gwaslab 3.5.7__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
@@ -111,6 +114,13 @@ def mqqplot(insumstats,
           region_marker_shapes=None,
           region_legend_marker=True,
           region_ref_alias = None,
+          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,
@@ -232,35 +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)
@@ -277,64 +278,45 @@ 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"]
-    if font_family is None:
-        font_family = fontfamily
-    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":600,"facecolor":"none"}
-    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
+    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)
+    
+    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:
@@ -613,7 +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): 
@@ -631,7 +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"]
@@ -777,9 +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):
@@ -814,6 +815,7 @@ def mqqplot(insumstats,
                                 ax3=ax3,
                                 region=region,
                                 vcf_path=vcf_path,
+                                ld_path=ld_path,
                                 marker_size=marker_size,
                                 build=build,
                                 cbar_scale=cbar_scale,
@@ -1149,6 +1151,7 @@ def _configure_fig_save_kwargs(mode="m",
                     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

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

@@ -35,6 +35,7 @@ def _plot_regional(
     ax3,
     region,
     vcf_path,
+    ld_path,
     marker_size,
     build,
     cut_line_color,
@@ -125,7 +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, 

gwaslab/viz_plot_stackedregional.py

@@ -86,11 +86,14 @@ def plot_stacked_mqq(   objects,
             if "P" in each_object.data.columns or "MLOG10P" in each_object.data.columns:
                 sumstats_list.append(each_object.data)
                 pm.append("m")
-        else:
+        if type(each_object) is pd.DataFrame:
             if "PIP" in each_object.columns:
                 sumstats_list.append(each_object)
                 pm.append("pip")
                 common_ylabel=False
+            else:
+                sumstats_list.append(each_object)
+                pm.append("m")
     
     if common_ylabel==True:
         rr_ylabel=False

{gwaslab-3.5.7.dist-info → gwaslab-3.5.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: gwaslab
-Version: 3.5.7
+Version: 3.5.8
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/
@@ -25,15 +25,15 @@ Requires-Dist: scikit-allel>=1.3.5
 Requires-Dist: pyensembl==2.2.3
 Requires-Dist: gtfparse==1.3.0
 Requires-Dist: h5py>=3.10.0
+Dynamic: license-file
 
 # GWASLab
 
-<img width="600" alt="image" src="https://user-images.githubusercontent.com/40289485/197167760-5f761f5e-5856-4b27-a540-8b9cd90bdadb.png">
+<img width="600" alt="image" src="https://github.com/user-attachments/assets/109262c6-c870-4078-94b5-66cf8c6b13c4" />
 
 ![badge](https://img.shields.io/pypi/v/gwaslab)
 [![Downloads](https://static.pepy.tech/badge/gwaslab)](https://pepy.tech/project/gwaslab)
 ![badge_pip](https://img.shields.io/pypi/dm/gwaslab)
-[![Hits](https://hits.seeyoufarm.com/api/count/incr/badge.svg?url=https%3A%2F%2Fcloufield.github.io%2Fgwaslab%2F&count_bg=%2379C83D&title_bg=%23555555&icon=&icon_color=%23E7E7E7&title=hits&edge_flat=false)](https://hits.seeyoufarm.com)
 ![badge_commit_m](https://img.shields.io/github/commit-activity/m/Cloufield/gwaslab)
 
 * A handy Python toolkit for handling GWAS summary statistics (sumstats).
@@ -42,7 +42,7 @@ Requires-Dist: h5py>=3.10.0
 
 Please check GWASLab documentation at [https://cloufield.github.io/gwaslab/](https://cloufield.github.io/gwaslab/)
 
-Note: GWASLab is being updated very frequently for now. I will release the first stable version soon! Please stay tuned.
+Note: GWASLab is being updated very frequently for now. We will release the first stable version soon! Please stay tuned.
 
 Warning: Known issues of GWASLab are summarized in [https://cloufield.github.io/gwaslab/KnownIssues/](https://cloufield.github.io/gwaslab/KnownIssues/) .
 
@@ -50,8 +50,10 @@ Warning: Known issues of GWASLab are summarized in [https://cloufield.github.io/
 
 ### install via pip
 
+The latest version of GWASLab now supports Python 3.9, 3.10, 3.11, and 3.12.
+
 ```
-pip install gwaslab==3.5.4
+pip install gwaslab==3.5.7
 ```
 
 ```python

gwaslab-3.5.8.dist-info/RECORD

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+gwaslab/bd_common_data.py,sha256=jqkdKib-tc8RKyYMPy8z2KF3YwCWIr-6STMCi4xR7KY,13899
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