                                                                     vcf=vcf, 
                                                                     plink_log=plink_log,
                                                                     n_cores=n_cores, 
                                                                     log=log,
                                                                     load_bim=False,
-                                                                    overwrite=overwrite,**kwargs)
+                                                                    overwrite=overwrite,
+                                                                    plink=plink,
+                                                                    plink2=plink2,
+                                                                    **kwargs)
         score_file_path_list =[]
         for index, chrom in enumerate(chrlist): 
             chr_sumstats = sumstats.loc[sumstats["CHR"]==chrom,:].copy()
@@ -61,7 +67,7 @@ def _calculate_prs(sumstats,
                                plink_log=plink_log, 
                                log=log, 
                                memory=memory, 
-                               mode=mode,filetype=filetype)
+                               mode=mode,filetype=filetype,plink2=plink2)
             score_file_path_list.append(score_file_path)
             if delete == True:
                 os.remove(model_path)
@@ -71,10 +77,10 @@ def _calculate_prs(sumstats,
 
 
 
-def _run_calculate_prs(study, chrom , model_path, bfile_prefix, n_cores, out, plink_log, log, memory,filetype, mode=None):
+def _run_calculate_prs(study, chrom , model_path, bfile_prefix, n_cores, out, plink_log, log, memory,filetype, plink2,mode=None):
     
     log.write(" -Start to calculate PRS for Chr {}...".format(chrom))
-    _checking_plink_version(v=2, log=log)
+    _checking_plink_version(plink2=plink2, log=log)
     
     if "@" in bfile_prefix:
         bpfile_to_use = bfile_prefix.replace("@",str(chrom))
@@ -92,13 +98,13 @@ def _run_calculate_prs(study, chrom , model_path, bfile_prefix, n_cores, out, pl
         memory_flag = "--memory {}".format(memory)
     
     script_vcf_to_bfile = """
-    plink2 \
+    {} \
         {} \
         --score {} 1 2 3 header {} cols=+scoresums,+denom ignore-dup-ids \
         --chr {} \
         --threads {} {}\
         --out {}
-    """.format(file_flag, model_path ,  mode if mode is not None else "", chrom, n_cores, memory_flag if memory is not None else "", output_prefix)
+    """.format(plink2, file_flag, model_path ,  mode if mode is not None else "", chrom, n_cores, memory_flag if memory is not None else "", output_prefix)
 
     try:
         output = subprocess.check_output(script_vcf_to_bfile, stderr=subprocess.STDOUT, shell=True,text=True)

gwaslab/util_ex_process_ref.py

@@ -20,7 +20,9 @@ def _process_plink_input_files(chrlist,
                                bgen_mode="ref-first", 
                                convert="bfile", 
                                memory=None, 
-                               load_bim=False):
+                               load_bim=False,
+                               plink="plink",
+                               plink2="plink2"):
     """
     Process input files (bfile,pfile,vcf,bgen) to either PLINK1 bed/bim/fam or PLINK2 pgen/psam/pvar. 
     
@@ -66,7 +68,9 @@ def _process_plink_input_files(chrlist,
                                                             convert=convert, 
                                                             memory=memory, 
                                                             overwrite=overwrite, 
-                                                            load_bim=load_bim)
+                                                            load_bim=load_bim,
+                                                            plink=plink,
+                                                            plink2=plink2)
         filetype = convert
     elif filetype == "bgen": 
         ref_file_prefix, plink_log, ref_bims = _process_bgen(ref_file_prefix=ref_file_prefix, 
@@ -81,7 +85,9 @@ def _process_plink_input_files(chrlist,
                                                             convert=convert, 
                                                             memory=memory, 
                                                             overwrite=overwrite, 
-                                                            load_bim=load_bim)
+                                                            load_bim=load_bim,
+                                                            plink=plink,
+                                                            plink2=plink2)
         filetype = convert
     return ref_file_prefix, plink_log, ref_bims, filetype
 
@@ -199,11 +205,13 @@ def _process_vcf(ref_file_prefix,
                  convert="bfile", 
                  memory=None, 
                  overwrite=False, 
-                 load_bim=False):
+                 load_bim=False,
+                 plink="plink",
+                 plink2="plink2"):
     log.write(" -Processing VCF : {}...".format(ref_file_prefix))
     
     #check plink version
-    log = _checking_plink_version(v=2,log=log)
+    log = _checking_plink_version(plink2=plink2,log=log)
     
     # file path prefix to return
     if is_wild_card==True:
@@ -243,14 +251,15 @@ def _process_vcf(ref_file_prefix,
         #if not existing or overwrite is True
         if (not is_file_exist) or overwrite:
             script_vcf_to_bfile = """
-            plink2 \
+            {} \
                 --vcf {} \
                 --chr {} \
                 {} \
                 --rm-dup force-first \
                 --threads {}{}\
                 --out {}
-            """.format(vcf_to_load, 
+            """.format(plink2,
+                        vcf_to_load, 
                        i, 
                        make_flag,
                        n_cores, memory_flag,
@@ -288,11 +297,13 @@ def _process_bgen(ref_file_prefix,
                   convert="bfile", 
                   memory=None, 
                   overwrite=False, 
-                  load_bim=False):
+                  load_bim=False,
+                  plink="plink",
+                 plink2="plink2"):
     log.write(" -Processing BGEN files : {}...".format(ref_file_prefix))
     
     #check plink version
-    log = _checking_plink_version(v=2,log=log)
+    log = _checking_plink_version(log=log,plink2=plink2)
     
     # file path prefix to return
     if is_wild_card==True:
@@ -338,14 +349,14 @@ def _process_bgen(ref_file_prefix,
         #if not existing or overwrite is True
         if (not is_file_exist) or overwrite:
             script_vcf_to_bfile = """
-            plink2 \
+            {} \
                 --bgen {} {} {}\
                 --chr {} \
                 {} \
                 --rm-dup force-first \
                 --threads {}{}\
                 --out {}
-            """.format(bgen_to_load, bgen_mode, sample_flag,
+            """.format(plink2,bgen_to_load, bgen_mode, sample_flag,
                        i, 
                        make_flag,
                        n_cores, memory_flag,

gwaslab/viz_aux_chromatin.py

@@ -63,6 +63,8 @@ def _plot_chromatin_state(region_chromatin_files,
                           fig, 
                           ax,
                           xlim_i,
+                          fontsize = 12,
+                          font_family = "Arial",
                           log=Log(),
                           verbose=True):
     '''
@@ -101,11 +103,10 @@ def _plot_chromatin_state(region_chromatin_files,
     
     ## add stripe label
     if len(region_chromatin_labels) == len(region_chromatin_files):
-        ax.set_yticks([i*0.1 for i in range(len(region_chromatin_labels))], 
-                      region_chromatin_labels)
+        ax.set_yticks([i*0.1 for i in range(len(region_chromatin_labels))], region_chromatin_labels, fontsize=fontsize, family=font_family)
     else:
         ax.set_yticks(ticks=[])
     
-    ax.set_xticks(ticks=[])
+    #ax.set_xticks(ticks=[])
     ax.invert_yaxis()
     return fig

gwaslab/viz_plot_mqqplot.py

@@ -23,8 +23,8 @@ from gwaslab.viz_aux_reposition_text import adjust_text_position
 from gwaslab.viz_aux_annotate_plot import annotate_single
 from gwaslab.viz_plot_qqplot import _plot_qq
 from gwaslab.hm_harmonize_sumstats import auto_check_vcf_chr_dict
-from gwaslab.viz_plot_regionalplot import _plot_regional
-from gwaslab.viz_plot_regionalplot import process_vcf
+from gwaslab.viz_plot_regional2 import _plot_regional
+from gwaslab.viz_plot_regional2 import process_vcf
 from gwaslab.viz_aux_quickfix import _get_largenumber
 from gwaslab.viz_aux_quickfix import _quick_fix_p_value
 from gwaslab.viz_aux_quickfix import _quick_fix_pos
@@ -51,6 +51,9 @@ from gwaslab.bd_common_data import get_number_to_chr
 from gwaslab.bd_common_data import get_recombination_rate
 from gwaslab.bd_common_data import get_gtf
 from gwaslab.g_version import _get_version
+from matplotlib.colors import ListedColormap
+from matplotlib.colors import LinearSegmentedColormap
+from matplotlib.colors import to_hex
 # 20230202 ######################################################################################################
 
 def mqqplot(insumstats,            
@@ -98,13 +101,13 @@ def mqqplot(insumstats,
           region_ld_threshold = None,
           region_ld_legend = True,
           region_ld_colors = None,
-          region_ld_colors1 = None,
-          region_ld_colors2 = None,
+          region_ld_colors_m = None,
           region_recombination = True,
           region_protein_coding = True,
           region_flank_factor = 0.05,
           region_anno_bbox_args = None,
-          cbar_title='LD $r^{2}$',
+          region_marker_shapes=None,
+          cbar_title='LD $r^{2}$ with variant',
           cbar_fontsize = None,
           cbar_font_family = None,
           track_n=4,
@@ -238,20 +241,39 @@ def mqqplot(insumstats,
         anno_args=dict()
     if colors is None:
         colors=["#597FBD","#74BAD3"]
-    if region_ref2 is not None:
-        region_ref_second = copy.copy(region_ref2),
+    
+    if region is not None:
+        if marker_size == (5,20):
+            marker_size=(45,65)
+    
+    # make region_ref a list of ref variants
+    if pd.api.types.is_list_like(region_ref):
+        if len(region_ref) == 0 :
+            region_ref.append(None)
+            if region_ref_second is not None:
+                region_ref.append(region_ref_second)
+    else:
+        region_ref = [region_ref]
+        if region_ref_second is not None:
+            region_ref.append(region_ref_second)
+    region_ref_index_dic = {value: index for index,value in enumerate(region_ref)}
+        
+    if region_marker_shapes is None:
+        # 9 shapes
+        region_marker_shapes = ['o', 's','^','D','*','P','X','h','8']
     if region_grid_line is None:
         region_grid_line = {"linewidth": 2,"linestyle":"--"}
     if region_lead_grid_line is None:
         region_lead_grid_line = {"alpha":0.5,"linewidth" : 2,"linestyle":"--","color":"#FF0000"}
     if region_ld_threshold is None:
         region_ld_threshold = [0.2,0.4,0.6,0.8]
+
     if region_ld_colors is None:     
         region_ld_colors = ["#E4E4E4","#020080","#86CEF9","#24FF02","#FDA400","#FF0000","#FF0000"]
-    if region_ld_colors1 is None:
-        region_ld_colors1 = ["#E4E4E4","#F8CFCF","#F5A2A5","#F17474","#EB4445","#E51819","#E51819"]
-    if region_ld_colors2 is None:
-        region_ld_colors2 = ["#E4E4E4","#D8E2F2","#AFCBE3","#86B3D4","#5D98C4","#367EB7","#367EB7"]
+    
+    # 7 colors    
+    region_ld_colors_m = ["#E51819","#367EB7","green","#F07818","#AD5691","yellow","purple"]
+    
     if region_title_args is None:
         region_title_args = {"size":10}
     if cbar_fontsize is None:
@@ -353,6 +375,7 @@ def mqqplot(insumstats,
     lines_to_plot = -np.log10(lines_to_plot)
 
     vcf_chr_dict = auto_check_vcf_chr_dict(vcf_path, vcf_chr_dict, verbose, log)
+    
 
 # Plotting mode selection : layout ####################################################################
     # ax1 : manhattanplot / brisbane plot
@@ -435,7 +458,7 @@ def mqqplot(insumstats,
         region_chr = region[0]
         region_start = region[1]
         region_end = region[2]
-        marker_size=(25,45)
+        
         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)
@@ -548,7 +571,6 @@ def mqqplot(insumstats,
                                vcf_path=vcf_path,
                                region=region, 
                                region_ref=region_ref, 
-                               region_ref_second=region_ref_second,
                                log=log ,
                                pos=pos,
                                ea=ea,
@@ -589,17 +611,27 @@ def mqqplot(insumstats,
         if vcf_path is not None:
             legend=None
             linewidth=1
-            palette = { i:region_ld_colors[i] for i in range(len(region_ld_colors))}
-            if region_ref_second is not None:
-                palette = {} 
-                for i in range(len(region_ld_colors)):
-                    palette[i]=region_ld_colors1[i]
-                    palette[100+i]=region_ld_colors2[i]
+            if len(region_ref) == 1:
+                palette = {100+i:region_ld_colors[i] for i in range(len(region_ld_colors))}
+            else:
+                palette = {}
+                region_color_maps = []
+                for group_index, colorgroup in enumerate(region_ld_colors_m):
+                    color_map_len = len(region_ld_threshold)+2   # default 6
+                    rgba = LinearSegmentedColormap.from_list("custom", ["white",colorgroup], color_map_len)(range(1,color_map_len)) # skip white
+                    output_hex_colors=[]
+                    for i in range(len(rgba)):
+                        output_hex_colors.append(to_hex(rgba[i]))
+                        # 1 + 5 + 1
+                        region_ld_colors_single = [region_ld_colors[0]] + output_hex_colors + [output_hex_colors[-1]]
+                    region_color_maps.append(region_ld_colors_single)
+                # gradient colors
+                for i, hex_colors in enumerate(region_color_maps):
+                    for j, hex_color in enumerate(hex_colors):
+                        palette[(i+1)*100 + j ] = hex_color
+
                 edgecolor="none"
-                if sumstats["SHAPE"].nunique() >1:
-                    scatter_args["markers"]=['o', 's']
-                else:
-                    scatter_args["markers"]=['o']
+                scatter_args["markers"]= region_marker_shapes[:len(region_ref)]
                 style="SHAPE"
                 
             
@@ -649,6 +681,7 @@ def mqqplot(insumstats,
         
         ## if not highlight    
         else:
+            ## density plot
             if density_color == True:
                 hue = "DENSITY_hue"
                 s = "DENSITY"
@@ -676,6 +709,7 @@ def mqqplot(insumstats,
                    linewidth=linewidth,
                    zorder=2,ax=ax1,edgecolor=edgecolor,**scatter_args)   
             else:
+                # major / regional
                 s = "s"
                 hue = 'chr_hue'
                 hue_norm=None
@@ -720,7 +754,7 @@ def mqqplot(insumstats,
         # if regional plot : pinpoint lead , add color bar ##################################################
         if (region is not None) and ("r" in mode):
             
-            ax1, ax3, ax4, cbar, lead_snp_i, lead_snp_i2 =_plot_regional(
+            ax1, ax3, ax4, cbar, lead_snp_is, lead_snp_is_color =_plot_regional(
                                 sumstats=sumstats,
                                 fig=fig,
                                 ax1=ax1,
@@ -744,8 +778,8 @@ def mqqplot(insumstats,
                                 rr_ylabel=rr_ylabel,
                                 mode=mode,
                                 region_step = region_step,
-                                region_ref=region_ref,
-                                region_ref_second=region_ref_second,
+                                region_ref = region_ref,
+                                region_ref_index_dic = region_ref_index_dic,
                                 region_grid = region_grid,
                                 region_grid_line = region_grid_line,
                                 region_lead_grid = region_lead_grid,
@@ -756,8 +790,8 @@ def mqqplot(insumstats,
                                 region_ld_legend = region_ld_legend,
                                 region_ld_threshold = region_ld_threshold,
                                 region_ld_colors = region_ld_colors,
-                                region_ld_colors1=region_ld_colors1,
-                                region_ld_colors2=region_ld_colors2,
+                                palette = palette,
+                                region_marker_shapes = region_marker_shapes,
                                 region_recombination = region_recombination,
                                 region_protein_coding=region_protein_coding,
                                 region_flank_factor =region_flank_factor,
@@ -771,8 +805,8 @@ def mqqplot(insumstats,
                             )
             
         else:
-            lead_snp_i= None
-            lead_snp_i2=None
+            lead_snp_is =[]
+            lead_snp_is_color = []
         
         log.write("Finished creating MQQ plot successfully!",verbose=verbose)
 
@@ -884,8 +918,8 @@ def mqqplot(insumstats,
         # regional plot cbar
         if cbar is not None:    
             cbar = _process_cbar(cbar, 
-                                 cbar_fontsize=fontsize, 
-                                 cbar_font_family=font_family, 
+                                 cbar_fontsize=cbar_fontsize, 
+                                 cbar_font_family=cbar_font_family, 
                                  cbar_title=cbar_title, 
                                  log=log, 
                                  verbose=verbose)         
@@ -1021,7 +1055,7 @@ def mqqplot(insumstats,
     garbage_collect.collect()
     # Return matplotlib figure object #######################################################################################
     if _get_region_lead==True:
-        return fig, log, lead_snp_i, lead_snp_i2
+        return fig, log, lead_snp_is, lead_snp_is_color
     
     log.write("Finished creating plot successfully!",verbose=verbose)
     return fig, log
@@ -1271,15 +1305,19 @@ def _process_line(ax1, sig_line, suggestive_sig_line, additional_line, lines_to_
 
 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 )
+    #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.get_yticklabels()
+    cbar.set_yticklabels(cbar_yticklabels, fontsize=cbar_fontsize, family=cbar_font_family )
+    cbar_xticklabels = cbar.get_xticklabels()
+    cbar.set_xticklabels(cbar_xticklabels, fontsize=cbar_fontsize, family=cbar_font_family )
+
+    cbar.set_title(cbar_title, fontsize=cbar_fontsize, family=cbar_font_family, loc="center", y=1.00 )
     return cbar
 
 def _process_xtick(ax1, chrom_df, xtick_chr_dict, fontsize, font_family, log=Log(),verbose=True):