gwaslab 3.5.5__py3-none-any.whl → 3.5.7__py3-none-any.whl

gwaslab/viz_plot_effect.py

@@ -0,0 +1,283 @@
+import pandas as pd
+import matplotlib.pyplot as plt
+import matplotlib.ticker as ticker
+import matplotlib.patches as patches
+import seaborn as sns
+import numpy as np
+import scipy as sp
+import copy
+from math import ceil
+from shutil import which
+from pyensembl import EnsemblRelease
+from allel import GenotypeArray
+from allel import read_vcf
+from allel import rogers_huff_r_between
+import matplotlib as mpl
+from scipy import stats
+from mpl_toolkits.axes_grid1.inset_locator import inset_axes
+from mpl_toolkits.axes_grid1.inset_locator import mark_inset
+from matplotlib.ticker import MaxNLocator
+import gc as garbage_collect
+from adjustText import adjust_text
+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_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
+from gwaslab.viz_aux_quickfix import _quick_fix_chr
+from gwaslab.viz_aux_quickfix import _quick_fix_eaf
+from gwaslab.viz_aux_quickfix import _quick_fix_mlog10p
+from gwaslab.viz_aux_quickfix import _quick_add_tchrpos
+from gwaslab.viz_aux_quickfix import _quick_merge_sumstats
+from gwaslab.viz_aux_quickfix import _quick_assign_i
+from gwaslab.viz_aux_quickfix import _quick_assign_i_with_rank
+from gwaslab.viz_aux_quickfix import _quick_extract_snp_in_region
+from gwaslab.viz_aux_quickfix import _quick_assign_highlight_hue_pair
+from gwaslab.viz_aux_quickfix import _quick_assign_marker_relative_size
+from gwaslab.viz_aux_quickfix import _cut
+from gwaslab.viz_aux_quickfix import _set_yticklabels
+from gwaslab.viz_aux_quickfix import _jagged_y
+from gwaslab.viz_aux_save_figure import save_figure
+from gwaslab.g_Log import Log
+from gwaslab.util_in_calculate_gc import lambdaGC
+from gwaslab.util_in_get_sig import getsig
+from gwaslab.util_in_get_sig import annogene
+from gwaslab.bd_common_data import get_chr_to_number
+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.util_in_filter_value import _filter_region
+from gwaslab.g_version import _get_version
+from matplotlib.colors import ListedColormap
+from matplotlib.colors import LinearSegmentedColormap
+from matplotlib.colors import to_hex
+from gwaslab.io_process_args import _extract_kwargs
+
+def _plot_effect(to_plot, 
+                 y=None, 
+                 y_sort=None, 
+                 group=None, 
+                 x="BETA", 
+                 se="SE", 
+                 eaf="EAF", 
+                 snpr2="SNPR2", 
+                 ylabel="Variant",
+                 eaf_panel=True, 
+                 snpvar_panel=True, 
+                 rename_dic=None, 
+                 err_args=None,
+                 font_args=None,
+                 save=None,
+                 title=None,
+                 save_args=None,
+                 eaf_args=None,
+                 snpr2_args=None,
+                 fig_args=None,
+                 scatter_args=None,
+                 effect_label=None,
+                 eaf_label=None,
+                 snpr2_label=None,
+                 log=Log(),
+                 verbose=True,
+                 legend_mode=1,
+                 ncol=2,
+                 size=None,
+                 hue=None,
+                 style=None,
+                 **args):
+
+    if err_args is None:
+        err_args={"ecolor":"#cccccc",
+                  "linewidth":0,
+                  "zorder":90,
+                  "elinewidth":1}
+    if eaf_args is None:
+        eaf_args={"color":"#74BAD3"}
+    if snpr2_args is None:
+        snpr2_args={"color":"#74BAD3"}
+    if font_args is None:
+        font_args={'fontsize':12,'family':'sans','fontname':'Arial'}
+    if fig_args is None:
+        fig_args={"figsize":(8,8),"dpi":300}
+    if scatter_args is None:
+        scatter_args={"s":20}
+    
+
+    legend_titles=[]
+    if hue is not None:
+        args["hue"] = hue
+        legend_titles.append(hue)
+
+    if size is not None:
+        args["size"] = size
+        legend_titles.append(size)
+
+    if style is not None:
+        args["style"] = style
+        legend_titles.append(style)
+
+        
+    save_kwargs =      _extract_kwargs("save", save_args, locals())
+    err_kwargs =       _extract_kwargs("err", err_args, locals())
+    scatter_kwargs =   _extract_kwargs("scatter", scatter_args, locals())
+    font_kwargs =      _extract_kwargs("font",font_args, locals())
+    
+    def concat_cols(cols):
+        string = "-".join(map(str,cols))
+        return string
+    
+    y_name = "-".join(y)
+    
+    to_plot[y_name] = to_plot[y].apply(lambda x: concat_cols(x), axis=1)
+    
+
+    # sort y 
+    if y_sort is None:
+        y_sort = ["CHR","POS","STUDY"]
+    
+    to_plot = to_plot.sort_values(by=y_sort)
+
+    if group is None:
+        group = ["CHR","POS"]
+        to_plot = to_plot.sort_values(by=group)
+    # Assign group IDs based on the sorted 'score'
+        
+    to_plot['_VAR_GROUP'] = to_plot.groupby(group).ngroup() + 1
+
+    to_plot["_VAR_INDEX"] = range(len(to_plot))
+    to_plot["_VAR_INDEX"]= to_plot["_VAR_INDEX"] + to_plot['_VAR_GROUP']
+
+    y="_VAR_INDEX"
+
+    if rename_dic is None:
+        rename_dic = {
+            "BETA":"Per-allele effect size",
+            "STUDY":"Study"
+                      }
+    ncols=1
+    if eaf_panel:
+        ncols+=1
+    if snpvar_panel:
+        ncols+=1
+
+    if ncols==1:
+        fig,ax1 = plt.subplots(ncols=ncols, **fig_args)
+    elif ncols==2:
+        if eaf_panel==True:
+            fig,axes = plt.subplots(ncols=ncols, dpi=400,sharey=True)
+            ax1=axes[0]
+            ax2=axes[1]
+        else:
+            fig,axes = plt.subplots(ncols=ncols, dpi=400,sharey=True)
+            ax1=axes[0]
+            ax3=axes[1]
+    else:
+        fig,axes = plt.subplots(ncols=ncols, dpi=400,sharey=True)
+        ax1=axes[0]
+        ax2=axes[1]
+        ax3=axes[2]
+
+    sns.scatterplot(data=to_plot, x=x, y=y, ax=ax1, zorder=100, **args)
+
+    ax1.errorbar(y=to_plot[y], x=to_plot[x], xerr=to_plot[se], 
+                  **err_kwargs)
+    
+    ax1.axvline(x=0,linestyle="dashed",c="grey")
+    ax1.set_yticks(to_plot[y], labels = to_plot[y_name])
+    ax1.set_ylabel(ylabel) 
+
+    if title is not None:
+        ax1.set_title(title)
+
+    if eaf_panel==True:
+        ax2.barh(y=to_plot[y], width=to_plot[eaf], zorder=100, **eaf_args)
+        ax2.set_xlabel(eaf)
+
+    if snpvar_panel==True:
+        ax3.barh(y=to_plot[y], width=to_plot[snpr2], zorder=100,**snpr2_args)
+        ax3.set_xlabel(snpr2)
+    
+    #try:
+    if legend_mode==1:
+        #if ncols==1:
+        sns.move_legend(
+            ax1, "upper left",
+            bbox_to_anchor=(1, 1), title=None, frameon=False, bbox_transform = axes[-1].transAxes
+            )
+            #else:
+##
+            #    sns.move_legend(
+            #        ax1, "lower left",
+            #        bbox_to_anchor=(0, ncols), title=None, frameon=False,
+            #    )
+        #elif legend_mode==2:
+        #    sns.move_legend(
+        #        ax1, "lower center",
+        #        bbox_to_anchor=(0, 1), ncol=ncol, title=None, frameon=False,
+        #        )
+    #except:
+    #    pass
+
+
+    #handles, labels = ax1.get_legend_handles_labels()
+    #if len(labels)>0:
+    #    #new_labels = []
+    #    #ncol = len(labels)
+    #    max_col=0
+    #    new_labels=[]
+    #    new_labels_i = []
+    #    previous_i = 0
+    #    max_string_len=0
+    #    for i in range(len(labels)):
+    #        if len(labels[i]) > max_string_len:
+    #            max_string_len = len(labels[i])
+    #        if labels[i] in legend_titles:
+    #            new_labels_i.append(i)
+    #            col_number = i - previous_i
+    #            if col_number > max_col:
+    #                max_col = col_number
+    #            previous_i = i
+    #    for i in labels:
+    #        new_labels.append(str(i).ljust(max_string_len))
+    #    print(new_labels)
+    #    new_labels_i.append(len(labels))
+#
+    #    legend_rows = []
+    #    #new_labels_i[index+1] - i
+    #    for index, i in enumerate(new_labels_i):
+    #        if index<len(new_labels_i)-1:
+    #            legend_row = ax1.legend(labels = new_labels[i:new_labels_i[index+1]],  
+    #                                    handles= handles[i:new_labels_i[index+1]],
+    #                                    loc="lower left", 
+    #                                    bbox_to_anchor=(-0.2, 1.02 + 0.05*index), 
+    #                                    ncol=max_col, 
+    #                                    scatterpoints=1, 
+    #                                    title=None, 
+    #                                    borderpad=0,
+    #                                    handletextpad=0.1,
+    #                                    handlelength=0.7,
+    #                                    borderaxespad =0,
+    #                                    alignment = "left",
+    #                                    fontsize=8,
+    #                                    frameon=False)
+    #            legend_rows.append(legend_row)
+    #    for legend_row in legend_rows[:-1]:
+    #        ax1.add_artist(legend_row)
+
+
+
+    if effect_label is not None:
+        ax1.set_xlabel(effect_label)
+    if eaf_label is not None:
+        ax2.set_xlabel(eaf_label)
+    if snpr2_label is not None:
+        ax3.set_xlabel(snpr2_label)
+
+    save_figure(fig, save, keyword="forest",save_args=save_kwargs, log=log, verbose=verbose)   
+    
+    return fig

gwaslab/viz_plot_miamiplot2.py

@@ -249,7 +249,7 @@ def plot_miami2(
     #####################################################################################################################
     ##plotting
     if figax is None:
-        fig_args["figsize"] = (15,10)
+        #fig_args["figsize"] = (15,10)
         fig, (ax1, ax5) = plt.subplots(2, 1, gridspec_kw={'height_ratios': [1, 1]},**fig_args)
         plt.subplots_adjust(hspace=region_hspace)    
     else:

gwaslab/viz_plot_mqqplot.py

@@ -110,9 +110,17 @@ def mqqplot(insumstats,
           region_anno_bbox_args = None,
           region_marker_shapes=None,
           region_legend_marker=True,
-          cbar_title='LD $r^{2}$ with variant',
+          region_ref_alias = None,
+          cbar_title='LD $\mathregular{r^2}$ with variant',
           cbar_fontsize = None,
+          cbar_scale=True,
           cbar_font_family = None,
+          cbar_bbox_to_anchor = (0,0,1,1),
+          cbar_equal_aspect = True,
+          cbar_w_scale=1,
+          cbar_h_scale=1,
+          cbar_downward_offset =1.3, 
+          cbar_borderpad=None,
           track_n=4,
           track_n_offset=0,
           track_fontsize_ratio=0.95,
@@ -197,7 +205,9 @@ def mqqplot(insumstats,
           title_pad=1.08, 
           title_fontsize=13,
           fontsize = 9,
-          font_family="Arial",
+          font_family=None,
+          fontfamily="Arial",
+          math_fontfamily="dejavusans",
           anno_fontsize = 9,
           figargs=None,
           fig_args= None,
@@ -222,6 +232,7 @@ def mqqplot(insumstats,
           ):
 
 # log.writeing meta info #######################################################################################
+    
     if chr_dict is None:          
         chr_dict = get_chr_to_number()
     if xtick_chr_dict is None:         
@@ -281,7 +292,8 @@ def mqqplot(insumstats,
     
     # 7 colors    
     region_ld_colors_m = ["#E51819","#367EB7","green","#F07818","#AD5691","yellow","purple"]
-    
+    if font_family is None:
+        font_family = fontfamily
     if region_title_args is None:
         region_title_args = {"size":10}
     if cbar_fontsize is None:
@@ -297,7 +309,7 @@ def mqqplot(insumstats,
     if maf_bin_colors is None:
         maf_bin_colors = ["#f0ad4e","#5cb85c", "#5bc0de","#000042"]
     if save_args is None:
-        save_args = {"dpi":400,"facecolor":"white"}
+        save_args = {"dpi":600,"facecolor":"none"}
     if highlight is None:
         highlight = list()
     if highlight_anno_args is None:
@@ -328,22 +340,15 @@ def mqqplot(insumstats,
     else:
         _if_quick_qc = False
 
-    if save is not None:
-        if type(save) is not bool:
-            if len(save)>3:
-                if save[-3:]=="pdf" or save[-3:]=="svg":
-                    fig_args["dpi"]=72
-                    scatter_args["rasterized"]=True
-                    qq_scatter_args["rasterized"]=True
-                else:
-                    fig_args["dpi"] = save_args["dpi"]
-    
     # configure dpi if saving the plot
-    fig_args, scatter_args, qq_scatter_args, save_args = _configure_fig_save_kwargs(save = save, 
+    fig_args, scatter_args, qq_scatter_args, save_args = _configure_fig_save_kwargs(mode=mode,
+                                                                                    save = save, 
                                                                                     fig_args = fig_args, 
                                                                                     scatter_args = scatter_args, 
                                                                                     qq_scatter_args = qq_scatter_args, 
-                                                                                    save_args = save_args)
+                                                                                    save_args = save_args,
+                                                                                    log=log,
+                                                                                    verbose=verbose)
 
 
     if len(anno_d) > 0 and arm_offset is None:
@@ -810,12 +815,16 @@ def mqqplot(insumstats,
                                 region=region,
                                 vcf_path=vcf_path,
                                 marker_size=marker_size,
-                                fontsize=fontsize,
                                 build=build,
-                                chrom_df=chrom_df,
-                                xtick_chr_dict=xtick_chr_dict,
+                                cbar_scale=cbar_scale,
+                                cbar_fontsize=cbar_fontsize,
+                                cbar_bbox_to_anchor=cbar_bbox_to_anchor,
+                                cbar_w_scale=cbar_w_scale,
+                                cbar_h_scale=cbar_h_scale,
+                                cbar_equal_aspect=cbar_equal_aspect,
+                                cbar_downward_offset =cbar_downward_offset, 
+                                cbar_borderpad=cbar_borderpad,
                                 cut_line_color=cut_line_color,
-                                vcf_chr_dict =vcf_chr_dict,
                                 gtf_path=gtf_path,
                                 gtf_chr_dict = gtf_chr_dict,
                                 gtf_gene_name=gtf_gene_name,
@@ -828,17 +837,16 @@ def mqqplot(insumstats,
                                 region_step = region_step,
                                 region_ref = region_ref,
                                 region_ref_index_dic = region_ref_index_dic,
+                                region_ref_alias = region_ref_alias,
                                 region_grid = region_grid,
                                 region_grid_line = region_grid_line,
                                 region_lead_grid = region_lead_grid,
                                 region_lead_grid_line = region_lead_grid_line,
-                                region_hspace=region_hspace,
                                 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,
                                 region_marker_shapes = region_marker_shapes,
                                 region_recombination = region_recombination,
@@ -846,8 +854,6 @@ def mqqplot(insumstats,
                                 region_flank_factor =region_flank_factor,
                                 track_font_family=track_font_family,
                                 taf=taf,
-                                tabix=tabix,
-                                chrom=chrom,
                                 pos=pos,
                                 verbose=verbose,
                                 log=log
@@ -906,10 +912,10 @@ def mqqplot(insumstats,
 
         # Configure X, Y axes #######################################################
         log.write("Start to process figure arts.",verbose=verbose)
-        if region is None:
-            # if Manhattan plot 
- 
-            ax1 = _process_xtick(ax1=ax1, 
+
+        ax1, ax3 = _process_xtick(ax1=ax1, 
+                                  ax3=ax3,
+                                  mode=mode,
                                  chrom_df=chrom_df, 
                                  xtick_chr_dict=xtick_chr_dict, 
                                  fontsize = fontsize, 
@@ -933,7 +939,8 @@ def mqqplot(insumstats,
                                    mode=mode, 
                                    bwindowsizekb=bwindowsizekb, 
                                    fontsize=fontsize, 
-                                   font_family=font_family, 
+                                   font_family=font_family,
+                                   math_fontfamily=math_fontfamily, 
                                    ax4=ax4,
                                    log=log, 
                                    verbose=verbose)      
@@ -1115,11 +1122,14 @@ def mqqplot(insumstats,
 
 ##############################################################################################################################################################################
 
-def _configure_fig_save_kwargs(save=None, 
+def _configure_fig_save_kwargs(mode="m",
+                                save=None, 
                                fig_args=None, 
                                scatter_args=None, 
                                qq_scatter_args=None, 
-                               save_args=None):
+                               save_args=None,
+                               log=Log(),
+                               verbose=True):
     if fig_args is None:
         fig_args = dict()
     if scatter_args is None:
@@ -1135,8 +1145,14 @@ def _configure_fig_save_kwargs(save=None,
                 if save[-3:]=="pdf" or save[-3:]=="svg":
                     # to save as vectorized plot
                     fig_args["dpi"]=72
-                    scatter_args["rasterized"]=True
-                    qq_scatter_args["rasterized"]=True
+                    
+                    if mode!="r":
+                        scatter_args["rasterized"]=True
+                        qq_scatter_args["rasterized"]=True
+                        log.write("Saving as pdf/svg: scatter plot will be rasterized for mqq...", verbose=verbose)
+                    else:
+                        scatter_args["rasterized"]=False
+                        qq_scatter_args["rasterized"]=False
                 else:
                     fig_args["dpi"] = save_args["dpi"]
     return fig_args, scatter_args, qq_scatter_args, save_args
@@ -1397,45 +1413,52 @@ 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.get_yticklabels()
-    cbar.set_yticklabels(cbar_yticklabels, fontsize=cbar_fontsize, family=cbar_font_family )
+    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_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 )
+    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):
+def _process_xtick(ax1, mode, chrom_df, xtick_chr_dict, fontsize, font_family="Arial", ax3=None , 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
+    
+    if mode!="r":
+        ax1.set_xticks(chrom_df.astype("float64"))
+        ax1.set_xticklabels(chrom_df.index.astype("Int64").map(xtick_chr_dict),
+                            fontsize=fontsize,
+                            family=font_family)    
+    
+    if ax3 is not None:
+        ax3.tick_params(axis='x', 
+                        labelsize=fontsize,
+                        labelfontfamily=font_family) 
+    
+    return ax1, ax3
 
 def _process_ytick(ax1, fontsize, font_family, ax4, log=Log(),verbose=True):
     log.write(" -Processing Y labels...",verbose=verbose)
-    #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.tick_params(axis='y', labelsize=fontsize,labelfontfamily=font_family)
-    #ax1.set_yticks(ax1_yticks,ax1_yticklabels,fontsize=fontsize,family=font_family) 
+    
+    ax1.tick_params(axis='y', 
+                    labelsize=fontsize,
+                    labelfontfamily=font_family)
+    
     if ax4 is not None:
-        #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) 
+        ax4.tick_params(axis='y', 
+                        labelsize=fontsize,
+                        labelfontfamily=font_family)
     return ax1, ax4
 
-def _process_xlabel(region, xlabel, ax1, gtf_path, mode, fontsize, font_family,  ax3=None , log=Log(),verbose=True):
+def _process_xlabel(region, xlabel, ax1, gtf_path, mode, fontsize, font_family="Arial",  ax3=None , log=Log(),verbose=True):
     log.write(" -Processing X labels...",verbose=verbose)
     if region is not None:
         if xlabel is None:
@@ -1450,19 +1473,29 @@ 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, ax4=None, log=Log(),verbose=True):
+def _process_ylabel(ylabel, ax1,  mode, bwindowsizekb, fontsize, font_family, math_fontfamily, 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"
-        ax1.set_ylabel(ylabel,ha="center",va="bottom",fontsize=fontsize,family=font_family)
+        ax1.set_ylabel(ylabel,ha="center",va="bottom",
+                       fontsize=fontsize,
+                       family=font_family,
+                       math_fontfamily=math_fontfamily)
     else:
         if ylabel is None:
-            ylabel ="$-log_{10}(P)$"
-        ax1.set_ylabel(ylabel,fontsize=fontsize,family=font_family)
+            ylabel ="$\mathregular{-log_{10}(P)}$"
+        ax1.set_ylabel(ylabel,
+                       fontsize=fontsize,
+                       family=font_family, 
+                       math_fontfamily=math_fontfamily)
+    
     if ax4 is not None:
         ax4_ylabel = ax4.get_ylabel()
-        ax4.set_ylabel(ax4_ylabel, fontsize=fontsize, family=font_family )
+        ax4.set_ylabel(ax4_ylabel, 
+                       fontsize=fontsize, 
+                       family=font_family,
+                       math_fontfamily=math_fontfamily )
     return ax1, ax4
 
 def _process_spine(ax1, mode):
@@ -1477,6 +1510,11 @@ def _process_spine(ax1, mode):
 
 
 def _process_layout(mode, figax, fig_args, mqqratio, region_hspace):
+    #ax1 m / r
+    #ax2 qq
+    #ax3 gene track
+    #ax4 recombination
+
     if  mode=="qqm": 
         fig, (ax2, ax1) = plt.subplots(1, 2,gridspec_kw={'width_ratios': [1, mqqratio]},**fig_args)
         ax3 = None