gsMap 1.73.1__py3-none-any.whl → 1.73.3__py3-none-any.whl

gsMap/__init__.py

@@ -2,4 +2,4 @@
 Genetics-informed pathogenic spatial mapping
 """
 
-__version__ = "1.73.1"
+__version__ = "1.73.3"

gsMap/diagnosis.py

@@ -51,8 +51,8 @@ def compute_gene_diagnostic_info(config: DiagnosisConfig):
     mk_score = mk_score.loc[trait_ldsc_result.index]
 
     # Filter out genes with no variation
-    non_zero_std_cols = mk_score.columns[mk_score.std() > 0]
-    mk_score = mk_score.loc[:, non_zero_std_cols]
+    has_variation = (~mk_score.eq(mk_score.iloc[0], axis=1)).any()
+    mk_score = mk_score.loc[:, has_variation]
 
     logger.info("Calculating correlation between gene marker scores and trait logp-values...")
     corr = mk_score.corrwith(trait_ldsc_result["logp"])
@@ -69,10 +69,6 @@ def compute_gene_diagnostic_info(config: DiagnosisConfig):
         }
     )
 
-    # Filter based on median GSS score
-    high_GSS_Gene_annotation_pair = high_GSS_Gene_annotation_pair[
-        high_GSS_Gene_annotation_pair["Median_GSS"] >= 1.0
-    ]
     high_GSS_Gene_annotation_pair = high_GSS_Gene_annotation_pair.merge(
         corr, left_on="Gene", right_index=True
     )
@@ -161,6 +157,20 @@ def generate_manhattan_plot(config: DiagnosisConfig):
         + gwas_data_to_plot["Annotation"].astype(str)
     )
 
+    # Verify data integrity
+    if gwas_data_with_gene_annotation_sort.empty:
+        logger.error("Filtered GWAS data is empty, cannot create Manhattan plot")
+        return
+
+    if len(gwas_data_to_plot) == 0:
+        logger.error("No SNPs passed filtering criteria for Manhattan plot")
+        return
+
+    # Log some diagnostic information
+    logger.info(f"Creating Manhattan plot with {len(gwas_data_to_plot)} SNPs")
+    logger.info(f"Columns available: {list(gwas_data_to_plot.columns)}")
+    logger.info(f"Chromosome column values: {gwas_data_to_plot['CHR'].unique()}")
+
     fig = ManhattanPlot(
         dataframe=gwas_data_to_plot,
         title="gsMap Diagnosis Manhattan Plot",

gsMap/generate_ldscore.py

@@ -57,7 +57,8 @@ def load_gtf(
     gtf = gtf[gtf["Feature"] == "gene"]
 
     # Find common genes between GTF and marker scores
-    common_gene = np.intersect1d(mk_score.index, gtf.gene_name)
+    # common_gene = np.intersect1d(mk_score.index, gtf.gene_name)
+    common_gene = list(set(mk_score.index) & set(gtf.gene_name))
     logger.info(f"Found {len(common_gene)} common genes between GTF and marker scores")
 
     # Filter GTF and marker scores to common genes
@@ -69,6 +70,9 @@ def load_gtf(
 
     # Process the GTF (open window around gene coordinates)
     gtf_bed = gtf[["Chromosome", "Start", "End", "gene_name", "Strand"]].copy()
+    gtf_bed["Chromosome"] = gtf_bed["Chromosome"].apply(
+        lambda x: f"chr{x}" if not str(x).startswith("chr") else x
+    )
     gtf_bed.loc[:, "TSS"] = gtf_bed["Start"]
     gtf_bed.loc[:, "TED"] = gtf_bed["End"]
 
@@ -128,7 +132,7 @@ def load_bim(bfile_root: str, chrom: int) -> tuple[pd.DataFrame, pr.PyRanges]:
         - bim_pr is a PyRanges object with BIM data
     """
     bim_file = f"{bfile_root}.{chrom}.bim"
-    logger.debug(f"Loading BIM file: {bim_file}")
+    logger.info(f"Loading BIM file: {bim_file}")
 
     bim = pd.read_csv(bim_file, sep="\t", header=None)
     bim.columns = ["CHR", "SNP", "CM", "BP", "A1", "A2"]
@@ -311,6 +315,8 @@ def get_ldscore(
         bfile_chr_prefix=f"{bfile_root}.{chrom}", keep_snps=keep_snps_index
     )
 
+    annot_matrix = annot_matrix[geno_array.kept_snps, :]
+
     # Configure LD window based on specified unit
     if ld_unit == "SNP":
         max_dist = ld_wind

gsMap/utils/manhattan_plot.py

@@ -308,13 +308,21 @@ class _ManhattanPlot:
         self.index = "INDEX"
         self.pos = "POSITION"
 
-        # Fixes the bug where one chromosome is missing by adding a sequential
-        # index column.
-        idx = 0
-        for i in self.data[chrm].unique():
-            idx = idx + 1
-            self.data.loc[self.data[chrm] == i, self.index] = int(idx)
-        # Set the type to be the same as provided for chrm column
+        self.data[self.index] = 0  # Initialize with zeros as default value
+
+        if not self.data.empty and len(self.data[chrm].unique()) > 0:
+            idx = 0
+            for i in self.data[chrm].unique():
+                idx = idx + 1
+                self.data.loc[self.data[chrm] == i, self.index] = int(idx)
+        else:
+            import logging
+
+            logger = logging.getLogger("gsMap.utils.manhattan_plot")
+            logger.warning(
+                "No chromosome data found or empty dataframe when creating Manhattan plot"
+            )
+
         self.data[self.index] = self.data[self.index].astype(self.data[chrm].dtype)
 
         # This section sets up positions and ticks. Ticks should be placed in

{gsmap-1.73.1.dist-info → gsmap-1.73.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gsMap
-Version: 1.73.1
+Version: 1.73.3
 Summary: Genetics-informed pathogenic spatial mapping
 Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
 Requires-Python: >=3.10

{gsmap-1.73.1.dist-info → gsmap-1.73.3.dist-info}/RECORD

@@ -1,12 +1,12 @@
-gsMap/__init__.py,sha256=JH9MEzz0OCzOzCkWe26fsjrbx9Bstvsy68Pjx82trOA,77
+gsMap/__init__.py,sha256=0XtiYZAbXor3EAyHAebfh1qGJuKOgeB3h1MPE6ukNNY,77
 gsMap/__main__.py,sha256=Vdhw8YA1K3wPMlbJQYL5WqvRzAKVeZ16mZQFO9VRmCo,62
 gsMap/cauchy_combination_test.py,sha256=SiUyqJKr4ATFtRgsCEJ43joGcSagCOnnurkB1FlQiB4,5105
 gsMap/config.py,sha256=LmBVMb0eda6bfrKkQuh7eZnZdvgecjCnozRd_clqvlY,51584
 gsMap/create_slice_mean.py,sha256=Nnmb7ACtS-9TurW5xQ4TqCinejPsYcvuT5Oxqa5Uges,5723
-gsMap/diagnosis.py,sha256=rQIjtM5inqrLlNULC88JVEO1XA64XOQWEgaKLx2oA_g,12553
+gsMap/diagnosis.py,sha256=YyT_TkPbb3c22DLpRYu9yynbNGrhytcCgxCoPwz9Bpc,12962
 gsMap/find_latent_representation.py,sha256=aZ5fFY2RhAsNaDeoehd5lN28556d6GGHK9xEUTvo6G4,5365
 gsMap/format_sumstats.py,sha256=1c9OgbqDQWOgXeSrbAhbJfChv_2IwXIgLE6Pbw2sx0s,13778
-gsMap/generate_ldscore.py,sha256=xxzbaANl638bRvRAowrTPmFA4dEC0zDBv6i8KQTJvJ8,45094
+gsMap/generate_ldscore.py,sha256=G108fVVdGj0Pn50TqFmAXLjQ7OTY9BWnilHoDeIn2D8,45348
 gsMap/latent_to_gene.py,sha256=sDPvOU4iF-HkfQY0nnkIVXpjyTQ9-PjQflwEFWrPg-A,12869
 gsMap/main.py,sha256=SzfAXhrlr4LXnSD4gkvAtUUPYXyra6a_MzVCxDBZjr0,1170
 gsMap/report.py,sha256=_1FYkzGhVGMnvHgEQ8z51iMrVEVlh48a31jLqbV2o9w,6953
@@ -22,10 +22,10 @@ gsMap/templates/report_template.html,sha256=QODZEbVxpW1xsLz7lDrD_DyUfzYoi9E17o2t
 gsMap/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 gsMap/utils/generate_r2_matrix.py,sha256=0zyoJDWUVavlQtR6_XXb7Ah9UhPyT3n0t6XCqlI1HXQ,17354
 gsMap/utils/jackknife.py,sha256=w_qMj9GlqViouHuOw1U80N6doWuCTXuPoAVU4P-5mm8,17673
-gsMap/utils/manhattan_plot.py,sha256=N7jd0Cn-7JMsTBgv41k1w0174rqnPT-v7xLIV2cfY5U,25241
+gsMap/utils/manhattan_plot.py,sha256=4ok5CHAaT_MadyMPnFZMR_llmE8Vf4-KiEfametgHq0,25480
 gsMap/utils/regression_read.py,sha256=rKA0nkUpTJf6WuGddhKrsBCExchDNEyojOWu_qddZNw,5474
-gsmap-1.73.1.dist-info/entry_points.txt,sha256=s_P2Za22O077tc1FPLKMinbdRVXaN_HTcDBgWMYpqA4,41
-gsmap-1.73.1.dist-info/licenses/LICENSE,sha256=fb5WP6qQytSKO5rM0ZSqQXg_92Fdt0aAeFNwSi3Lpmc,1069
-gsmap-1.73.1.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
-gsmap-1.73.1.dist-info/METADATA,sha256=34Y4_egICgzOwwCJ2L3u8j9OvKsUBPPlLJfi-t-gm98,8196
-gsmap-1.73.1.dist-info/RECORD,,
+gsmap-1.73.3.dist-info/entry_points.txt,sha256=s_P2Za22O077tc1FPLKMinbdRVXaN_HTcDBgWMYpqA4,41
+gsmap-1.73.3.dist-info/licenses/LICENSE,sha256=fb5WP6qQytSKO5rM0ZSqQXg_92Fdt0aAeFNwSi3Lpmc,1069
+gsmap-1.73.3.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
+gsmap-1.73.3.dist-info/METADATA,sha256=-MD9qe4n_qOVF1dAQ6gcSLtCl1DZDMeoRw2EVijGDms,8196
+gsmap-1.73.3.dist-info/RECORD,,