gsMap 1.73.0__py3-none-any.whl → 1.73.2__py3-none-any.whl

gsMap/latent_to_gene.py

@@ -104,6 +104,7 @@ def compute_regional_mkscore(
     ranks,
     frac_whole,
     adata_X_bool,
+    pearson_residuals,
 ):
     """
     Compute gmean ranks of a region.
@@ -129,7 +130,8 @@ def compute_regional_mkscore(
         # Simultaneously consider the ratio of expression fractions and ranks
         gene_ranks_region = gene_ranks_region * frac_region
 
-    mkscore = np.exp(gene_ranks_region**1.5) - 1
+    mkscore = np.exp(gene_ranks_region) - 1 if not pearson_residuals else gene_ranks_region
+
     return mkscore.astype(np.float16, copy=False)
 
 
@@ -246,11 +248,18 @@ def run_latent_to_gene(config: LatentToGeneConfig):
     # Create mappings
     n_cells = adata.n_obs
     n_genes = adata.n_vars
-
+    pearson_residuals = True if "pearson_residuals" in adata.layers else False
     ranks = np.zeros((n_cells, adata.n_vars), dtype=np.float16)
-    for i in tqdm(range(n_cells), desc="Computing ranks per cell"):
-        data = adata_X[i, :].toarray().flatten()
-        ranks[i, :] = rankdata(data, method="average")
+
+    if pearson_residuals:
+        logger.info("Using pearson residuals for ranking.")
+        data = adata.layers["pearson_residuals"]
+        for i in tqdm(range(n_cells), desc="Computing ranks per cell"):
+            ranks[i, :] = rankdata(data[i, :], method="average")
+    else:
+        for i in tqdm(range(n_cells), desc="Computing ranks per cell"):
+            data = adata_X[i, :].toarray().flatten()
+            ranks[i, :] = rankdata(data, method="average")
 
     if gM is None:
         gM = gmean(ranks, axis=0)
@@ -280,6 +289,7 @@ def run_latent_to_gene(config: LatentToGeneConfig):
             ranks,
             frac_whole,
             adata_X_bool,
+            pearson_residuals,
         )
 
     logger.info("------Computing marker scores...")

gsMap/run_all_mode.py

@@ -68,6 +68,7 @@ def run_pipeline(config: RunAllModeConfig):
             annotation=config.annotation,
             data_layer=config.data_layer,
             n_comps=config.n_comps,
+            pearson_residuals=config.pearson_residuals,
         )
 
         # Step 1: Find latent representations

gsMap/utils/generate_r2_matrix.py

@@ -465,7 +465,7 @@ class PlinkBEDFile(GenotypeArrayInMemory):
         return Y
 
 
-def load_bfile(bfile_chr_prefix):
+def load_bfile(bfile_chr_prefix, keep_snps=None, keep_indivs=None, mafMin=None):
     PlinkBIMFile = ID_List_Factory(
         ["CHR", "SNP", "CM", "BP", "A1", "A2"], 1, ".bim", usecols=[0, 1, 2, 3, 4, 5]
     )
@@ -483,7 +483,7 @@ def load_bfile(bfile_chr_prefix):
     # Load genotype array
     array_file = bfile_chr_prefix + ".bed"
     geno_array = PlinkBEDFile(
-        array_file, n, array_snps, keep_snps=None, keep_indivs=None, mafMin=None
+        array_file, n, array_snps, keep_snps=keep_snps, keep_indivs=keep_indivs, mafMin=mafMin
     )
 
     return array_snps, array_indivs, geno_array

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-1.73.0.dist-info → gsmap-1.73.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gsMap
-Version: 1.73.0
+Version: 1.73.2
 Summary: Genetics-informed pathogenic spatial mapping
 Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
 Requires-Python: >=3.10
@@ -97,6 +97,14 @@ conda activate gsMap
 pip install gsMap
 ```
 
+Install using conda:
+
+```bash
+conda create -n gsMap python>=3.10
+conda activate gsMap
+conda install bioconda::gsmap
+```
+
 Install from source:
 
 ```bash

{gsmap-1.73.0.dist-info → gsmap-1.73.2.dist-info}/RECORD

@@ -1,31 +1,31 @@
-gsMap/__init__.py,sha256=knR7dQ3TSoHO6p9wIF50N1FMi0Y-hqQLVLblUN0V3xE,77
+gsMap/__init__.py,sha256=xjO1mrd3lI32sCY5mQ8rHHD4yyTbUr94E758a72nT4c,77
 gsMap/__main__.py,sha256=Vdhw8YA1K3wPMlbJQYL5WqvRzAKVeZ16mZQFO9VRmCo,62
 gsMap/cauchy_combination_test.py,sha256=SiUyqJKr4ATFtRgsCEJ43joGcSagCOnnurkB1FlQiB4,5105
-gsMap/config.py,sha256=QaDM3Um6p3rcQO-HTMts8-mQ85RmPCJ2RK2kjC32Bgg,51246
-gsMap/create_slice_mean.py,sha256=bkobWq1kPSvVUZb5RUxYR6ckGGmsftVYCcHfU4xpT6w,5676
-gsMap/diagnosis.py,sha256=RcoIQoK2rtHpEqmSVwOG_amfKWuu1r5T8e2POPfIpOM,13362
-gsMap/find_latent_representation.py,sha256=ktC1nQ_dDqL0uwV6f-E2EwLKX7fwX8TRj9jWGpDrKJw,4745
+gsMap/config.py,sha256=LmBVMb0eda6bfrKkQuh7eZnZdvgecjCnozRd_clqvlY,51584
+gsMap/create_slice_mean.py,sha256=Nnmb7ACtS-9TurW5xQ4TqCinejPsYcvuT5Oxqa5Uges,5723
+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=lqw5KGegptZlNjXBoVDLT0UB9Rft-KaIPuEd9GkvEm4,27937
-gsMap/latent_to_gene.py,sha256=CqvlH2qriuzWTt-hjfzgMD1VEd4PNSSG4A4ODvSbUfA,12398
+gsMap/generate_ldscore.py,sha256=xxzbaANl638bRvRAowrTPmFA4dEC0zDBv6i8KQTJvJ8,45094
+gsMap/latent_to_gene.py,sha256=sDPvOU4iF-HkfQY0nnkIVXpjyTQ9-PjQflwEFWrPg-A,12869
 gsMap/main.py,sha256=SzfAXhrlr4LXnSD4gkvAtUUPYXyra6a_MzVCxDBZjr0,1170
 gsMap/report.py,sha256=_1FYkzGhVGMnvHgEQ8z51iMrVEVlh48a31jLqbV2o9w,6953
-gsMap/run_all_mode.py,sha256=0fJWV6TL7o2OAUXyhC0okHav6gydVUXOinP-HJ-DaAQ,9325
+gsMap/run_all_mode.py,sha256=LhMTT85B6yoDG9MvKmclQWYdQyNIP0FFdHpYVGTCJTs,9381
 gsMap/setup.py,sha256=lsIQCChHwR0ojWZs7xay8rukRaLlueuLkc83bp-B2ZE,103
 gsMap/spatial_ldsc_multiple_sumstats.py,sha256=-mawOBjn8-Y5Irl8mv8ye83hfiEJ1mkLrRIQiI-XaMM,17973
 gsMap/visualize.py,sha256=N55s-xmzSd_DtIesrGewfDeoytYUcMd2acDsjEpChCA,7242
 gsMap/GNN/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 gsMap/GNN/adjacency_matrix.py,sha256=MfkhgpAHJcC-3l_iZDQQYD30w4bpe29-8s6kkGxiwQw,3231
 gsMap/GNN/model.py,sha256=75In9sxBkaqqpCQSrQEUO-zsQQVQnkXVbKsAgyAZjiQ,2918
-gsMap/GNN/train.py,sha256=S6s-AufN9GJNcgC5Mqe6MjcJAsaNnbDlHUoYHcvxFmA,3069
+gsMap/GNN/train.py,sha256=4qipaxaz3rQOtlRpTYCfl1Oz4kz_A6vNB1aw8_gGK_k,3076
 gsMap/templates/report_template.html,sha256=QODZEbVxpW1xsLz7lDrD_DyUfzYoi9E17o2tLJlf8OQ,8016
 gsMap/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-gsMap/utils/generate_r2_matrix.py,sha256=Hwp70pQfMoWjvDa8LyrtZsvws3YHKj5oGYB_LB2CSqs,17293
+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-1.73.0.dist-info/entry_points.txt,sha256=s_P2Za22O077tc1FPLKMinbdRVXaN_HTcDBgWMYpqA4,41
-gsmap-1.73.0.dist-info/licenses/LICENSE,sha256=fb5WP6qQytSKO5rM0ZSqQXg_92Fdt0aAeFNwSi3Lpmc,1069
-gsmap-1.73.0.dist-info/WHEEL,sha256=_2ozNFCLWc93bK4WKHCO-eDUENDlo-dgc9cU3qokYO4,82
-gsmap-1.73.0.dist-info/METADATA,sha256=Z6rfdCCrlRN1_DRzoIhCwshs9b94LDJVwHNYRLF5bko,8075
-gsmap-1.73.0.dist-info/RECORD,,
+gsmap-1.73.2.dist-info/entry_points.txt,sha256=s_P2Za22O077tc1FPLKMinbdRVXaN_HTcDBgWMYpqA4,41
+gsmap-1.73.2.dist-info/licenses/LICENSE,sha256=fb5WP6qQytSKO5rM0ZSqQXg_92Fdt0aAeFNwSi3Lpmc,1069
+gsmap-1.73.2.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
+gsmap-1.73.2.dist-info/METADATA,sha256=giDX_EkW5AutmnHHukvC2Kw29fY-q939rA9cWJP5pMY,8196
+gsmap-1.73.2.dist-info/RECORD,,

{gsmap-1.73.0.dist-info → gsmap-1.73.2.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: flit 3.11.0
+Generator: flit 3.12.0
 Root-Is-Purelib: true
 Tag: py3-none-any