gwaslab 3.6.7__tar.gz → 3.6.8__tar.gz

{gwaslab-3.6.7/src/gwaslab.egg-info → gwaslab-3.6.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gwaslab
-Version: 3.6.7
+Version: 3.6.8
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <gwaslab@gmail.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/

{gwaslab-3.6.7 → gwaslab-3.6.8}/pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gwaslab"
-version = "3.6.7"
+version = "3.6.8"
 authors = [
   { name="Yunye", email="gwaslab@gmail.com" },
 ]

{gwaslab-3.6.7 → gwaslab-3.6.8}/src/gwaslab/g_version.py

@@ -17,8 +17,8 @@ def _get_version():
 def gwaslab_info():
     # version meta information
     dic={
-   "version":"3.6.7",
-   "release_date":"20250827"
+   "version":"3.6.0",
+   "release_date":"20250902"
     }
     return dic   
 

{gwaslab-3.6.7 → gwaslab-3.6.8}/src/gwaslab/util/util_ex_phewwas.py

@@ -7,6 +7,11 @@ def _extract_associations(sumstats, rsid="rsID", log = Log(), verbose=True):
 
     assoc, traits, studies, variants = get_associations_from_gwascatalog(sumstats, rsid=rsid, log=log, verbose=verbose)
     
+    if len(assoc)==0:
+        # if no associations
+        log.write("No associations!")
+        return None, None
+    
     assoc = _fix_beta(assoc)
 
     traits_agg = traits.groupby("associationId")[["trait","shortForm"]].agg(lambda x: ",".join(x)).reset_index()
@@ -14,7 +19,7 @@ def _extract_associations(sumstats, rsid="rsID", log = Log(), verbose=True):
     assoc_traits_agg= pd.merge(assoc, traits_agg, on ="associationId",how="left")
     
     assoc_traits_agg= pd.merge(assoc_traits_agg, studies, on ="associationId", how="left")
-
+    
     assoc_traits_agg= pd.merge(assoc_traits_agg, variants, on ="associationId",how="left")
     
     assoc_traits_agg = assoc_traits_agg.rename(columns={"trait":"GWASCATALOG_TRAIT",
@@ -101,7 +106,12 @@ def get_associations_from_gwascatalog(sumstats, rsid="rsID", log=Log(), verbose=
     return association, traits, studies, variants
 
 def _fix_beta(association):
-
+    if "betaNum" not in association:
+        association["betaNum"] = pd.NA
+    if "orPerCopyNum" not in association:
+        association["orPerCopyNum"] = pd.NA
+    if "range" not in association:
+        association["range"] = pd.NA
     is_or_available = (association["betaNum"].isna()) & (~association["orPerCopyNum"].isna())
     is_range_available = (association["betaNum"].isna()) & (association["orPerCopyNum"].isna()) & (~association["range"].isna())
 
@@ -114,4 +124,4 @@ def parse_range(x):
     high = np.log(range_list[1])
     low = np.log(range_list[0])
     beta = (high + low)/2
-    return beta
+    return beta

{gwaslab-3.6.7 → gwaslab-3.6.8}/src/gwaslab/viz/viz_plot_mqqplot.py

@@ -100,6 +100,8 @@ def mqqplot(insumstats,
           qq_scatter_args=None,
           qqscatterargs=None,
           qq_line_color = "grey",
+          qq_xlabels = None,
+          qq_xlim = None,
           # region
           region = None,
           region_title=None,
@@ -204,6 +206,8 @@ def mqqplot(insumstats,
           highlight_color="#CB132D",
           highlight_windowkb = 500,
           highlight_anno_args = None,
+          highlight_lim = None,
+          highlight_lim_mode = "absolute",
           pinpoint= None,
           pinpoint_color ="red",
           stratified=False,
@@ -531,6 +535,8 @@ def mqqplot(insumstats,
                                                     highlight=highlight, 
                                                     highlight_chrpos=highlight_chrpos, 
                                                     highlight_windowkb=highlight_windowkb, 
+                                                    highlight_lim = highlight_lim, 
+                                                    highlight_lim_mode = highlight_lim_mode,
                                                     snpid=snpid, 
                                                     chrom=chrom, 
                                                     pos=pos)
@@ -1096,6 +1102,8 @@ def mqqplot(insumstats,
                     linewidth=sc_linewidth,
                     ytick3 = ytick3,
                     ylabels = ylabels,
+                    xlabels = qq_xlabels,
+                    xlim = qq_xlim,
                     ylabels_converted = ylabels_converted,
                     verbose=verbose,
                     qq_scatter_args=qq_scatter_args,
@@ -1335,19 +1343,38 @@ def _process_p_value(sumstats, mode,p, mlog10p, scaled, log, verbose ):
 
     return sumstats
 
-def _process_highlight(sumstats, highlight, highlight_chrpos, highlight_windowkb, snpid, chrom, pos):
+def _process_highlight(sumstats, highlight, highlight_chrpos, highlight_windowkb,  highlight_lim,  highlight_lim_mode, snpid, chrom, pos):
         if pd.api.types.is_list_like(highlight[0]):
             if highlight_chrpos == False:
                 # highlight for multiple sets
                 for i, highlight_set in enumerate(highlight):
                     to_highlight = sumstats.loc[sumstats[snpid].isin(highlight_set),:]
                     #assign colors: 0 is hightlight color
-                    for index,row in to_highlight.iterrows():
+                    #assign colors: i is highlight color
+                    for j, (index, row) in enumerate(to_highlight.iterrows()):
                         target_chr = int(row[chrom])
                         target_pos = int(row[pos])
                         right_chr=sumstats[chrom]==target_chr
-                        up_pos=sumstats[pos]>target_pos-highlight_windowkb*1000
-                        low_pos=sumstats[pos]<target_pos+highlight_windowkb*1000
+                        # Check if highlight_lim is provided for this group and SNP
+                        if (highlight_lim is not None and 
+                            i < len(highlight_lim) and 
+                            j < len(highlight_lim[i]) and 
+                            highlight_lim[i][j] is not None):
+                            # Use custom limits for this SNP
+                            if highlight_lim_mode == "absolute":
+                                # Absolute positions: (start_pos, end_pos)
+                                start_pos, end_pos = highlight_lim[i][j]
+                                up_pos = sumstats[pos] >= start_pos
+                                low_pos = sumstats[pos] <= end_pos
+                            else:
+                                # Offset mode: (lower_kb, upper_kb) relative to SNP position
+                                lower_kb, upper_kb = highlight_lim[i][j]
+                                up_pos = sumstats[pos] > target_pos + lower_kb * 1000
+                                low_pos = sumstats[pos] < target_pos + upper_kb * 1000
+                        else:
+                            # Use default highlight_windowkb
+                            up_pos = sumstats[pos] > target_pos - highlight_windowkb * 1000
+                            low_pos = sumstats[pos] < target_pos + highlight_windowkb * 1000
                         sumstats.loc[right_chr&up_pos&low_pos,"HUE"]=i
             else:
                 for i, highlight_chrpos_tuple in enumerate(highlight):
@@ -1371,13 +1398,30 @@ def _process_highlight(sumstats, highlight, highlight_chrpos, highlight_windowkb
         else:
             # highlight for one set
             to_highlight = sumstats.loc[sumstats[snpid].isin(highlight),:]
-            #assign colors: 0 is hightlight color
-            for index,row in to_highlight.iterrows():
+            #assign colors: 0 is highlight color
+            for j, (index, row) in enumerate(to_highlight.iterrows()):
                 target_chr = int(row[chrom])
                 target_pos = int(row[pos])
                 right_chr=sumstats[chrom]==target_chr
-                up_pos=sumstats[pos]>target_pos-highlight_windowkb*1000
-                low_pos=sumstats[pos]<target_pos+highlight_windowkb*1000
+                # Check if highlight_lim is provided for this SNP
+                if (highlight_lim is not None and 
+                    j < len(highlight_lim) and 
+                    highlight_lim[j] is not None):
+                    # Use custom limits for this SNP
+                    if highlight_lim_mode == "absolute":
+                        # Absolute positions: (start_pos, end_pos)
+                        start_pos, end_pos = highlight_lim[j]
+                        up_pos = sumstats[pos] >= start_pos
+                        low_pos = sumstats[pos] <= end_pos
+                    else:
+                        # Offset mode: (lower_kb, upper_kb) relative to SNP position
+                        lower_kb, upper_kb = highlight_lim[j]
+                        up_pos = sumstats[pos] > target_pos + lower_kb * 1000
+                        low_pos = sumstats[pos] < target_pos + upper_kb * 1000
+                else:
+                    # Use default highlight_windowkb
+                    up_pos = sumstats[pos] > target_pos - highlight_windowkb * 1000
+                    low_pos = sumstats[pos] < target_pos + highlight_windowkb * 1000
                 sumstats.loc[right_chr&up_pos&low_pos,"HUE"]=0
         return sumstats
 

{gwaslab-3.6.7 → gwaslab-3.6.8}/src/gwaslab/viz/viz_plot_qqplot.py

@@ -39,6 +39,8 @@ def _plot_qq(
     linewidth,
     ytick3,
     ylabels,
+    xlabels,
+    xlim,
     ylabels_converted,
     qq_scatter_args,
     expected_min_mlog10p,
@@ -155,32 +157,12 @@ def _plot_qq(
                         log=log,
                         verbose=verbose
                         )
-
-    #if cut == 0: 
-    #    ax2.set_ylim(skip, ceil(maxy*1.2) )
-    #    
-    #if cut:
-    #    qcutline = ax2.axhline(y=cut, linewidth = linewidth, linestyle="--",color=cut_line_color,zorder=1)
-    #    step=2
-    #    if ((maxticker-cut)/cutfactor + cut) > cut:
-    #        if ystep == 0:
-    #            if (cut - skip ) // step > 10:
-    #                step = (cut - skip ) // 10
-    #        else:
-    #            step = ystep
-#
-    #        ax2.set_yticks([x for x in range(skip,cut-step,step)]+[cut]+[(maxticker-cut)/cutfactor + cut])
-    #        ax2.set_yticklabels([x for x in range(skip,cut-step,step)]+[cut]+[maxticker],fontsize=fontsize,family=font_family)
-    #    else:
-    #        if ystep == 0:
-    #            if (cut - skip ) // step > 10:
-    #                step = (cut - skip ) // 10
-    #        else:
-    #            step = ystep
-#
-    #        ax2.set_yticks([x for x in range(skip,cut-step,step)]+[cut])
-    #        ax2.set_yticklabels([x for x in range(skip,cut-step,step)]+[cut],fontsize=fontsize,family=font_family)
-    #    ax2.set_ylim(bottom = skip)
+    if xlim is not None:
+        ax2.set_xlim(xlim)
+        
+    if xlabels is not None:
+        ax2.set_xticks(xlabels)
+        ax2.set_xticklabels(xlabels,fontsize=fontsize,family=font_family)
 
     ax2.tick_params(axis='both', which='both', labelsize=fontsize,labelfontfamily=font_family)
     #

{gwaslab-3.6.7 → gwaslab-3.6.8}/src/gwaslab/viz/viz_plot_trumpetplot.py

@@ -57,6 +57,8 @@ def plottrumpet(mysumstats,
                 highlight_color="#CB132D",
                 highlight_windowkb = 500,
                 highlight_anno_args = None,
+                highlight_lim = None,
+                highlight_lim_mode = "absolute",
                 pinpoint= None,
                 pinpoint_color ="red",
                 scatter_args=None,
@@ -235,6 +237,8 @@ def plottrumpet(mysumstats,
                                                     highlight=highlight, 
                                                     highlight_chrpos=highlight_chrpos, 
                                                     highlight_windowkb=highlight_windowkb, 
+                                                    highlight_lim=highlight_lim,
+                                                    highlight_lim_mode=highlight_lim_mode,
                                                     snpid=snpid, 
                                                     chrom=chrom, 
                                                     pos=pos)

{gwaslab-3.6.7 → gwaslab-3.6.8/src/gwaslab.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gwaslab
-Version: 3.6.7
+Version: 3.6.8
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <gwaslab@gmail.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/