gsMap 1.71.1__py3-none-any.whl → 1.71.2__py3-none-any.whl

gsMap/latent_to_gene.py

@@ -1,234 +1,252 @@
-import logging
-from pathlib import Path
-
-import numpy as np
-import pandas as pd
-import scanpy as sc
-from scipy.stats import gmean
-from scipy.stats import rankdata
-from sklearn.metrics.pairwise import cosine_similarity
-from sklearn.neighbors import NearestNeighbors
-from tqdm import tqdm
-
-from gsMap.config import LatentToGeneConfig
-
-logger = logging.getLogger(__name__)
-
-
-def find_neighbors(coor, num_neighbour):
-    """
-    Find Neighbors of each cell (based on spatial coordinates).
-    """
-    nbrs = NearestNeighbors(n_neighbors=num_neighbour).fit(coor)
-    distances, indices = nbrs.kneighbors(coor, return_distance=True)
-    cell_indices = np.arange(coor.shape[0])
-    cell1 = np.repeat(cell_indices, indices.shape[1])
-    cell2 = indices.flatten()
-    distance = distances.flatten()
-    spatial_net = pd.DataFrame({'Cell1': cell1, 'Cell2': cell2, 'Distance': distance})
-    return spatial_net
-
-
-def build_spatial_net(adata, annotation, num_neighbour):
-    """
-    Build spatial neighbourhood matrix for each spot (cell) based on the spatial coordinates.
-    """
-    logger.info(f'------Building spatial graph based on spatial coordinates...')
-
-    coor = adata.obsm['spatial']
-    if annotation is not None:
-        logger.info(f'Cell annotations are provided...')
-        spatial_net_list = []
-        # Cells with annotations
-        for ct in adata.obs[annotation].dropna().unique():
-            idx = np.where(adata.obs[annotation] == ct)[0]
-            coor_temp = coor[idx, :]
-            spatial_net_temp = find_neighbors(coor_temp, min(num_neighbour, coor_temp.shape[0]))
-            # Map back to original indices
-            spatial_net_temp['Cell1'] = idx[spatial_net_temp['Cell1'].values]
-            spatial_net_temp['Cell2'] = idx[spatial_net_temp['Cell2'].values]
-            spatial_net_list.append(spatial_net_temp)
-            logger.info(f'{ct}: {coor_temp.shape[0]} cells')
-
-        # Cells labeled as nan
-        if pd.isnull(adata.obs[annotation]).any():
-            idx_nan = np.where(pd.isnull(adata.obs[annotation]))[0]
-            logger.info(f'Nan: {len(idx_nan)} cells')
-            spatial_net_temp = find_neighbors(coor, num_neighbour)
-            spatial_net_temp = spatial_net_temp[spatial_net_temp['Cell1'].isin(idx_nan)]
-            spatial_net_list.append(spatial_net_temp)
-        spatial_net = pd.concat(spatial_net_list, axis=0)
-    else:
-        logger.info(f'Cell annotations are not provided...')
-        spatial_net = find_neighbors(coor, num_neighbour)
-
-    return spatial_net
-
-
-def find_neighbors_regional(cell_pos, spatial_net_dict, coor_latent, config, cell_annotations):
-    num_neighbour = config.num_neighbour
-    annotations = config.annotation
-
-    cell_use_pos = spatial_net_dict.get(cell_pos, [])
-    if len(cell_use_pos) == 0:
-        return []
-
-    cell_latent = coor_latent[cell_pos, :].reshape(1, -1)
-    neighbors_latent = coor_latent[cell_use_pos, :]
-    similarity = cosine_similarity(cell_latent, neighbors_latent).reshape(-1)
-
-    if annotations is not None:
-        cell_annotation = cell_annotations[cell_pos]
-        neighbor_annotations = cell_annotations[cell_use_pos]
-        mask = neighbor_annotations == cell_annotation
-        if not np.any(mask):
-            return []
-        similarity = similarity[mask]
-        cell_use_pos = cell_use_pos[mask]
-
-    if len(similarity) == 0:
-        return []
-
-    indices = np.argsort(-similarity)  # descending order
-    top_indices = indices[:num_neighbour]
-    cell_select_pos = cell_use_pos[top_indices]
-    return cell_select_pos
-
-
-def compute_regional_mkscore(cell_pos, spatial_net_dict, coor_latent, config, cell_annotations,
-                             ranks, frac_whole, adata_X_bool):
-    """
-    Compute gmean ranks of a region.
-    """
-    cell_select_pos = find_neighbors_regional(
-        cell_pos, spatial_net_dict, coor_latent, config, cell_annotations
-    )
-    if len(cell_select_pos) == 0:
-        return np.zeros(ranks.shape[1], dtype=np.float16)
-
-    # Ratio of expression ranks
-    ranks_tg = ranks[cell_select_pos, :]
-    gene_ranks_region = gmean(ranks_tg, axis=0)
-    gene_ranks_region[gene_ranks_region <= 1] = 0
-
-    if not config.no_expression_fraction:
-        # Ratio of expression fractions
-        frac_focal = adata_X_bool[cell_select_pos, :].sum(axis=0).A1 / len(cell_select_pos)
-        frac_region = frac_focal / frac_whole
-        frac_region[frac_region <= 1] = 0
-        frac_region[frac_region > 1] = 1
-
-        # 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
-    return mkscore.astype(np.float16, copy=False)
-
-
-def run_latent_to_gene(config: LatentToGeneConfig):
-    logger.info('------Loading the spatial data...')
-    adata = sc.read_h5ad(config.hdf5_with_latent_path)
-
-    if config.annotation is not None:
-        logger.info(f'------Cell annotations are provided as {config.annotation}...')
-        adata = adata[~pd.isnull(adata.obs[config.annotation]), :]
-
-    # Homologs transformation
-    if config.homolog_file is not None:
-        logger.info(f'------Transforming the {config.species} to HUMAN_GENE_SYM...')
-        homologs = pd.read_csv(config.homolog_file, sep='\t')
-        if homologs.shape[1] != 2:
-            raise ValueError(
-                "Homologs file must have two columns: one for the species and one for the human gene symbol.")
-
-        homologs.columns = [config.species, 'HUMAN_GENE_SYM']
-        homologs.set_index(config.species, inplace=True)
-        adata = adata[:, adata.var_names.isin(homologs.index)]
-        logger.info(f"{adata.shape[1]} genes retained after homolog transformation.")
-        if adata.shape[1] < 100:
-            raise ValueError("Too few genes retained in ST data (<100).")
-        adata.var_names = homologs.loc[adata.var_names, 'HUMAN_GENE_SYM'].values
-        adata = adata[:, ~adata.var_names.duplicated()]
-
-    # Create mappings
-    n_cells = adata.n_obs
-    n_genes = adata.n_vars
-
-    if config.annotation is not None:
-        cell_annotations = adata.obs[config.annotation].values
-    else:
-        cell_annotations = None
-
-    # Build the spatial graph
-    spatial_net = build_spatial_net(adata, config.annotation, config.num_neighbour_spatial)
-    spatial_net_dict = spatial_net.groupby('Cell1')['Cell2'].apply(np.array).to_dict()
-
-    # Extract the latent representation
-    coor_latent = adata.obsm[config.latent_representation]
-    coor_latent = coor_latent.astype(np.float32)
-
-    # Compute ranks
-    logger.info('------Ranking the spatial data...')
-    adata_X = adata.X.tocsr()
-    ranks = np.zeros((n_cells, n_genes), dtype=np.float32)
-
-    for i in tqdm(range(n_cells), desc="Computing ranks per cell"):
-        data = adata_X[i, :].toarray().flatten()
-        ranks[i, :] = rankdata(data, method='average')
-
-    # Geometric mean across slices
-    if config.gM_slices is not None:
-        logger.info('Geometrical mean across multiple slices is provided.')
-        gM_df = pd.read_parquet(config.gM_slices)
-        if config.species is not None:
-            homologs = pd.read_csv(config.homolog_file, sep='\t', header=None)
-            if homologs.shape[1] < 2:
-                raise ValueError(
-                    "Homologs file must have at least two columns: one for the species and one for the human gene symbol.")
-            homologs.columns = [config.species, 'HUMAN_GENE_SYM']
-            homologs.set_index(config.species, inplace=True)
-            gM_df = gM_df.loc[gM_df.index.isin(homologs.index)]
-            gM_df.index = homologs.loc[gM_df.index, 'HUMAN_GENE_SYM'].values
-        common_genes = np.intersect1d(adata.var_names, gM_df.index)
-        gM_df = gM_df.loc[common_genes]
-        gM = gM_df['G_Mean'].values
-        adata = adata[:, common_genes]
-        ranks = ranks[:, np.isin(adata.var_names, common_genes)]
-    else:
-        gM = gmean(ranks, axis=0)
-
-    # Compute the fraction of each gene across cells
-    adata_X_bool = adata_X.astype(bool)
-    frac_whole = np.asarray(adata_X_bool.sum(axis=0)).flatten() / n_cells
-
-    # Normalize the ranks
-    ranks = ranks / gM
-
-    # Compute marker scores in parallel
-    logger.info('------Computing marker scores...')
-
-    def compute_mk_score_wrapper(cell_pos):
-        return compute_regional_mkscore(
-            cell_pos, spatial_net_dict, coor_latent, config, cell_annotations, ranks, frac_whole, adata_X_bool
-        )
-
-    mk_scores = [compute_mk_score_wrapper(cell_pos) for cell_pos in tqdm(range(n_cells), desc="Calculating marker scores")]
-    mk_score = np.vstack(mk_scores).T
-
-    # Remove mitochondrial genes
-    gene_names = adata.var_names.values.astype(str)
-    mt_gene_mask = ~(np.char.startswith(gene_names, 'MT-') | np.char.startswith(gene_names, 'mt-'))
-    mk_score = mk_score[mt_gene_mask, :]
-    gene_names = gene_names[mt_gene_mask]
-
-    # Save the marker scores
-    logger.info(f'------Saving marker scores ...')
-    output_file_path = Path(config.mkscore_feather_path)
-    output_file_path.parent.mkdir(parents=True, exist_ok=True, mode=0o755)
-    mk_score_df = pd.DataFrame(mk_score, index=gene_names, columns=adata.obs_names)
-    mk_score_df.reset_index(inplace=True)
-    mk_score_df.rename(columns={'index': 'HUMAN_GENE_SYM'}, inplace=True)
-    mk_score_df.to_feather(output_file_path)
-
-    # Save the modified adata object to disk
-    adata.write(config.hdf5_with_latent_path)
+import logging
+from pathlib import Path
+
+import numpy as np
+import pandas as pd
+import scanpy as sc
+import scipy
+from scipy.stats import gmean
+from scipy.stats import rankdata
+from sklearn.metrics.pairwise import cosine_similarity
+from sklearn.neighbors import NearestNeighbors
+from tqdm import tqdm
+
+from gsMap.config import LatentToGeneConfig
+
+logger = logging.getLogger(__name__)
+
+
+def find_neighbors(coor, num_neighbour):
+    """
+    Find Neighbors of each cell (based on spatial coordinates).
+    """
+    nbrs = NearestNeighbors(n_neighbors=num_neighbour).fit(coor)
+    distances, indices = nbrs.kneighbors(coor, return_distance=True)
+    cell_indices = np.arange(coor.shape[0])
+    cell1 = np.repeat(cell_indices, indices.shape[1])
+    cell2 = indices.flatten()
+    distance = distances.flatten()
+    spatial_net = pd.DataFrame({'Cell1': cell1, 'Cell2': cell2, 'Distance': distance})
+    return spatial_net
+
+
+def build_spatial_net(adata, annotation, num_neighbour):
+    """
+    Build spatial neighbourhood matrix for each spot (cell) based on the spatial coordinates.
+    """
+    logger.info(f'------Building spatial graph based on spatial coordinates...')
+
+    coor = adata.obsm['spatial']
+    if annotation is not None:
+        logger.info(f'Cell annotations are provided...')
+        spatial_net_list = []
+        # Cells with annotations
+        for ct in adata.obs[annotation].dropna().unique():
+            idx = np.where(adata.obs[annotation] == ct)[0]
+            coor_temp = coor[idx, :]
+            spatial_net_temp = find_neighbors(coor_temp, min(num_neighbour, coor_temp.shape[0]))
+            # Map back to original indices
+            spatial_net_temp['Cell1'] = idx[spatial_net_temp['Cell1'].values]
+            spatial_net_temp['Cell2'] = idx[spatial_net_temp['Cell2'].values]
+            spatial_net_list.append(spatial_net_temp)
+            logger.info(f'{ct}: {coor_temp.shape[0]} cells')
+
+        # Cells labeled as nan
+        if pd.isnull(adata.obs[annotation]).any():
+            idx_nan = np.where(pd.isnull(adata.obs[annotation]))[0]
+            logger.info(f'Nan: {len(idx_nan)} cells')
+            spatial_net_temp = find_neighbors(coor, num_neighbour)
+            spatial_net_temp = spatial_net_temp[spatial_net_temp['Cell1'].isin(idx_nan)]
+            spatial_net_list.append(spatial_net_temp)
+        spatial_net = pd.concat(spatial_net_list, axis=0)
+    else:
+        logger.info(f'Cell annotations are not provided...')
+        spatial_net = find_neighbors(coor, num_neighbour)
+
+    return spatial_net.groupby('Cell1')['Cell2'].apply(np.array).to_dict()
+
+
+def find_neighbors_regional(cell_pos, spatial_net_dict, coor_latent, config, cell_annotations):
+    num_neighbour = config.num_neighbour
+    annotations = config.annotation
+
+    cell_use_pos = spatial_net_dict.get(cell_pos, [])
+    if len(cell_use_pos) == 0:
+        return []
+
+    cell_latent = coor_latent[cell_pos, :].reshape(1, -1)
+    neighbors_latent = coor_latent[cell_use_pos, :]
+    similarity = cosine_similarity(cell_latent, neighbors_latent).reshape(-1)
+
+    if annotations is not None:
+        cell_annotation = cell_annotations[cell_pos]
+        neighbor_annotations = cell_annotations[cell_use_pos]
+        mask = neighbor_annotations == cell_annotation
+        if not np.any(mask):
+            return []
+        similarity = similarity[mask]
+        cell_use_pos = cell_use_pos[mask]
+
+    if len(similarity) == 0:
+        return []
+
+    indices = np.argsort(-similarity)  # descending order
+    top_indices = indices[:num_neighbour]
+    cell_select_pos = cell_use_pos[top_indices]
+    return cell_select_pos
+
+
+def compute_regional_mkscore(cell_pos, spatial_net_dict, coor_latent, config, cell_annotations,
+                             ranks, frac_whole, adata_X_bool):
+    """
+    Compute gmean ranks of a region.
+    """
+    cell_select_pos = find_neighbors_regional(
+        cell_pos, spatial_net_dict, coor_latent, config, cell_annotations
+    )
+    if len(cell_select_pos) == 0:
+        return np.zeros(ranks.shape[1], dtype=np.float16)
+
+    # Ratio of expression ranks
+    ranks_tg = ranks[cell_select_pos, :]
+    gene_ranks_region = gmean(ranks_tg, axis=0)
+    gene_ranks_region[gene_ranks_region <= 1] = 0
+
+    if not config.no_expression_fraction:
+        # Ratio of expression fractions
+        frac_focal = adata_X_bool[cell_select_pos, :].sum(axis=0).A1 / len(cell_select_pos)
+        frac_region = frac_focal / frac_whole
+        frac_region[frac_region <= 1] = 0
+        frac_region[frac_region > 1] = 1
+
+        # 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
+    return mkscore.astype(np.float16, copy=False)
+
+
+def run_latent_to_gene(config: LatentToGeneConfig):
+    logger.info('------Loading the spatial data...')
+    adata = sc.read_h5ad(config.hdf5_with_latent_path)
+    logger.info(f'Loaded spatial data with {adata.n_obs} cells and {adata.n_vars} genes.')
+
+    if config.annotation is not None:
+        logger.info(f'------Cell annotations are provided as {config.annotation}...')
+        initial_cell_count = adata.n_obs
+        adata = adata[~pd.isnull(adata.obs[config.annotation]), :]
+        logger.info(f'Removed null annotations. Cells retained: {adata.n_obs} (initial: {initial_cell_count}).')
+
+    # Homologs transformation
+    if config.homolog_file is not None:
+        logger.info(f'------Transforming the {config.species} to HUMAN_GENE_SYM...')
+        homologs = pd.read_csv(config.homolog_file, sep='\t')
+        if homologs.shape[1] != 2:
+            raise ValueError("Homologs file must have two columns: one for the species and one for the human gene symbol.")
+
+        homologs.columns = [config.species, 'HUMAN_GENE_SYM']
+        homologs.set_index(config.species, inplace=True)
+        adata = adata[:, adata.var_names.isin(homologs.index)]
+        logger.info(f"{adata.shape[1]} genes retained after homolog transformation.")
+        if adata.shape[1] < 100:
+            raise ValueError("Too few genes retained in ST data (<100).")
+        adata.var_names = homologs.loc[adata.var_names, 'HUMAN_GENE_SYM'].values
+        adata = adata[:, ~adata.var_names.duplicated()]
+
+    # Create mappings
+    n_cells = adata.n_obs
+    n_genes = adata.n_vars
+
+    if config.annotation is not None:
+        cell_annotations = adata.obs[config.annotation].values
+        logger.info(f'Using cell annotations for {len(cell_annotations)} cells.')
+    else:
+        cell_annotations = None
+
+    # Build the spatial graph
+    logger.info('------Building the spatial graph...')
+    spatial_net_dict = build_spatial_net(adata, config.annotation, config.num_neighbour_spatial)
+    logger.info('Spatial graph built successfully.')
+
+    # Extract the latent representation
+    logger.info('------Extracting the latent representation...')
+    coor_latent = adata.obsm[config.latent_representation]
+    coor_latent = coor_latent.astype(np.float32)
+    logger.info('Latent representation extracted.')
+
+    # Geometric mean across slices
+    gM = None
+    if config.gM_slices is not None:
+        logger.info('Geometrical mean across multiple slices is provided.')
+        gM_df = pd.read_parquet(config.gM_slices)
+        if config.species is not None:
+            homologs = pd.read_csv(config.homolog_file, sep='\t')
+            if homologs.shape[1] < 2:
+                raise ValueError("Homologs file must have at least two columns: one for the species and one for the human gene symbol.")
+            homologs.columns = [config.species, 'HUMAN_GENE_SYM']
+            homologs.set_index(config.species, inplace=True)
+            gM_df = gM_df.loc[gM_df.index.isin(homologs.index)]
+            gM_df.index = homologs.loc[gM_df.index, 'HUMAN_GENE_SYM'].values
+        common_genes = np.intersect1d(adata.var_names, gM_df.index)
+        gM_df = gM_df.loc[common_genes]
+        gM = gM_df['G_Mean'].values
+        adata = adata[:, common_genes]
+        logger.info(f'{len(common_genes)} common genes retained after loading the cross slice geometric mean.')
+
+    # Compute ranks after taking common genes with gM_slices
+    logger.info('------Ranking the spatial data...')
+    if not scipy.sparse.issparse(adata.X):
+        adata_X = scipy.sparse.csr_matrix(adata.X)
+    elif isinstance(adata.X, scipy.sparse.csr_matrix):
+        adata_X = adata.X  # Avoid copying if already CSR
+    else:
+        adata_X = adata.X.tocsr()
+
+    ranks = np.zeros((n_cells, adata.n_vars), dtype=np.float32)
+
+    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)
+
+    # Compute the fraction of each gene across cells
+    adata_X_bool = adata_X.astype(bool)
+    frac_whole = np.asarray(adata_X_bool.sum(axis=0)).flatten() / n_cells
+    logger.info('Gene expression proportion of each gene across cells computed.')
+
+    # Normalize the ranks
+    ranks /= gM
+
+    # Compute marker scores in parallel
+    logger.info('------Computing marker scores...')
+    def compute_mk_score_wrapper(cell_pos):
+        return compute_regional_mkscore(
+            cell_pos, spatial_net_dict, coor_latent, config, cell_annotations, ranks, frac_whole, adata_X_bool
+        )
+
+    mk_scores = [compute_mk_score_wrapper(cell_pos) for cell_pos in tqdm(range(n_cells), desc="Calculating marker scores")]
+    mk_score = np.vstack(mk_scores).T
+    logger.info('Marker scores computed.')
+
+    # Remove mitochondrial genes
+    gene_names = adata.var_names.values.astype(str)
+    mt_gene_mask = ~(np.char.startswith(gene_names, 'MT-') | np.char.startswith(gene_names, 'mt-'))
+    mk_score = mk_score[mt_gene_mask, :]
+    gene_names = gene_names[mt_gene_mask]
+    logger.info(f'Removed mitochondrial genes. Remaining genes: {len(gene_names)}.')
+
+    # Save the marker scores
+    logger.info(f'------Saving marker scores ...')
+    output_file_path = Path(config.mkscore_feather_path)
+    output_file_path.parent.mkdir(parents=True, exist_ok=True, mode=0o755)
+    mk_score_df = pd.DataFrame(mk_score, index=gene_names, columns=adata.obs_names)
+    mk_score_df.reset_index(inplace=True)
+    mk_score_df.rename(columns={'index': 'HUMAN_GENE_SYM'}, inplace=True)
+    mk_score_df.to_feather(output_file_path)
+    logger.info(f'Marker scores saved to {output_file_path}.')
+
+    # Save the modified adata object to disk
+    adata.write(config.hdf5_with_latent_path)
+    logger.info(f'Modified adata object saved to {config.hdf5_with_latent_path}.')

gsMap/main.py

@@ -1,31 +1,31 @@
-from gsMap import (__version__)
-from gsMap.config import *
-
-def main():
-    parser = create_parser()
-    args = parser.parse_args()
-    if args.subcommand is None:
-        parser.print_help()
-        exit(1)
-    args.func(
-        args
-    )
-
-def create_parser():
-    parser = argparse.ArgumentParser(description=" gsMap: genetically informed spatial mapping of cells for complex traits",
-                                     formatter_class=argparse.RawTextHelpFormatter,
-                                     prog='gsMap'
-                                     )
-    parser.add_argument('--version', '-v', action='version', version=f'gsMap version {__version__}')
-    subparsers = parser.add_subparsers(dest="subcommand", help="Subcommands", title="Available subcommands")
-    for subcommand in cli_function_registry.values():
-        subcommand_parser = subparsers.add_parser(subcommand.name, help=subcommand.description,
-                                                  formatter_class=argparse.ArgumentDefaultsHelpFormatter
-                                                  )
-        subcommand.add_args_function(subcommand_parser)
-        subcommand_parser.set_defaults(func=subcommand.func)
-    return parser
-
-
-if __name__ == "__main__":
-    main()
+from gsMap import (__version__)
+from gsMap.config import *
+
+def main():
+    parser = create_parser()
+    args = parser.parse_args()
+    if args.subcommand is None:
+        parser.print_help()
+        exit(1)
+    args.func(
+        args
+    )
+
+def create_parser():
+    parser = argparse.ArgumentParser(description=" gsMap: genetically informed spatial mapping of cells for complex traits",
+                                     formatter_class=argparse.RawTextHelpFormatter,
+                                     prog='gsMap'
+                                     )
+    parser.add_argument('--version', '-v', action='version', version=f'gsMap version {__version__}')
+    subparsers = parser.add_subparsers(dest="subcommand", help="Subcommands", title="Available subcommands")
+    for subcommand in cli_function_registry.values():
+        subcommand_parser = subparsers.add_parser(subcommand.name, help=subcommand.description,
+                                                  formatter_class=argparse.ArgumentDefaultsHelpFormatter
+                                                  )
+        subcommand.add_args_function(subcommand_parser)
+        subcommand_parser.set_defaults(func=subcommand.func)
+    return parser
+
+
+if __name__ == "__main__":
+    main()