gwaslab 3.6.8__py3-none-any.whl → 3.6.9__py3-none-any.whl

gwaslab/g_Sumstats.py

@@ -102,7 +102,7 @@ from gwaslab.viz.viz_plot_mqqplot import mqqplot
 from gwaslab.viz.viz_plot_trumpetplot import plottrumpet
 from gwaslab.viz.viz_plot_compare_af import plotdaf
 from gwaslab.viz.viz_plot_credible_sets import _plot_cs
-
+from gwaslab.viz.viz_plot_associations import _plot_associations
 from gwaslab.io.io_read_pipcs import _read_pipcs
 from gwaslab.io.io_load_ld import tofinemapping_using_ld
 from gwaslab.io.io_preformat_input import preformat
@@ -811,6 +811,9 @@ class Sumstats():
         self.associations = associations_full
         
         return associations_summary
+    def plot_associations(self,**kwargs):
+
+        _plot_associations(self.associations, **kwargs)
 
     def check_cis(self, gls=False, **kwargs):
         if "SNPID" in self.data.columns:

gwaslab/g_version.py

@@ -17,8 +17,8 @@ def _get_version():
 def gwaslab_info():
     # version meta information
     dic={
-   "version":"3.6.0",
-   "release_date":"20250902"
+   "version":"3.6.9",
+   "release_date":"20251012"
     }
     return dic   
 

gwaslab/util/util_ex_phewwas.py

@@ -25,15 +25,19 @@ def _extract_associations(sumstats, rsid="rsID", log = Log(), verbose=True):
     assoc_traits_agg = assoc_traits_agg.rename(columns={"trait":"GWASCATALOG_TRAIT",
                                                         "riskFrequency":"RAF",
                                                         "betaNum":"Beta",
-                                                        "pvalue":"P-value"
+                                                        "pvalue":"P-value",
+                                                        "betaUnit":"Unit"
                                                         })
     
     summary_columns=['GWASCATALOG_TRAIT','associationId', 'rsID', "geneName", 
-                     'RA', 'RAF','Beta', 'P-value','cohort','initialSampleSize','publicationInfo.pubmedId',
+                     'RA', 'RAF','Beta',"Unit", 'P-value','cohort','initialSampleSize','publicationInfo.pubmedId',
                      "functionalClass","gene.geneName"]
     
     assoc_traits_agg_summary = assoc_traits_agg[summary_columns]
 
+    assoc_traits_agg_summary = _align_beta(sumstats, assoc_traits_agg_summary, log, verbose)
+    assoc_traits_agg = _align_beta(sumstats, assoc_traits_agg, log, verbose)
+
     return assoc_traits_agg, assoc_traits_agg_summary
 
 def get_associations_from_gwascatalog(sumstats, rsid="rsID", log=Log(), verbose=True):
@@ -125,3 +129,41 @@ def parse_range(x):
     low = np.log(range_list[0])
     beta = (high + low)/2
     return beta
+
+def _align_beta(sumstats, assoc_traits_agg_summary, log, verbose):
+    # merge with sumstats
+    log.write("Merging GWAS Catalog associationms with Sumstats...",)
+    assoc_traits_agg_summary = pd.merge(sumstats[["rsID","CHR","POS","EA","NEA","BETA"]], assoc_traits_agg_summary, on = "rsID", how="inner")
+    # check direction 
+    assoc_traits_agg_summary["GC_Beta_GL_RA"] = np.nan
+    assoc_traits_agg_summary["GC_Beta_GL_EA"] = np.nan
+
+    # get sumstats RA
+    assoc_traits_agg_summary["_GL_RA_BETA"] = assoc_traits_agg_summary["BETA"].abs()
+    assoc_traits_agg_summary["_GL_RA"] = assoc_traits_agg_summary["EA"]
+    assoc_traits_agg_summary["_GL_NRA"] = assoc_traits_agg_summary["NEA"]
+    is_GL_RA_flipped = assoc_traits_agg_summary["BETA"]<0
+    assoc_traits_agg_summary.loc[is_GL_RA_flipped, "_GL_RA"] = assoc_traits_agg_summary.loc[is_GL_RA_flipped, "NEA"]
+    assoc_traits_agg_summary.loc[is_GL_RA_flipped, "_GL_NRA"] = assoc_traits_agg_summary.loc[is_GL_RA_flipped, "EA"]
+    
+    is_matched = assoc_traits_agg_summary["_GL_RA"] == assoc_traits_agg_summary["RA"]
+    log.write(" -GL_RA matched RA for {} variants ".format(sum(is_matched)), verbose=verbose)
+    assoc_traits_agg_summary.loc[is_matched, "GC_Beta_GL_RA"] = assoc_traits_agg_summary.loc[is_matched, "Beta"]
+    
+    is_flipped = assoc_traits_agg_summary["_GL_NRA"] == assoc_traits_agg_summary["RA"]
+    log.write(" -GL_NRA matched RA for {} variants... Aligning with Sumstats Risk allele (BETA>0) in GC_Beta_GL_RA... ".format(sum(is_flipped)), verbose=verbose)
+    assoc_traits_agg_summary.loc[is_flipped, "GC_Beta_GL_RA"] = - assoc_traits_agg_summary.loc[is_flipped, "Beta"]
+
+    is_matched = assoc_traits_agg_summary["EA"] == assoc_traits_agg_summary["RA"]
+    log.write(" -EA matched RA for {} variants ".format(sum(is_matched)), verbose=verbose)
+    assoc_traits_agg_summary.loc[is_matched, "GC_Beta_GL_EA"] = assoc_traits_agg_summary.loc[is_matched, "Beta"]
+    
+    is_flipped = assoc_traits_agg_summary["NEA"] == assoc_traits_agg_summary["RA"]
+    log.write(" -NEA matched RA for {} variants... Aligning with Sumstats Risk allele (BETA>0) in GC_Beta_GL_RA... ".format(sum(is_flipped)), verbose=verbose)
+    assoc_traits_agg_summary.loc[is_flipped, "GC_Beta_GL_EA"] = - assoc_traits_agg_summary.loc[is_flipped, "Beta"]
+
+    not_match = (assoc_traits_agg_summary["_GL_RA"] != assoc_traits_agg_summary["RA"])& (assoc_traits_agg_summary["_GL_NRA"] != assoc_traits_agg_summary["RA"])
+    log.write(" -NEA and EA not matching RA for {} variants... ".format(sum(not_match)), verbose=verbose)
+
+
+    return assoc_traits_agg_summary

gwaslab/viz/viz_aux_save_figure.py

@@ -53,7 +53,8 @@ def get_default_path(keyword,fmt="png"):
                         "afc":"allele_frequency_comparision",
                         "gwheatmap":"genome_wide_heatmap",
                         "scatter":"scatter",
-                        "forest":"forest"
+                        "forest":"forest",
+                        "gwaslab":"gwaslab"
                         }
     prefix = path_dictionary[keyword]
     count = 1

gwaslab/viz/viz_plot_associations.py

@@ -0,0 +1,61 @@
+import seaborn as sns
+import matplotlib.pyplot as plt
+from gwaslab.io.io_process_args import _update_args
+from gwaslab.io.io_process_args import _update_arg
+from gwaslab.g_Log import Log
+
+def _plot_associations(associations, 
+                       values="Beta",
+                        fig_args=None,
+                        log=Log(),
+                        verbose=True,
+                        sort="P-value",
+                        fontsize=12,
+                        font_family="Arial",
+                        cmap=None,
+                        ylabel="Traits",
+                        xlabel="rsID - Gene Name",
+                        **args               
+                       ):
+    
+    log.write("Start to create heatmap for associations...", verbose=verbose)
+    
+    cmap = _update_arg(cmap, "RdBu")
+
+    log.write(f" -Value to plot: {values}", verbose=verbose)
+    log.write(f" -Total number of associations :{len(associations)} ", verbose=verbose)
+    log.write(f" -Sorting associations by :{sort} ", verbose=verbose)
+
+    associations = associations.sort_values(by=[sort]).drop_duplicates(subset=["rsID","GWASCATALOG_TRAIT"])
+
+    log.write(f" -Keeping unique rsID-traits pairs :{len(associations)} ", verbose=verbose)
+
+    associations = associations.dropna(subset=[values])
+    log.write(f" -Keeping associations without NA in {values} :{len(associations)} ", verbose=verbose)
+
+    log.write(f" -Total number of unique variants for plotting :{associations["rsID"].nunique()} ", verbose=verbose)
+    log.write(f" -Total number of unique traits for plotting:{associations["GWASCATALOG_TRAIT"].nunique()} ", verbose=verbose)
+
+    matrix_beta = associations.pivot_table(index=['rsID','gene.geneName'], 
+                                    columns='GWASCATALOG_TRAIT', 
+                                    values=[values])
+
+    matrix_beta = matrix_beta.astype("float64")
+    
+    matrix_beta.columns = matrix_beta.columns.droplevel(0)
+
+    height = max(2, len(matrix_beta)//2)
+    width = max(2, len(matrix_beta.columns)//2)
+
+    fig_args = _update_args(fig_args, dict(figsize=(width,height)))
+    fig,ax = plt.subplots(**fig_args)
+    
+    sns.heatmap(matrix_beta.T, annot=True, fmt=".2f",cmap="RdBu",ax=ax)
+    
+
+    ax.set_xlabel(xlabel,fontsize=fontsize, fontfamily=font_family)
+    ax.set_ylabel(ylabel,fontsize=fontsize, fontfamily=font_family)
+
+
+    log.write("Finished creating heatmap for associations.", verbose=verbose)
+    return fig, ax

gwaslab/viz/viz_plot_template.py

@@ -0,0 +1,98 @@
+import seaborn as sns
+import matplotlib.pyplot as plt
+from gwaslab.io.io_process_args import _update_args
+from gwaslab.io.io_process_args import _update_arg
+from gwaslab.g_Log import Log
+from gwaslab.viz.viz_aux_save_figure import save_figure
+
+def _plot( associations, 
+            values="Beta",
+            sort="P-value",
+            mode="gwaslab",
+            fontsize=12,
+            font_family="Arial",
+            cmap=None,
+            ylabel="Y",
+            xlabel="X",
+            xlim=None,
+            ylim=None,
+            yticks=None,
+            xticks=None,
+            title="Title",
+            title_pad=1.08, 
+            title_fontsize=13,
+            linewidth=None,
+            linestyle=None,
+            linecolor=None,
+            dpi=200,
+            fig_args= None,
+            scatter_args=None,
+            save=None,
+            save_args=None,
+            log=Log(),
+            verbose=True,
+            **args               
+            ):
+    
+    # update args
+    
+    cmap = _update_arg(cmap, "RdBu")
+
+    fig_args = _update_args(fig_args, dict(figsize=(10,10)))
+
+    # create fig and ax    
+    fig,ax = plt.subplots(**fig_args)
+
+    # draw lines
+    horizontal_line = ax.axhline(y=1, linewidth = linewidth,
+                            linestyle="--",
+                            color=linecolor,zorder=1000)
+    vertical_line   = ax.axvline(x=1, linewidth = linewidth,
+                            linestyle="--",
+                            color=linecolor,zorder=1000)
+
+    # ticks
+    if xticks is not None:
+        ax.set_xticks(xticks)
+        ax.set_xticklabels(xticks,
+                            fontsize=fontsize,
+                            family=font_family)    
+    
+    if yticks is not None:
+        ax.set_xticks(yticks)
+        ax.set_xticklabels(yticks,
+                            fontsize=fontsize,
+                            family=font_family)    
+
+    # labels
+    ax.set_xlabel(xlabel,
+                  fontsize=fontsize, 
+                  fontfamily=font_family)
+    ax.set_ylabel(ylabel,
+                  fontsize=fontsize, 
+                  fontfamily=font_family)
+
+    ax.tick_params(axis='x', 
+                    labelsize=fontsize,
+                    labelfontfamily=font_family)
+    ax.tick_params(axis='y', 
+                    labelsize=fontsize,
+                    labelfontfamily=font_family)
+    
+    # title
+    title_pad = title_pad -0.05
+    fig.suptitle(title , 
+                 fontsize = title_fontsize, 
+                 x=0.5,
+                 y=title_pad)
+    
+    # spines
+    ax.spines["top"].set_visible(False)
+    ax.spines["right"].set_visible(False)
+    ax.spines["left"].set_visible(True)
+    ax.spines["bottom"].set_visible(True)
+
+    save_figure(fig = fig, save = save, keyword=mode, save_args=save_args, log = log, verbose=verbose)
+
+    log.write("Finished creating plots.", verbose=verbose)
+    return fig, ax

{gwaslab-3.6.8.dist-info → gwaslab-3.6.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gwaslab
-Version: 3.6.8
+Version: 3.6.9
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <gwaslab@gmail.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/

{gwaslab-3.6.8.dist-info → gwaslab-3.6.9.dist-info}/RECORD

@@ -2,7 +2,7 @@ gwaslab/__init__.py,sha256=tr8AGz-BqvOc5V0aUHNC-xW--LIAiUXrFo8HTR4SI9k,2861
 gwaslab/cache_manager.py,sha256=HOTnSkCOyGEPLRl90WT8D_6pAdI8d8AzenMIDGuCeWc,28113
 gwaslab/g_Log.py,sha256=C3Zv-_6c3C9ms8bgQ-ytplz22sjk7euqXYkWr9zNeAs,1573
 gwaslab/g_Phenotypes.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-gwaslab/g_Sumstats.py,sha256=7gRp2DIBxcBVYC6H5_4_3lde-VkGSKCiFCHOM3vLE1Q,45366
+gwaslab/g_Sumstats.py,sha256=XH0QrEAofxvMwb07ISp1AUkagfgeCH971VmB2pb2fEA,45529
 gwaslab/g_SumstatsMulti.py,sha256=CDnYMK0L8bV-LNOwO4h9yJahOVHR-sPAxZMNaeKFb3U,15098
 gwaslab/g_SumstatsPair.py,sha256=3-4aFh6pMZ4phcqHCCfyFPC3ySuck43wuTsfLG-ZAyY,13470
 gwaslab/g_SumstatsSet.py,sha256=xuGLpsHyhY2SjMVsFHGdL3iCa-Leb_3bu_R8totkzBY,30180
@@ -14,8 +14,7 @@ gwaslab/g_meta.py,sha256=pXtSsQfFPv2UJmOxKMmLtcsp_Ku_H73YP7PnlfMd0sg,6472
 gwaslab/g_meta_update.py,sha256=W1m6mh5jNUeZAW4T6F6kKZ10gE4l8YieoEC2mAfkzGg,2495
 gwaslab/g_vchange_status.py,sha256=lc3G65-QBV5k5yK-ySGIxiUT0hMBmESLhMKYncwjSwU,1986
 gwaslab/g_vchange_status_polars.py,sha256=kxyGQCur0ibVFBCyZghA-XNf_kLDXKK-l7VC-Om2IdA,1839
-gwaslab/g_version.py,sha256=pW2dwSPMZRQYVnUfhCRZJgqUZrsdoO-wzycgeKdD8L8,1964
-gwaslab/hm_harmonize_sumstats.py,sha256=WkUGNxftEGF5NAJktbEqQfniwcoD6zWHd-4bGrBxOtM,84472
+gwaslab/g_version.py,sha256=NJBby5_kMtMdDdDRyQc5s8LAjWzRq3QNF7LWqk1I_5o,1964
 gwaslab/run_script.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 gwaslab/bd/bd_common_data.py,sha256=mlw977K-ihKf7TQEn6FwUCyJ2vcnq6KIhrX6J3bRMVA,14226
 gwaslab/bd/bd_config.py,sha256=t3YeDMGRSP8k3lw4rHHilIM4jAXSzFOF9DtuuIbpDS8,924
@@ -65,7 +64,7 @@ gwaslab/util/util_ex_infer_ancestry.py,sha256=AXLEhuJUBT6XIYjADB-envFRGIZ-misneg
 gwaslab/util/util_ex_ldproxyfinder.py,sha256=8E4g82gCmolAvrg52urNMJX11MZMwOAPGQaZ4cfggiU,16918
 gwaslab/util/util_ex_ldsc.py,sha256=ss1QlwH7duLuVx_Ckb9mDbyz2neK8tv0WefUGCqzZUc,21685
 gwaslab/util/util_ex_match_ldmatrix.py,sha256=uVfHKxWQRtUQ0lUkt1o2LtZPSd3fh1yQ1rElFa4FDao,17525
-gwaslab/util/util_ex_phewwas.py,sha256=Reg3TUMDpLuUCNGHxpVa_fxrlzpeXFOUShTDXUcxiLk,5887
+gwaslab/util/util_ex_phewwas.py,sha256=oLbAgh_ULLWNP0m6bmD9xtx3EdDcH3HSIeTjxHX_0HU,8745
 gwaslab/util/util_ex_plink_filter.py,sha256=pK1Yxtv9-J4rMOdVAG7VU9PktvI6-y4FxBiVEH0QuRs,1673
 gwaslab/util/util_ex_process_h5.py,sha256=LqfQKBjXnbPSRUVJy9hhRhuoS5wG93yoIguiFDZN1A4,2837
 gwaslab/util/util_ex_process_ref.py,sha256=qtDRxJT0O2NgW4fd6VkRMxIHhSdzhSwz6bfa4iLQvcc,17132
@@ -98,7 +97,8 @@ gwaslab/viz/viz_aux_chromatin.py,sha256=aWZaXOSvGyZY7wQcoFDaqHRYCSHZbi_K4Q70HruN
 gwaslab/viz/viz_aux_property.py,sha256=UIaivghnLXYpTwkKnXRK0F28Jbn9L6OaICk3K73WZaU,33
 gwaslab/viz/viz_aux_quickfix.py,sha256=6xgJYHBEz6iTRkuIAS1e28PQJH1eIViBCOMvczxI-BQ,18698
 gwaslab/viz/viz_aux_reposition_text.py,sha256=iRIP-Rkltlei068HekJcVubiqPrunBqvAoSQ1eHk04M,4304
-gwaslab/viz/viz_aux_save_figure.py,sha256=HwIRDMYpeXfkBgb7mqzLN7OVPMz163U-ZVOlQJABzeg,2811
+gwaslab/viz/viz_aux_save_figure.py,sha256=IOhojOCPPUDjZZYw7i4BgzCpAeasNpnzBTyrpiSoH_4,2856
+gwaslab/viz/viz_plot_associations.py,sha256=06sE8987NEj4v-4_OFo6rliN2RVsf_WoTmLmnfVvQVU,2472
 gwaslab/viz/viz_plot_compare_af.py,sha256=pnL6pEQOSXZ1Zm2UTX-TdvTYSFD9zSY2vaJZSo4Ry_w,5348
 gwaslab/viz/viz_plot_compare_effect.py,sha256=KF0Ug4OwVwfl205Z5nRqGwXBLceuwJXYXj6378sT1Sg,69629
 gwaslab/viz/viz_plot_credible_sets.py,sha256=CjTtO5Dk2R-_GpZ0KN2NW0bN-EDga1OCjt9U8zDiTcw,5864
@@ -114,10 +114,11 @@ gwaslab/viz/viz_plot_regionalplot.py,sha256=UZSeXHfQlGWAYW_tMt00lZt8_vhiB6QcVLvM
 gwaslab/viz/viz_plot_rg_heatmap.py,sha256=AvVAlOOAwhqGWCses7MfdIXLVQSIA2SFE6bd7K1NaLw,13865
 gwaslab/viz/viz_plot_scatter_with_reg.py,sha256=0cpE6ui7yuJ1lhoLu_klac2OSzd5QDx6V51fyplB3GI,8366
 gwaslab/viz/viz_plot_stackedregional.py,sha256=bgVQir_Wj3TxB3o7NJFf7b8HETlWjppgfwLsbUyr3oo,20668
+gwaslab/viz/viz_plot_template.py,sha256=3tOT4pWcxN8je6XEcqPTQ7PJXEG25cwXUnDnoIhqjMA,2917
 gwaslab/viz/viz_plot_trumpetplot.py,sha256=_FKVkxckEFE11jZDwcHhF_bLuYbzxTWDaRTs6ylNEGg,42982
-gwaslab-3.6.8.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-gwaslab-3.6.8.dist-info/licenses/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
-gwaslab-3.6.8.dist-info/METADATA,sha256=wH3szvvkbal87X3T_iWS3KFB-vKDcy0OtCqqh7M2Gh4,7073
-gwaslab-3.6.8.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-gwaslab-3.6.8.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
-gwaslab-3.6.8.dist-info/RECORD,,
+gwaslab-3.6.9.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+gwaslab-3.6.9.dist-info/licenses/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
+gwaslab-3.6.9.dist-info/METADATA,sha256=V7VQ4hyHm_LDCykfxBuRaDvqPdc4yKdrfKple7nROAI,7073
+gwaslab-3.6.9.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+gwaslab-3.6.9.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
+gwaslab-3.6.9.dist-info/RECORD,,