gwaslab 3.5.6__py3-none-any.whl → 3.5.8__py3-none-any.whl

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.io_load_ld import process_ld
 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
@@ -42,6 +43,8 @@ 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.io_process_args import _update_args
+from gwaslab.io_process_args import _update_arg
 from gwaslab.viz_aux_save_figure import save_figure
 from gwaslab.g_Log import Log
 from gwaslab.util_in_calculate_gc import lambdaGC
@@ -111,7 +114,14 @@ def mqqplot(insumstats,
           region_marker_shapes=None,
           region_legend_marker=True,
           region_ref_alias = None,
-          cbar_title='LD $r^{2}$ with variant',
+          ld_path=None,
+          ld_map_path=None,
+          ld_fmt = "npz",
+          ld_if_square =  False,
+          ld_if_add_T = False,
+          ld_map_rename_dic = None,
+          ld_map_kwargs = None,
+          cbar_title='LD $\mathregular{r^2}$ with variant',
           cbar_fontsize = None,
           cbar_scale=True,
           cbar_font_family = None,
@@ -205,7 +215,9 @@ 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,
@@ -230,34 +242,26 @@ def mqqplot(insumstats,
           ):
 
 # log.writeing meta info #######################################################################################
-    if chr_dict is None:          
-        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:   
-        rr_chr_dict = get_number_to_chr()
-    if fig_args is None:
-        fig_args= dict(figsize=(15,5))
-    if figargs is not None:
-        fig_args = figargs
+    chr_dict = _update_args(chr_dict, get_chr_to_number())
+    xtick_chr_dict = _update_args(xtick_chr_dict, get_number_to_chr())
+    gtf_chr_dict = _update_args(gtf_chr_dict, get_number_to_chr())
+    rr_chr_dict = _update_args(rr_chr_dict, get_number_to_chr())
+
+    fig_args = _update_args(fig_args, dict(figsize=(15,5)))
+    fig_args = _update_args(figargs, fig_args)
     if "dpi" not in fig_args.keys():
         fig_args["dpi"] = dpi
-    if region_anno_bbox_args is None:
-        region_anno_bbox_args = {"ec":"None","fc":"None"}
-    if anno_set is None:
-        anno_set=list()
-    if anno_alias is None:
-        anno_alias=dict()
-    if anno_d is None:
-        anno_d=dict()
-    if anno_args is None:
-        anno_args=dict()
-    if colors is None:
-        colors=["#597FBD","#74BAD3"]
-    if arrow_kwargs is None:
-        arrow_kwargs=dict()
+
+    anno_set = _update_arg(anno_set, list())
+    anno_alias = _update_args(anno_alias, dict())
+    anno_d = _update_args(anno_d,dict())
+    anno_args = _update_args(anno_args,dict())
+    arrow_kwargs = _update_args(arrow_kwargs,dict())
+
+    colors = _update_arg(colors, ["#597FBD","#74BAD3"])
+
+    ld_map_kwargs = _update_args(ld_map_kwargs,dict())
+
     if region is not None:
         if marker_size == (5,20):
             marker_size=(45,65)
@@ -274,84 +278,59 @@ def mqqplot(insumstats,
             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"]
+    taf = _update_args(taf, [track_n,track_n_offset,track_fontsize_ratio,track_exon_ratio,track_text_offset])
+    region_marker_shapes = _update_arg(region_marker_shapes, ['o', '^','s','D','*','P','X','h','8'])
+    region_grid_line = _update_args(region_grid_line,  {"linewidth": 2,"linestyle":"--"})
+    region_lead_grid_line = _update_args(region_lead_grid_line, {"alpha":0.5,"linewidth" : 2,"linestyle":"--","color":"#FF0000"})
+    region_ld_threshold = _update_arg(region_ld_threshold, [0.2,0.4,0.6,0.8])
+    region_anno_bbox_args = _update_args(region_anno_bbox_args, {"ec":"None","fc":"None"})
+    region_ld_colors = _update_arg(region_ld_colors, ["#E4E4E4","#020080","#86CEF9","#24FF02","#FDA400","#FF0000","#FF0000"])
+    region_ld_colors_m = _update_arg(region_ld_colors_m,  ["#E51819","#367EB7","green","#F07818","#AD5691","yellow","purple"])
+    region_title_args = _update_args(region_title_args,  {"size":fontsize})
+
+    font_family = _update_arg(font_family, fontfamily)
+    cbar_fontsize = _update_arg(cbar_fontsize, fontsize)
+    cbar_font_family = _update_arg(cbar_font_family, font_family)
+    track_font_family = _update_arg(track_font_family, font_family)
     
-    # 7 colors    
-    region_ld_colors_m = ["#E51819","#367EB7","green","#F07818","#AD5691","yellow","purple"]
+    build = _update_arg(build,"19")
+
+    save_args = _update_args(save_args, {"dpi":600,"transparent":True})
+    save_args = _update_args(saveargs , save_args)
+
+    pinpoint = _update_arg(pinpoint,list())
+    highlight = _update_arg(highlight,list())
+    highlight_anno_args = _update_args(highlight_anno_args)
     
-    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 = [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:
-        maf_bin_colors = ["#f0ad4e","#5cb85c", "#5bc0de","#000042"]
-    if save_args is None:
-        save_args = {"dpi":400,"facecolor":"white"}
-    if highlight is None:
-        highlight = list()
-    if highlight_anno_args is None:
-        highlight_anno_args = {}
-    if pinpoint is None:
-        pinpoint = list()  
-    if build is None:
-        build = "19"
-    if scatter_args is None:
-        scatter_args={}
-    if scatterargs is not None:
-        scatter_args = scatterargs
-    if qq_scatter_args is None:
-        qq_scatter_args={}
-    if qqscatterargs is not None:
-        qq_scatter_args = qqscatterargs
-    if saveargs is not None:
-        save_args = saveargs
+    maf_bins = _update_arg(maf_bins,[(0, 0.01), (0.01, 0.05), (0.05, 0.25),(0.25,0.5)])
+    maf_bin_colors = _update_arg(maf_bin_colors,["#f0ad4e","#5cb85c", "#5bc0de","#000042"])
+    qq_scatter_args = _update_args(qq_scatter_args)
+    qq_scatter_args = _update_args(qqscatterargs, qq_scatter_args)
+
+    scatter_args = _update_args(scatter_args)
+    scatter_args = _update_args(scatter_args, scatterargs)
+
     if sig_level is None:
         sig_level_plot=sig_level_plot
         sig_level_lead=sig_level_lead 
     else:
         sig_level_plot = sig_level
         sig_level_lead = sig_level     
-
+    
     if check==True and _if_quick_qc==True:
         _if_quick_qc = True
     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:
@@ -616,7 +595,25 @@ def mqqplot(insumstats,
                                verbose=verbose,
                                vcf_chr_dict=vcf_chr_dict,
                                tabix=tabix)
-
+    elif ld_path is not None:
+        sumstats = process_ld(
+            ld_path=ld_path,
+            ld_map_path = ld_map_path, 
+            sumstats=sumstats, 
+            region=region, 
+            region_ref=region_ref, 
+            log=log ,
+            pos=pos,
+            ea=ea,
+            nea=nea,
+            region_ld_threshold=region_ld_threshold,
+            verbose=verbose,
+            ld_fmt = ld_fmt,
+            ld_if_square =  ld_if_square,
+            ld_if_add_T = ld_if_add_T,
+            ld_map_rename_dic = ld_map_rename_dic,
+            ld_map_kwargs = ld_map_kwargs
+        )
     #sort & add id
     ## Manhatann plot ###################################################
     if ("m" in mode) or ("r" in mode): 
@@ -634,7 +631,7 @@ def mqqplot(insumstats,
         sumstats["chr_hue"]=sumstats[chrom].astype("string")
 
         if "r" in mode:
-            if vcf_path is None:
+            if vcf_path is None and ld_path is None:
                 sumstats["LD"]=100
                 sumstats["SHAPE"]=1
             sumstats["chr_hue"]=sumstats["LD"]
@@ -780,9 +777,10 @@ def mqqplot(insumstats,
                        sizes=marker_size,
                        hue_norm=hue_norm,
                        linewidth=linewidth,
-                       edgecolor = edgecolor,
+                       edgecolor = edgecolor, 
                        zorder=2,ax=ax1,**scatter_args)   
         
+        ax1.set_rasterization_zorder(0)
         
         ## if pinpoint variants
         if (len(pinpoint)>0):
@@ -817,10 +815,9 @@ def mqqplot(insumstats,
                                 ax3=ax3,
                                 region=region,
                                 vcf_path=vcf_path,
+                                ld_path=ld_path,
                                 marker_size=marker_size,
-                                fontsize=fontsize,
                                 build=build,
-                                chrom_df=chrom_df,
                                 cbar_scale=cbar_scale,
                                 cbar_fontsize=cbar_fontsize,
                                 cbar_bbox_to_anchor=cbar_bbox_to_anchor,
@@ -829,9 +826,7 @@ def mqqplot(insumstats,
                                 cbar_equal_aspect=cbar_equal_aspect,
                                 cbar_downward_offset =cbar_downward_offset, 
                                 cbar_borderpad=cbar_borderpad,
-                                xtick_chr_dict=xtick_chr_dict,
                                 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,
@@ -849,13 +844,11 @@ def mqqplot(insumstats,
                                 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,
@@ -863,8 +856,6 @@ 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
@@ -923,10 +914,10 @@ 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, 
@@ -950,7 +941,8 @@ 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)      
@@ -1132,11 +1124,14 @@ 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:
@@ -1152,8 +1147,15 @@ 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
+                        qq_scatter_args["antialiased"]=False,
+                        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
@@ -1414,45 +1416,52 @@ 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:
@@ -1467,19 +1476,29 @@ 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):
@@ -1494,6 +1513,11 @@ 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

gwaslab/viz_plot_qqplot.py

@@ -94,15 +94,15 @@ def _plot_qq(
             
             expected = -np.log10(np.linspace(minit,upper_bound_p,max(len(databin_raw),len(databin))))[:len(observed)]
 
-            label ="("+str(lower)+","+str(upper) +"]"
+            label ="( "+str(lower)+","+str(upper) +" ]"
             ax2.scatter(expected,observed,s=marker_size[1],color=maf_bin_colors[i],label=label,**qq_scatter_args)
-            ax2_legend= ax2.legend(loc="best",fontsize=fontsize,markerscale=3,frameon=False)
+            ax2_legend= ax2.legend(loc="best",fontsize=fontsize,markerscale=1.5,frameon=False, handletextpad=0.4, borderaxespad=0.4)
             plt.setp(ax2_legend.texts, family=font_family)
 
     qq_x = max(skip, expected_min_mlog10p)
     ax2.plot([qq_x,-np.log10(minit)],[qq_x,-np.log10(minit)],linestyle="--",color=qq_line_color)
-    ax2.set_xlabel("Expected $-log_{10}(P)$",fontsize=fontsize,family=font_family)
-    ax2.set_ylabel("Observed $-log_{10}(P)$",fontsize=fontsize,family=font_family)
+    ax2.set_xlabel("Expected $\mathregular{-log_{10}(P)}$",fontsize=fontsize,family=font_family)
+    ax2.set_ylabel("Observed $\mathregular{-log_{10}(P)}$",fontsize=fontsize,family=font_family)
     ax2.spines["top"].set_visible(False)
     ax2.spines["right"].set_visible(False)
     ax2.spines["left"].set_visible(True)
@@ -127,7 +127,7 @@ def _plot_qq(
                             verbose=verbose)
         
         # annotate lambda gc to qq plot
-        ax2.text(0.10, 1.03,"$\\lambda_{GC}$ = "+"{:.4f}".format(lambdagc),
+        ax2.text(0.10, 1.03,"$\mathregular{\\lambda_{GC}}$ = "+"{:.4f}".format(lambdagc),
                     horizontalalignment='left',
                     verticalalignment='top',
                     transform=ax2.transAxes,
@@ -179,7 +179,7 @@ def _plot_qq(
     #        ax2.set_yticklabels([x for x in range(skip,cut-step,step)]+[cut],fontsize=fontsize,family=font_family)
     #    ax2.set_ylim(bottom = skip)
 
-    ax2.tick_params(axis='both', which='both', labelsize=fontsize)
+    ax2.tick_params(axis='both', which='both', labelsize=fontsize,labelfontfamily=font_family)
     #
     if qtitle:
         ax2.set_title(qtitle,fontsize=title_fontsize,pad=10,family=font_family)

gwaslab/viz_plot_regional2.py

@@ -35,13 +35,10 @@ def _plot_regional(
     ax3,
     region,
     vcf_path,
+    ld_path,
     marker_size,
-    fontsize,
     build,
-    chrom_df,
-    xtick_chr_dict,
     cut_line_color,
-    vcf_chr_dict = None,
     gtf_path="default",
     gtf_chr_dict = get_number_to_chr(),
     gtf_gene_name=None,
@@ -50,7 +47,6 @@ def _plot_regional(
     rr_chr_dict = get_number_to_chr(),
     rr_lim = (0,100),
     rr_ylabel = True,
-    rr_title=None,
     region_ld_legend=True,
     region_title=None,
     mode="mqq",
@@ -64,9 +60,7 @@ def _plot_regional(
     region_lead_grid = True,
     region_lead_grid_line = {"alpha":0.5,"linewidth" : 2,"linestyle":"--","color":"#FF0000"},
     region_title_args = None,
-    region_hspace=0.02,
     region_ld_threshold = [0.2,0.4,0.6,0.8],
-    region_ld_colors = ["#E4E4E4","#020080","#86CEF9","#24FF02","#FDA400","#FF0000","#FF0000"],
     region_marker_shapes=None,
     cbar_fontsize=None,
     cbar_scale=False,
@@ -84,8 +78,6 @@ def _plot_regional(
     track_font_family="Arial",
     taf=[4,0,0.95,1,1],
     # track_n, track_n_offset,font_ratio,exon_ratio,text_offset
-    tabix=None,
-    chrom="CHR",
     pos="POS",
     verbose=True,
     log=Log()
@@ -134,7 +126,7 @@ def _plot_regional(
 
         ##########################################################################################################
 
-        if (vcf_path is not None) and region_ld_legend:
+        if ((vcf_path is not None) or (ld_path is not None)) and region_ld_legend:
             ## plot cbar
             ax1, cbar = _add_ld_legend(sumstats=sumstats, 
                             ax1=ax1, 
@@ -225,7 +217,7 @@ def _plot_regional(
         if "r" in mode:
             if gtf_path is not None: 
                 ax3.set_xticks(np.linspace(gene_track_start_i+region[1], gene_track_start_i+region[2], num=region_step))
-                ax3.set_xticklabels(region_ticks,rotation=45,fontsize=fontsize,family="sans-serif")
+                ax3.set_xticklabels(region_ticks,rotation=45)
             
             if region_grid==True:
                 for i in np.linspace(gene_track_start_i+region[1], gene_track_start_i+region[2], num=region_step):
@@ -241,7 +233,7 @@ def _plot_regional(
         else:
             # set x ticks m plot
             ax1.set_xticks(np.linspace(gene_track_start_i+region[1], gene_track_start_i+region[2], num=region_step))
-            ax1.set_xticklabels(region_ticks,rotation=45,fontsize=fontsize,family="sans-serif")
+            ax1.set_xticklabels(region_ticks,rotation=45)
     
         ax1.set_xlim([gene_track_start_i+region[1], gene_track_start_i+region[2]])
 
@@ -498,7 +490,7 @@ def _add_ld_legend(sumstats, ax1, region_ld_threshold, region_ref,region_ref_ind
     return ax1, cbar
 
 # -############################################################################################################################################################################
-def  _plot_recombination_rate(sumstats,pos, region, ax1, rr_path, rr_chr_dict, rr_header_dict, build,rr_lim,rr_ylabel=True):
+def  _plot_recombination_rate(sumstats,pos, region, ax1, rr_path, rr_chr_dict, rr_header_dict, build,rr_lim, rr_ylabel=True):
     ax4 = ax1.twinx()
     most_left_snp = sumstats["i"].idxmin()
     

gwaslab/viz_plot_rg_heatmap.py

@@ -37,7 +37,7 @@ def plot_rg(ldscrg,
         corrections=None,
         panno_texts=None,
         equal_aspect=True,
-        cmap = matplotlib.cm.get_cmap('RdBu'),
+        cmap = None,
         full_cell =None,
         log=Log(),
         panno_args=None,
@@ -57,6 +57,11 @@ def plot_rg(ldscrg,
     
     log.write("Start to create ldsc genetic correlation heatmap..." ,verbose=verbose)
     # configure arguments
+    if cmap is None:
+        try: #matplotlib <3.9
+            cmap = matplotlib.cm.get_cmap('RdBu')
+        except:
+            cmap = matplotlib.colormaps.get_cmap('RdBu')
     if fig_args is None:
         fig_args = {"dpi":300}
     if colorbar_args is None: