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

gwaslab/viz_plot_qqplot.py

@@ -45,7 +45,7 @@ def _plot_qq(
 
     # QQ plot #########################################################################################################
     # ax2 qqplot
-    if verbose:log.write("Start to create QQ plot with "+str(len(sumstats))+" variants:")
+    log.write("Start to create QQ plot with "+str(len(sumstats))+" variants:",verbose=verbose )
     
     # plotting qq plots using processed data after cut and skip
     
@@ -59,6 +59,7 @@ def _plot_qq(
     upper_bound_p = np.power(10.0, -expected_min_mlog10p)
 
     if stratified is False:
+        log.write(" -Plotting all variants...",verbose=verbose)
         # sort x,y for qq plot
         # high to low
         observed = p_toplot.sort_values(ascending=False)
@@ -68,13 +69,13 @@ def _plot_qq(
     
         expected_all = -np.log10(np.linspace(minit,upper_bound_p,len(p_toplot_raw)))[:len(observed)]
 
-        if verbose:log.write("Expected range of P: (0,{})".format(upper_bound_p))
+        log.write(" -Expected range of P: (0,{})".format(upper_bound_p),verbose=verbose)
         #p_toplot = sumstats["scaled_P"]
         ax2.scatter(expected_all,observed,s=marker_size[1],color=colors[0],**qq_scatter_args)
 
     else:
         # stratified qq plot
-        
+        log.write(" -Plotting variants stratified by MAF...",verbose=verbose)
         observed = p_toplot.sort_values(ascending=False)
         expected_all = -np.log10(np.linspace(minit,upper_bound_p,len(p_toplot_raw)))[:len(observed)]
 
@@ -115,15 +116,15 @@ def _plot_qq(
 
         if expected_min_mlog10p!=0:
             level = 1 -  np.power(10.0,-np.nanmedian(expected_all))
-            if verbose: log.write(" -Level for calculating lambda GC : {}".format(1 - level))
+            log.write(" -Level for calculating lambda GC : {}".format(1 - level),verbose=verbose)
 
-        if verbose and not include_chrXYMT : log.write(" -Excluding chrX,Y, MT from calculation of lambda GC.")
+        if verbose and not include_chrXYMT : log.write(" -Excluding chrX,Y, MT from calculation of lambda GC.",verbose=verbose)
         lambdagc = lambdaGC(p_toplot_raw, 
                             mode="MLOG10P", 
                             level=level, 
                             include_chrXYMT=include_chrXYMT,
                             log=log,
-                            verbose=True)
+                            verbose=verbose)
         
         # annotate lambda gc to qq plot
         ax2.text(0.10, 1.03,"$\\lambda_{GC}$ = "+"{:.4f}".format(lambdagc),
@@ -147,7 +148,9 @@ def _plot_qq(
                         font_family=font_family,
                         ylabels=ylabels,
                         ytick3=ytick3,
-                        ylabels_converted=ylabels_converted
+                        ylabels_converted=ylabels_converted,
+                        log=log,
+                        verbose=verbose
                         )
 
     #if cut == 0: 
@@ -181,7 +184,7 @@ def _plot_qq(
     if qtitle:
         ax2.set_title(qtitle,fontsize=title_fontsize,pad=10,family=font_family)
 
-    if verbose: log.write("Finished creating QQ plot successfully!")
+    log.write("Finished creating QQ plot successfully!",verbose=verbose)
     
     # Creating QQ plot Finished #############################################################################################
     return ax2

gwaslab/viz_plot_regionalplot.py

@@ -64,6 +64,7 @@ def _plot_regional(
     region_recombination = True,
     region_protein_coding=True,
     region_flank_factor = 0.05,
+    track_font_family="Arial",
     taf=[4,0,0.95,1,1],
     # track_n, track_n_offset,font_ratio,exon_ratio,text_offset
     tabix=None,
@@ -104,21 +105,25 @@ def _plot_regional(
 
         if (vcf_path is not None) and region_ld_legend:
             if region_ref_second is None:
-                ax1 = _add_ld_legend(sumstats=sumstats, 
+                ax1, cbar = _add_ld_legend(sumstats=sumstats, 
                                 ax1=ax1, 
                                 region_ld_threshold=region_ld_threshold, 
                                 region_ld_colors=region_ld_colors)
             else:
-                ax1 = _add_ld_legend(sumstats=sumstats, 
+                
+                ax1, cbar1 = _add_ld_legend(sumstats=sumstats, 
                                 ax1=ax1, 
                                 region_ld_threshold=region_ld_threshold, 
                                 region_ld_colors=region_ld_colors1,
                                 position=1)
-                ax1 = _add_ld_legend(sumstats=sumstats, 
+                ax1, cbar2 = _add_ld_legend(sumstats=sumstats, 
                                 ax1=ax1, 
                                 region_ld_threshold=region_ld_threshold, 
                                 region_ld_colors=region_ld_colors2,
                                 position=2)
+                cbar = [cbar1, cbar2]
+        else:
+            cbar=None
         if region_title is not None:
                 ax1 = _add_region_title(region_title, ax1=ax1,region_title_args=region_title_args )
     ## recombinnation rate ##################################################       
@@ -176,6 +181,7 @@ def _plot_regional(
                         gene_track_start_i=gene_track_start_i,
                         gtf_chr_dict=gtf_chr_dict,
                         gtf_gene_name=gtf_gene_name, 
+                        track_font_family=track_font_family,
                         taf=taf,
                         build=build, 
                         verbose=verbose, 
@@ -231,7 +237,7 @@ def _plot_regional(
                     avoid_points=False,
                     lim =1000)     
     
-    return ax1, ax3, lead_snp_i, lead_snp_i2
+    return ax1, ax3, ax4, cbar, lead_snp_i, lead_snp_i2
 
 # + ###########################################################################################################################################################################
 def _get_lead_id(sumstats=None, region_ref=None, log=None):
@@ -336,7 +342,7 @@ def _add_ld_legend(sumstats, ax1, region_ld_threshold, region_ld_colors,position
                                 facecolor='white',
                                 zorder=999998)
     ax1.add_patch(rect)
-    return ax1
+    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):
@@ -385,6 +391,7 @@ def _plot_gene_track(
     region_ld_colors2,
     gene_track_start_i,
     gtf_chr_dict,gtf_gene_name, 
+    track_font_family,
     taf,
     build, 
     verbose=True, 
@@ -452,15 +459,15 @@ def _plot_gene_track(
         if row["end"] >= region[2]:
             #right side
             texts_to_adjust_right.append(ax3.text(x=gene_track_start_i+region[2],
-                    y=row["stack"]*2+taf[4],s=gene_anno,ha="right",va="center",color="black",style='italic', size=font_size_in_points))
+                    y=row["stack"]*2+taf[4],s=gene_anno,ha="right",va="center",color="black",style='italic', size=font_size_in_points,family=track_font_family))
             
         elif row["start"] <= region[1] :
             #left side
             texts_to_adjust_left.append(ax3.text(x=gene_track_start_i+region[1],
-                    y=row["stack"]*2+taf[4],s=gene_anno,ha="left",va="center",color="black",style='italic', size=font_size_in_points))
+                    y=row["stack"]*2+taf[4],s=gene_anno,ha="left",va="center",color="black",style='italic', size=font_size_in_points,family=track_font_family))
         else:
             texts_to_adjust_middle.append(ax3.text(x=(gene_track_start_i+row["start"]+gene_track_start_i+row["end"])/2,
-                    y=row["stack"]*2+taf[4],s=gene_anno,ha="center",va="center",color="black",style='italic',size=font_size_in_points))
+                    y=row["stack"]*2+taf[4],s=gene_anno,ha="center",va="center",color="black",style='italic',size=font_size_in_points,family=track_font_family))
     
     # plot exons
     for index,row in exons.iterrows():
@@ -535,7 +542,7 @@ def process_vcf(sumstats, vcf_path, region,region_ref, region_ref_second, log, v
             # no position match
             return None
     if verbose: log.write(" -Matching variants using POS, NEA, EA ...")
-    sumstats["REFINDEX"] = sumstats.loc[:,[pos,nea,ea]].apply(lambda x: match_varaint(x),axis=1)
+    sumstats["REFINDEX"] = sumstats[[pos,nea,ea]].apply(lambda x: match_varaint(x),axis=1)
     #############################################################################################
     #sumstats["REFINDEX"] = sumstats[pos].apply(lambda x: np.where(ref_genotype["variants/POS"] == x )[0][0] if np.any(ref_genotype["variants/POS"] == x) else None)
     

gwaslab/viz_plot_trumpetplot.py

@@ -66,7 +66,7 @@ def plottrumpet(mysumstats,
                 anno_source = "ensembl",
                 anno_max_iter=100,
                 arm_scale=1,
-                repel_force=0.05,
+                repel_force=0.01,
                 ylabel="Effect size",
                 xlabel="Minor allele frequency",
                 xticks = None,
@@ -99,7 +99,7 @@ def plottrumpet(mysumstats,
             xticks = [0,0.01,0.05,0.1,0.2,0.5]
             xticklabels = xticks            
     if figargs is None:
-        figargs={"figsize":(10,15)}
+        figargs={"figsize":(10,8)}
     if scatter_args is None:
         scatter_args ={}
     if hue is not None:
@@ -307,6 +307,7 @@ def plottrumpet(mysumstats,
     
     if ylim is not None:
         ax.set_ylim(ylim)
+
     if yticks is not None:
         ax.set_yticks(yticks, yticklabels)
 
@@ -337,8 +338,8 @@ def plottrumpet(mysumstats,
             texts_d=[]
 
             if len(variants_toanno)>0:
-                
-                maxy = max(variants_toanno[beta].abs().max(),1.5)
+                maxy = variants_toanno[beta].abs().max()
+                #maxy = max(variants_toanno[beta].abs().max(),1.5)
                 variants_toanno["ADJUSTED_i"] = np.nan 
                 y_span = 0.5
                 
@@ -348,6 +349,9 @@ def plottrumpet(mysumstats,
                     variants_toanno = variants_toanno.sort_values(by=maf, key= np.abs, ascending = True)
                 
                 if anno_style == "expand":
+
+                    min_factor=None
+                    
                     if len(variants_toanno.loc[variants_toanno[beta]>0, "ADJUSTED_i"])>1:
                         variants_toanno.loc[variants_toanno[beta]>0, "ADJUSTED_i"] = adjust_text_position(variants_toanno.loc[variants_toanno[beta]>0,maf].values.copy(), 
                                                                                 y_span, 
@@ -355,7 +359,7 @@ def plottrumpet(mysumstats,
                                                                                 max_iter=anno_max_iter,
                                                                                 log=log,
                                                                                 amode=xscale,
-                                                                                verbose=verbose)
+                                                                                verbose=verbose,min_factor=min_factor)
 
                     if len(variants_toanno.loc[variants_toanno[beta]<0, "ADJUSTED_i"])>1:
                         variants_toanno.loc[variants_toanno[beta]<0, "ADJUSTED_i"] = adjust_text_position(variants_toanno.loc[variants_toanno[beta]<0,maf].values.copy(), 
@@ -364,10 +368,12 @@ def plottrumpet(mysumstats,
                                                                 max_iter=anno_max_iter,
                                                                 log=log,
                                                                 amode=xscale,
-                                                                verbose=verbose)
+                                                                verbose=verbose,min_factor=min_factor)
 
                 
                 for variants_toanno_half in [variants_toanno.loc[variants_toanno[beta]<0,:], variants_toanno.loc[variants_toanno[beta]>0,:]]:
+                    if len(variants_toanno_half)<1:
+                        continue
                     last_pos = min(variants_toanno_half[maf])/2
                     for index, row in variants_toanno_half.iterrows():
                         
@@ -395,6 +401,7 @@ def plottrumpet(mysumstats,
                         
                         if anno_style=="tight":
                             texts_d.append(ax.text(row[maf], row[beta], row[anno]))
+
                 if anno_style=="tight":
                     adjust_text(texts_d, 
                                 autoalign =True,
@@ -404,6 +411,8 @@ def plottrumpet(mysumstats,
                                 expand_points=(0.5,0.5),
                                 force_objects=(0.5,0.5), 
                                 ax=ax)
+    
+
     ############  Annotation ##################################################################################################
     if mode=="q":
         save_figure(fig, save, keyword="trumpet_q",save_args=save_args, log=log, verbose=verbose)

{gwaslab-3.4.36.dist-info → gwaslab-3.4.38.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gwaslab
-Version: 3.4.36
+Version: 3.4.38
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/
@@ -8,13 +8,13 @@ Project-URL: Github, https://github.com/Cloufield/gwaslab
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Requires-Python: <=3.10,>=3.8
+Requires-Python: <=3.10,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: pandas !=1.5,>=1.3
 Requires-Dist: numpy >=1.21.2
 Requires-Dist: matplotlib !=3.7.2,>=3.5
-Requires-Dist: seaborn >=0.11.1
+Requires-Dist: seaborn >=0.12
 Requires-Dist: scipy >=1.12
 Requires-Dist: pySAM <0.20,>=0.18.1
 Requires-Dist: Biopython >=1.79

gwaslab-3.4.38.dist-info/RECORD

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