gwaslab 3.5.1__tar.gz → 3.5.3__tar.gz

{gwaslab-3.5.1/src/gwaslab.egg-info → gwaslab-3.5.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gwaslab
-Version: 3.5.1
+Version: 3.5.3
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/

{gwaslab-3.5.1 → gwaslab-3.5.3}/pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gwaslab"
-version = "3.5.1"
+version = "3.5.3"
 authors = [
   { name="Yunye", email="yunye@gwaslab.com" },
 ]

{gwaslab-3.5.1 → gwaslab-3.5.3}/src/gwaslab/__init__.py

@@ -46,3 +46,4 @@ from gwaslab.util_ex_process_h5 import process_vcf_to_hfd5
 from gwaslab.util_ex_run_susie import _run_susie_rss as run_susie_rss
 from gwaslab.io_read_tabular import _read_tabular as read_tabular
 from gwaslab.util_in_meta import meta_analyze
+from gwaslab.viz_plot_scatter_with_reg import scatter

{gwaslab-3.5.1 → gwaslab-3.5.3}/src/gwaslab/g_Sumstats.py

@@ -389,6 +389,12 @@ class Sumstats():
             self.data =flipallelestats(self.data,log=self.log,**flipallelestats_args)
             
             gc.collect()
+            
+        if (ref_seq is not None or ref_infer is not None) and (ref_rsid_tsv is not None or ref_rsid_vcf is not None):
+
+            self.data = fixID(self.data, log=self.log, **{"fixid":True, "fixsep":True, "overwrite":True})
+
+            gc.collect()
         
         #####################################################
         if ref_rsid_tsv is not None:
@@ -833,4 +839,4 @@ class Sumstats():
     def to_format(self, path, build=None, verbose=True, **kwargs):
         if build is None:
             build = self.meta["gwaslab"]["genome_build"]
-        _to_format(self.data, path, log=self.log, verbose=verbose, meta=self.meta, build=build, **kwargs)
+        _to_format(self.data, path, log=self.log, verbose=verbose, meta=self.meta, build=build, **kwargs)

{gwaslab-3.5.1 → gwaslab-3.5.3}/src/gwaslab/g_version.py

@@ -15,8 +15,8 @@ def _get_version():
 def gwaslab_info():
     # version meta information
     dic={
-   "version":"3.5.1",
-   "release_date":"20241120"
+   "version":"3.5.3",
+   "release_date":"20241217"
     }
     return dic   
 

{gwaslab-3.5.1 → gwaslab-3.5.3}/src/gwaslab/io_process_args.py

@@ -1,23 +1,40 @@
 import copy
-def _merge_and_sync_dic(list_of_dics:list, default:dict) -> dict:
-    temp = copy.copy(default)
-    for dic in list_of_dics:
-        if isinstance(dic, dict):
-            temp.update(dic)
-    return temp
 
 def _list_func_args(func):
     return func.__code__.co_varnames
 
 def _extract_kwargs(prefix:str, default:dict, kwargs:dict) -> dict:
+    # prefix: keyword
+    # default: default dict
+    # kwargs: all local kwargs  + args + kwargs
+
     extracted = []
+    extracted_single=dict()
     for key,value in kwargs.items():
+        # kwargs or args
         if key=="kwargs" or key=="args":
             for key_nested,value_nested in kwargs[key].items():
                 if prefix in key_nested and "arg" in key_nested:
-                    extracted.append(value_nested)
+
+                    if len(key_nested.split("_"))<3:
+                        extracted.append(value_nested)
+                    ##
+                    ## prefix_arg_fontsize
+                    else:
+                        print(key_nested.split("_")[-1], value)
+                        extracted_single[key_nested.split("_")[-1]] = value_nested
         else:
+            # local kwargs
             if prefix in key and "arg" in key:
                 extracted.append(value)
+    if len(extracted_single.keys()) >0:
+        extracted.append(extracted_single)
     merged_arg = _merge_and_sync_dic(extracted, default)
-    return merged_arg
+    return merged_arg
+
+def _merge_and_sync_dic(list_of_dics:list, default:dict) -> dict:
+    temp = copy.copy(default)
+    for dic in list_of_dics:
+        if isinstance(dic, dict):
+            temp.update(dic)
+    return temp

{gwaslab-3.5.1 → gwaslab-3.5.3}/src/gwaslab/io_to_formats.py

@@ -28,6 +28,7 @@ from gwaslab.util_in_filter_value import _extract
 def _to_format(sumstats,
               path="./sumstats",
               fmt="gwaslab",   
+              tab_fmt="tsv",
               extract=None,
               exclude=None,
               cols=None,
@@ -39,7 +40,6 @@ def _to_format(sumstats,
               n=None,
               no_status=False,
               output_log=True,
-              to_csvargs=None,
               float_formats=None,
               xymt_number=False,
               xymt=None,
@@ -47,20 +47,30 @@ def _to_format(sumstats,
               meta=None,
               ssfmeta=False,
               md5sum=False,
+              gzip=True,
               bgzip=False,
               tabix=False,
               tabix_indexargs={},
+              to_csvargs=None,
+              to_tabular_kwargs=None,
               log=Log(),
               verbose=True):
     
-    if  to_csvargs is None:
-        to_csvargs = {}
+    if to_csvargs is None:
+        to_csvargs=dict()
+    if tabix_indexargs is None:
+        tabix_indexargs=dict()
+    if to_tabular_kwargs is None:
+        to_tabular_kwargs=dict()
     if  float_formats is None:
-        float_formats={}
+        float_formats=dict()
     if cols is None:
         cols=[]
     if xymt is None:
         xymt = ["X","Y","MT"]
+    non_gzip_tab_fmt = ["parquet"]
+    non_md5sum_tab_fmt = ["parquet"]
+
     onetime_log = copy.deepcopy(log)
 
     #######################################################################################################
@@ -154,6 +164,7 @@ def _to_format(sumstats,
         tofmt(output,
               path=path,
               fmt=fmt,
+              tab_fmt=tab_fmt,
               cols=cols,
               suffix=suffix,
               build=build,
@@ -164,9 +175,13 @@ def _to_format(sumstats,
                 chr_prefix=chr_prefix,
                 meta=meta,
                 ssfmeta=ssfmeta,
+                gzip=gzip,
                 bgzip=bgzip,
+                non_gzip_tab_fmt=non_gzip_tab_fmt,
+                non_md5sum_tab_fmt=non_md5sum_tab_fmt,
                 tabix=tabix,
                 tabix_indexargs=tabix_indexargs,
+                to_tabular_kwargs=to_tabular_kwargs,
                 md5sum=md5sum,
                 xymt_number=xymt_number,
                 xymt=xymt)
@@ -186,6 +201,7 @@ def tofmt(sumstats,
           path=None,
           suffix=None,
           fmt=None,
+          tab_fmt="csv",
           cols=[],
           xymt_number=False,
           xymt=["X","Y","MT"],
@@ -194,15 +210,16 @@ def tofmt(sumstats,
           ssfmeta=False,
           md5sum=False,
           bgzip=False,
+          gzip=True,
+          non_gzip_tab_fmt=None,
+          non_md5sum_tab_fmt=None,
           tabix=False,
-          tabix_indexargs={},
+          tabix_indexargs=None,
           verbose=True,
           no_status=False,
           log=Log(),
-          to_csvargs=None):
-    
-    if to_csvargs is None:
-        to_csvargs=dict()
+          to_csvargs=None,
+          to_tabular_kwargs=None):
     
     if fmt in ["ssf"]: 
         xymt_number=True
@@ -336,36 +353,86 @@ def tofmt(sumstats,
         _bgzip_tabix_md5sum(path, fmt, bgzip, md5sum, tabix, tabix_indexargs, log, verbose)
     
     ####################################################################################################################
-    elif fmt in get_formats_list():      
+    elif fmt in get_formats_list() :      
         # tabular 
         log.write(" -"+fmt+" format will be loaded...",verbose=verbose)
         meta_data,rename_dictionary = get_format_dict(fmt,inverse=True)
         print_format_info(fmt=fmt, meta_data=meta_data,rename_dictionary=rename_dictionary,verbose=verbose, log=log, output=True)
         
-        yaml_path = path + "."+suffix+".tsv-meta.yaml"
-        path = path + "."+suffix+".tsv.gz"
+        # determine if gzip or not / create path for output
+        if gzip ==True and tab_fmt not in non_gzip_tab_fmt:
+            path = path + "."+suffix+".{}.gz".format(tab_fmt)
+        else:
+            path = path + "."+suffix+".{}".format(tab_fmt)
+
+        yaml_path = path + "."+suffix+".{}-meta.yaml".format(tab_fmt)
         log.write(" -Output path:",path, verbose=verbose) 
-        
+
         sumstats,to_csvargs = _configure_output_cols_and_args(sumstats, rename_dictionary, cols, no_status, path, meta_data, to_csvargs, log, verbose)
         
         log.write(" -Writing sumstats to: {}...".format(path),verbose=verbose)
-        try:
-            fast_to_csv(sumstats, path, to_csvargs=to_csvargs, compress=True, write_in_chunks=True)
-        except:
-            log.write(f"Error in using fast_to_csv. Falling back to original implementation.",verbose=verbose)
-            sumstats.to_csv(path, index=None, **to_csvargs)
-
-        if md5sum == True: 
-            md5_value = md5sum_file(path,log,verbose)
-        else:
-            md5_value = calculate_md5sum_file(path)
         
+        #if tab_fmt=="tsv" or tab_fmt=="csv":
+        #    try:
+        #        log.write(f"  -Fast to csv mode...",verbose=verbose)
+        #        fast_to_csv(sumstats, path, to_csvargs=to_csvargs, compress=True, write_in_chunks=True)
+        #    except:
+        #        log.write(f"Error in using fast_to_csv. Falling back to original implementation.",verbose=verbose)
+        #        sumstats.to_csv(path, index=None, **to_csvargs)
+#
+        #elif tab_fmt=="parquet":
+        #    sumstats.to_parquet(path, index=None, **to_tabular_kwargs)
+        _write_tabular(sumstats,rename_dictionary, path, tab_fmt, to_csvargs, to_tabular_kwargs, log, verbose)
+        
+        if tab_fmt not in non_md5sum_tab_fmt and "@" not in path:
+            if md5sum == True: 
+                # write a md5sum file
+                md5_value = md5sum_file(path,log,verbose)
+            else:
+                # calculate md5sum without saveing a file
+                md5_value = calculate_md5sum_file(path)
+        else:
+            md5_value = "NA"
+
         ## update ssf-style meta data and export to yaml file
         _configure_ssf_meta(sumstats, fmt, ssfmeta, meta, meta_data, path, md5_value, yaml_path, log, verbose)
         
         return sumstats  
     
 ####################################################################################################################
+def _write_tabular(sumstats,rename_dictionary, path, tab_fmt, to_csvargs, to_tabular_kwargs, log, verbose):
+    chr_header = rename_dictionary["CHR"]
+    if tab_fmt=="tsv" or tab_fmt=="csv":
+        try:
+            log.write(f"  -Fast to csv mode...",verbose=verbose)
+            if "@" in path:
+                log.write(f"  -@ detected: writing each chromosome to a single file...",verbose=verbose)
+                log.write("  -Chromosomes:{}...".format(list(sumstats["CHR"].unique())),verbose=verbose)
+                for single_chr in list(sumstats["CHR"].unique()):
+                    single_path = path.replace("@",single_chr)
+
+                    fast_to_csv(sumstats.loc[sumstats[chr_header]==single_chr,:],
+                                 single_path, 
+                                 to_csvargs=to_csvargs, compress=True, write_in_chunks=True)
+            else:
+                fast_to_csv(sumstats, path, to_csvargs=to_csvargs, compress=True, write_in_chunks=True)
+        except:
+            log.write(f"Error in using fast_to_csv. Falling back to original implementation.",verbose=verbose)
+            if "@" in path:
+                log.write(f"  -@ detected: writing each chromosome to a single file...",verbose=verbose)
+                log.write("  -Chromosomes:{}...".format(list(sumstats["CHR"].unique())),verbose=verbose)
+                for single_chr in list(sumstats["CHR"].unique()):
+                    single_path = path.replace("@",single_chr)
+
+                    sumstats.loc[sumstats[chr_header]==single_chr,:].to_csv(path, index=None, **to_csvargs)
+            else:
+                sumstats.to_csv(path, index=None, **to_csvargs)
+
+    elif tab_fmt=="parquet":
+        sumstats.to_parquet(path, index=None, **to_tabular_kwargs)
+
+
+
 def fast_to_csv(dataframe, path, to_csvargs=None, compress=True, write_in_chunks=True):
         df_numpy = dataframe.to_numpy()
 

{gwaslab-3.5.1 → gwaslab-3.5.3}/src/gwaslab/viz_aux_annotate_plot.py

@@ -31,6 +31,7 @@ def annotate_single(
     arm_scale_d,
     arm_offset,
     anno_adjust,
+    anno_xshift,
     anno_fixed_arm_length,
     maxy,
     anno_fontsize,
@@ -158,6 +159,8 @@ def annotate_single(
             if anno_fixed_arm_length is not None:
                 xytext=(row["i"],row["scaled_P"] + 0.2 + anno_fixed_arm_length)
 
+            if anno_xshift is not None:
+                xytext = (xytext[0] +(anno_xshift*y_span), xytext[1])
             ################################################################################################################################
             # if not changing the directions of some annotation arror arms 
             if anno_count not in anno_d.keys():

{gwaslab-3.5.1 → gwaslab-3.5.3}/src/gwaslab/viz_aux_chromatin.py

@@ -99,7 +99,7 @@ def _plot_chromatin_state(region_chromatin_files,
             color=color_dict_i[row["STATE_i"]]
             ax.plot([offset_i + row["START"] ,offset_i + row["END"]],
                     [i*0.1,i*0.1],
-                    c=color/255,linewidth=points_for_01,solid_capstyle="butt")
+                    c=color/255,linewidth=points_for_01,solid_capstyle="butt",rasterized=True)
     
     ## add stripe label
     if len(region_chromatin_labels) == len(region_chromatin_files):

{gwaslab-3.5.1 → gwaslab-3.5.3}/src/gwaslab/viz_aux_quickfix.py

@@ -1,6 +1,8 @@
 import pandas as pd
 import numpy as np
 from gwaslab.g_Log import Log
+from matplotlib import ticker
+import matplotlib.pyplot as plt
 from gwaslab.bd_common_data import get_chr_to_number
 from gwaslab.bd_common_data import get_number_to_chr
 from math import ceil
@@ -350,7 +352,7 @@ def _cut(series, mode,cutfactor,cut,skip, ylabels, cut_log, verbose, lines_to_pl
                 #sumstats.loc[sumstats["scaled_P"]>cut,"scaled_P"] = (sumstats.loc[sumstats["scaled_P"]>cut,"scaled_P"]-cut)/cutfactor +  cut
                 
                 maxy = (maxticker-cut)/cutfactor + cut
-    
+
     return series, maxy, maxticker, cut, cutfactor,ylabels,lines_to_plot
 
 #def _cut_line(level, mode,cutfactor,cut,skip, ylabels, cut_log, verbose, log):
@@ -379,10 +381,9 @@ def _set_yticklabels(cut,
     log.write(" -Processing Y tick lables...",verbose=verbose)
     # if no cut
     if cut == 0: 
-            ax1.set_ylim(skip, ceil(maxy*1.2) )
-
+            ax1.set_ylim((skip, ceil(maxy*1.2)) )
     # if cut     
-    if cut:
+    if cut!=0:
         # add cut line
         
         cutline = ax1.axhline(y=cut, linewidth = sc_linewidth,linestyle="--",color=cut_line_color,zorder=1)
@@ -432,14 +433,15 @@ def _set_yticklabels(cut,
         else:
             ax1.set_yticks(ticks1+ticks2)
             ax1.set_yticklabels(tickslabel1+tickslabel2,fontsize=fontsize,family=font_family)
-        ax1.set_ylim(bottom = skip)
     
     if ylabels is not None:  
         ax1.set_yticks(ylabels_converted)
         ax1.set_yticklabels(ylabels,fontsize=fontsize,family=font_family)
     
+    ylim_top = ax1.get_ylim()[1]
+    ax1.set_ybound(lower=skip,upper=ylim_top)
     ax1.tick_params(axis='y', labelsize=fontsize)
-    
+
     return ax1
 
 def _jagged_y(cut,skip,ax1,mode,mqqratio,jagged_len,jagged_wid, log=Log(), verbose=True):

{gwaslab-3.5.1 → gwaslab-3.5.3}/src/gwaslab/viz_aux_save_figure.py

@@ -51,7 +51,8 @@ def get_default_path(keyword,fmt="png"):
                         "miami":"miami",
                         "esc":"effect_size_comparision",
                         "afc":"allele_frequency_comparision",
-                        "gwheatmap":"genome_wide_heatmap"
+                        "gwheatmap":"genome_wide_heatmap",
+                        "scatter":"scatter"
                         }
     prefix = path_dictionary[keyword]
     count = 1

{gwaslab-3.5.1 → gwaslab-3.5.3}/src/gwaslab/viz_plot_mqqplot.py

@@ -25,6 +25,7 @@ from gwaslab.viz_plot_qqplot import _plot_qq
 from gwaslab.hm_harmonize_sumstats import auto_check_vcf_chr_dict
 from gwaslab.viz_plot_regional2 import _plot_regional
 from gwaslab.viz_plot_regional2 import process_vcf
+from gwaslab.viz_plot_regional2 import _get_lead_id
 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
@@ -107,6 +108,7 @@ def mqqplot(insumstats,
           region_flank_factor = 0.05,
           region_anno_bbox_args = None,
           region_marker_shapes=None,
+          region_legend_marker=True,
           cbar_title='LD $r^{2}$ with variant',
           cbar_fontsize = None,
           cbar_font_family = None,
@@ -138,6 +140,7 @@ def mqqplot(insumstats,
           anno_source = "ensembl",
           anno_gtf_path=None,
           anno_adjust=False,
+          anno_xshift=None,
           anno_max_iter=100,
           arrow_kwargs=None,
           arm_offset=None,
@@ -233,7 +236,7 @@ def mqqplot(insumstats,
     if "dpi" not in fig_args.keys():
         fig_args["dpi"] = dpi
     if region_anno_bbox_args is None:
-        region_anno_bbox_args = dict()
+        region_anno_bbox_args = {"ec":"None","fc":"None"}
     if anno_set is None:
         anno_set=list()
     if anno_alias is None:
@@ -264,7 +267,7 @@ def mqqplot(insumstats,
         
     if region_marker_shapes is None:
         # 9 shapes
-        region_marker_shapes = ['o', 's','^','D','*','P','X','h','8']
+        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:
@@ -626,7 +629,8 @@ def mqqplot(insumstats,
             sumstats["chr_hue"]=sumstats["LD"]
                 
         ## default seetings
-        
+        # assign to_plot for scatter plot
+        to_plot = None
         palette = sns.color_palette(colors,n_colors=sumstats[chrom].nunique())  
 
         legend = None
@@ -639,7 +643,18 @@ def mqqplot(insumstats,
             legend=None
             linewidth=1
             if len(region_ref) == 1:
+                # hide lead variants -> add back in region plot 
                 palette = {100+i:region_ld_colors[i] for i in range(len(region_ld_colors))}
+                scatter_args["markers"]= {(i+1):m for i,m in enumerate(region_marker_shapes[:2])}
+                if region_ref[0] is None:
+                    id_to_hide = sumstats["scaled_P"].idxmax()
+                    to_plot = sumstats.drop(id_to_hide, axis=0)
+                else:
+                    #id_to_hide = sumstats[sumstats["SNPID"]==region_ref[0],"scaled_P"].idxmax()
+                    id_to_hide = _get_lead_id(sumstats, region_ref, log=log, verbose=verbose)
+                    if id_to_hide is not None:
+                        to_plot = sumstats.drop(id_to_hide, axis=0)
+                style="SHAPE"
             else:
                 palette = {}
                 region_color_maps = []
@@ -652,21 +667,24 @@ def mqqplot(insumstats,
                         # 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
+                
+                # gradient color dict
                 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"
+                # create a marker shape dict
                 scatter_args["markers"]= {(i+1):m for i,m in enumerate(region_marker_shapes[:len(region_ref)])}
                 style="SHAPE"
 
-            
+        
         ## if highlight 
         highlight_i = pd.DataFrame()
         if len(highlight) >0:
+            to_plot = sumstats
             log.write(" -Creating background plot...",verbose=verbose)
-            plot = sns.scatterplot(data=sumstats, x='i', y='scaled_P',
+            plot = sns.scatterplot(data=to_plot, x='i', y='scaled_P',
                                hue='chr_hue',
                                palette=palette,
                                legend=legend,
@@ -678,7 +696,7 @@ def mqqplot(insumstats,
             if pd.api.types.is_list_like(highlight[0]) and highlight_chrpos==False:
                 for i, highlight_set in enumerate(highlight):
                     log.write(" -Highlighting set {} target loci...".format(i+1),verbose=verbose)
-                    sns.scatterplot(data=sumstats.loc[sumstats["HUE"]==i], x='i', y='scaled_P',
+                    sns.scatterplot(data=to_plot.loc[to_plot["HUE"]==i], x='i', y='scaled_P',
                         hue="HUE",
                         palette={i:highlight_color[i%len(highlight_color)]},
                         legend=legend,
@@ -687,10 +705,10 @@ def mqqplot(insumstats,
                         sizes=(marker_size[0]+1,marker_size[1]+1),
                         linewidth=linewidth,
                         zorder=3+i,ax=ax1,edgecolor=edgecolor,**scatter_args)  
-                highlight_i = sumstats.loc[~sumstats["HUE"].isna(),"i"].values
+                highlight_i = to_plot.loc[~to_plot["HUE"].isna(),"i"].values
             else:
                 log.write(" -Highlighting target loci...",verbose=verbose)
-                sns.scatterplot(data=sumstats.loc[sumstats["HUE"]==0], x='i', y='scaled_P',
+                sns.scatterplot(data=to_plot.loc[to_plot["HUE"]==0], x='i', y='scaled_P',
                     hue="HUE",
                     palette={0:highlight_color},
                     legend=legend,
@@ -701,7 +719,7 @@ def mqqplot(insumstats,
                     zorder=3,ax=ax1,edgecolor=edgecolor,**scatter_args)  
                 # for annotate
                 if highlight_chrpos==False:
-                    highlight_i = sumstats.loc[sumstats[snpid].isin(highlight),"i"].values
+                    highlight_i = to_plot.loc[to_plot[snpid].isin(highlight),"i"].values
                 else:
                     highlight_i = []
         
@@ -739,7 +757,8 @@ def mqqplot(insumstats,
                 s = "s"
                 hue = 'chr_hue'
                 hue_norm=None
-                to_plot = sumstats
+                if to_plot is None:
+                    to_plot = sumstats
                 log.write(" -Creating background plot...",verbose=verbose)
                 plot = sns.scatterplot(data=to_plot, x='i', y='scaled_P',
                        hue=hue,
@@ -814,6 +833,7 @@ def mqqplot(insumstats,
                                 region_title=region_title,
                                 region_title_args=region_title_args,
                                 region_ld_legend = region_ld_legend,
+                                region_legend_marker=region_legend_marker,
                                 region_ld_threshold = region_ld_threshold,
                                 region_ld_colors = region_ld_colors,
                                 palette = palette,
@@ -996,6 +1016,7 @@ def mqqplot(insumstats,
                                 arm_scale_d=arm_scale_d,
                                 arm_offset=arm_offset,
                                 anno_adjust=anno_adjust,
+                                anno_xshift=anno_xshift,
                                 anno_fixed_arm_length=anno_fixed_arm_length,
                                 maxy=maxy,
                                 anno_fontsize= anno_fontsize,
@@ -1396,14 +1417,19 @@ def _process_xtick(ax1, chrom_df, xtick_chr_dict, fontsize, font_family, log=Log
 
 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_yticklabels = ax1.get_yticklabels()
+    #print(ax1_yticklabels)
+    #plt.draw()
+    #ax1_yticks = ax1.get_yticks()
+    #print(ax1_yticks)
     #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) 
+    ax1.tick_params(axis='y', labelsize=fontsize,labelfontfamily=font_family)
+    #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) 
+        #ax4_yticklabels = ax4.get_yticklabels()
+        #ax4_yticks = ax4.get_yticks()
+        ax4.tick_params(axis='y', labelsize=fontsize,labelfontfamily=font_family)
+        #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):