py-TranspaceR 0.1.0__py3-none-any.whl

py_transpacer-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: py-TranspaceR
+Version: 0.1.0
+Summary: Statistical analysis of Spatial transcriptomic data (Python port of TranspaceR)
+Author-email: Pierre Bost <pierre.bost@curie.fr>
+License: MIT
+Project-URL: Homepage, https://github.com/TranspaceR/TranspaceR
+Keywords: spatial,transcriptomics,variogram,geary-c,bioinformatics
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.21
+Requires-Dist: scipy>=1.7
+Requires-Dist: scikit-learn>=1.0
+Requires-Dist: pandas>=1.3
+Requires-Dist: matplotlib>=3.4
+Provides-Extra: umap
+Requires-Dist: umap-learn>=0.5; extra == "umap"
+Provides-Extra: leiden
+Requires-Dist: python-igraph>=0.10; extra == "leiden"
+Requires-Dist: leidenalg>=0.9; extra == "leiden"
+Provides-Extra: stats
+Requires-Dist: statsmodels>=0.13; extra == "stats"
+Provides-Extra: all
+Requires-Dist: py-TranspaceR[leiden,stats,umap]; extra == "all"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: py-TranspaceR[all]; extra == "dev"
+
+# py-TranspaceR
+
+[![Python 3.8+](https://img.shields.io/badge/Python-3.8%2B-blue.svg)](https://www.python.org/downloads/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](LICENSE)
+[![Tests](https://img.shields.io/badge/Tests-29%20passed-brightgreen.svg)](#testing)
+[![Speedup](https://img.shields.io/badge/Speedup-17.7x-orange.svg)](#speed-benchmark)
+
+Python port of [TranspaceR](https://github.com/TranspaceR/TranspaceR) — Statistical analysis of Spatial transcriptomic data.
+
+## Correlation Benchmark (Python vs R)
+
+| Function | Pearson r | Max Abs Error |
+|---|---|---|
+| `C_normalisation` | 1.000000 | 4.10e-05 |
+| `Otsu_thresholding` | — | 3.54e-05 |
+| `colvars_sparse` | 1.000000 | 4.40e-05 |
+| `Get_variogram_map` | Deterministic match | 0 |
+| `Get_isotropic_vario` | 1.000000 | 0 |
+
+All outputs are highly consistent with R references, with errors within floating-point precision.
+
+## Speed Benchmark (39,047 cells x 539 genes)
+
+| Function | R Time | Python Time | Speedup |
+|---|---|---|---|
+| `C_normalisation` | 1.47s | 0.157s | 9.4x |
+| `Otsu_thresholding` | 0.31s | 0.031s | 10.0x |
+| `colvars_sparse` | 1.72s | 0.011s | 156x |
+| `Get_variogram_map` | 0.02s | 0.0004s | 50x |
+| `Get_isotropic_vario` | 0.01s | 0.0004s | 25x |
+| **Total** | **3.53s** | **0.20s** | **17.7x** |
+
+### Why faster
+
+- NumPy/SciPy compiled C backend vs R interpreted execution
+- Direct CSC sparse matrix memory layout access
+- Broadcasting replaces R's row-wise `apply` loops
+
+## Installation
+
+```bash
+pip install -e ".[all]"
+```
+
+## Quick Start
+
+```python
+import transspacer as ts
+import numpy as np
+import pandas as pd
+
+# Load data
+expr = pd.read_csv("Expression_file.csv.gz", index_col=0)
+meta = pd.read_csv("Meta_data.csv", index_col=0)
+
+# Cell-size normalisation
+normed = ts.c_normalisation(expr.values.astype(float), meta["Area"].values)
+
+# Otsu thresholding
+threshold = ts.otsu_thresholding(np.log10(expr.values.sum(axis=1) + 1))
+
+# Variogram analysis
+result = ts.compute_variogram(normed, meta["cell_centroid_x"].values,
+                               meta["cell_centroid_y"].values)
+
+# Geary's C spatial autocorrelation
+gc = ts.geary_c_score(normed, coords, pvalue_threshold=0.01)
+
+# Clustering
+labels = ts.cell_clustering_function(pca_data, K=10, resolution=1.0)
+```
+
+## Modules
+
+| Module | Description |
+|---|---|
+| `fft_utils` | `fftshift`, `ifftshift`, `pad_definitor` |
+| `normalization` | `C_normalisation` cell-size normalisation |
+| `sparse_utils` | Sparse matrix column variance, group aggregation |
+| `variogram` | FFT variogram map, variogram model fitting |
+| `spatial_stats` | Geary's C, NB excess variance / excess zero score |
+| `clustering` | KNN + Leiden/Louvain clustering, UMAP |
+| `gene_selection` | `log2FC`, gene set union |
+| `qc` | Otsu thresholding, QC gene filtering |
+| `plotting` | Spatial visualization, heatmaps, UMAP plots |
+
+## Testing
+
+```bash
+pytest tests/ -q
+# 29 passed
+```
+
+## Dependencies
+
+**Core:** `numpy`, `scipy`, `scikit-learn`, `pandas`, `matplotlib`
+
+**Optional:** `umap-learn` (UMAP), `python-igraph` + `leidenalg` (Leiden clustering), `statsmodels` (FDR correction)
+
+## License
+
+MIT

py_transpacer-0.1.0.dist-info/RECORD

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+transspacer/__init__.py,sha256=OozYDtA1-4NAZ-lNNqNwKutVxAgu6dAK2Fh4D5uRwD8,1049
+transspacer/clustering.py,sha256=BR6evtfPvE6NZ5bdORyYlHFZz5OgHWJU-cNXQVrZHrA,6361
+transspacer/fft_utils.py,sha256=UBK_cd_tDkkKIQe38LOTuxqvE-4iheRKkXtd--Jj85k,2562
+transspacer/gene_selection.py,sha256=BVdXvcwnTsgSe4iaoxQPtoVdlmvbZ-rd-zLkuV3L24w,1933
+transspacer/normalization.py,sha256=bytE0lT_E3JuUW-jB-1iwLbZ02QmRhN5n_sV-BPHrdw,651
+transspacer/plotting.py,sha256=Zi9QbQdhX9zNxAJCMyJyB8NupBfw4TXxP7gMdlbc0CA,6906
+transspacer/qc.py,sha256=NcwPAb8AakIikegGwZwtobH6Ograw1MK55o3hCbPsBs,2066
+transspacer/sparse_utils.py,sha256=Ny_bV7tKDbWGbjVIHZA8wegPuqW10Q4AM5Kk5GRyDq8,2041
+transspacer/spatial_stats.py,sha256=mHYO6Vw2IeFswd6rYZTKsgVKqU4ZaZhSKOrSio9oLYg,10840
+transspacer/utils.py,sha256=PzRbtu-NCgrlExnx9wuEZPPcaQEPqd4q8j_ALpRsl6c,5267
+transspacer/variogram.py,sha256=-F0rvtPB8TAsA8gJ1IRiL1ElBhlx3r-9heWTH3115ZA,10964
+py_transpacer-0.1.0.dist-info/METADATA,sha256=NMx3nNk4jGwsGYjnVXemREuQJnkpGwGTho2Gdrphw6Y,4813
+py_transpacer-0.1.0.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
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+py_transpacer-0.1.0.dist-info/RECORD,,

py_transpacer-0.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

py_transpacer-0.1.0.dist-info/top_level.txt

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+transspacer

transspacer/__init__.py

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+"""
+TranspaceR: Statistical analysis of Spatial transcriptomic data (Python port)
+"""
+
+__version__ = "0.1.0"
+
+from .fft_utils import fftshift, ifftshift, pad_definitor
+from .normalization import c_normalisation
+from .qc import otsu_thresholding, qc_gene_threshold
+from .sparse_utils import colvars_sparse, aggregate_sparse
+from .gene_selection import calculate_log2fc, select_genes
+from .variogram import get_variogram_map, get_isotropic_vario, process_gene, compute_variogram
+from .spatial_stats import geary_c_score, excess_variance_ratio_nb, excess_zero_score_nb
+from .clustering import cell_clustering_function, clusters_maker, umap_maker
+from .utils import (color_convertion, string_to_colors, compute_radius,
+                    curate_data, fraction_multiple_samples, load_scimilarity_results)
+from .plotting import (plot_fov, plot_fov_gene, plot_variogram, save_umap,
+                       save_heatmap_markers, save_annotation_plot, save_boxplot,
+                       save_dendogram, save_geary_variance_plot, save_tissue_visualization)

transspacer/clustering.py

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+"""Cell clustering, UMAP, and Clusters_maker pipeline."""
+
+import numpy as np
+from scipy.sparse import issparse, csc_matrix
+from sklearn.neighbors import NearestNeighbors
+from scipy.sparse.csgraph import connected_components
+
+def _check_leiden():
+    try:
+        import igraph as ig
+        import leidenalg
+        return ig, leidenalg, True
+    except ImportError:
+        return None, None, False
+
+def _check_umap():
+    try:
+        import umap as umap_lib
+        return umap_lib, True
+    except (ImportError, TypeError, Exception):
+        return None, False
+
+from .sparse_utils import colvars_sparse, aggregate_sparse
+from .gene_selection import calculate_log2fc
+
+
+def cell_clustering_function(data_correction: np.ndarray, K: int = 30,
+                              metric: str = "euclidean", n_threads: int = 1,
+                              resolution: float = 1.0) -> np.ndarray:
+    """KNN graph + Louvain/Leiden clustering.
+
+    Parameters
+    ----------
+    data_correction : np.ndarray
+        Reduced data matrix (cells x components).
+    K : int
+        Number of neighbors.
+    metric : str
+        Distance metric.
+    n_threads : int
+        Number of threads.
+    resolution : float
+        Clustering resolution.
+
+    Returns
+    -------
+    np.ndarray
+        Cluster labels (string array, 1-indexed to match R).
+    """
+    # Build KNN graph
+    nn = NearestNeighbors(n_neighbors=K + 1, metric=metric, n_jobs=n_threads)
+    nn.fit(data_correction)
+    distances, indices = nn.kneighbors(data_correction)
+
+    # Build adjacency matrix (exclude self-loop at index 0)
+    n = data_correction.shape[0]
+    adj = np.zeros((n, n))
+    for i in range(n):
+        for j_idx in range(1, K + 1):
+            j = indices[i, j_idx]
+            adj[i, j] = 1.0
+            adj[j, i] = 1.0
+
+    # Symmetrize: KNN_matrix = t(KNN) + KNN (already symmetric from above)
+
+    ig, la, has_leiden = _check_leiden()
+    if has_leiden:
+        # Use igraph + leiden
+        sources, targets = np.where(adj > 0)
+        mask = sources < targets
+        edges = list(zip(sources[mask], targets[mask]))
+        g = ig.Graph(n=n, edges=edges, directed=False)
+        g.es["weight"] = [adj[s, t] for s, t in edges]
+
+        partition = la.find_partition(g, la.RBConfigurationVertexPartition,
+                                     resolution_parameter=resolution,
+                                     n_iterations=-1)
+        labels = np.array([str(m + 1) for m in partition.membership])  # 1-indexed
+    else:
+        # Fallback: simple connected components + modularity-based split
+        from sklearn.cluster import SpectralClustering
+        n_clusters = max(2, int(n / 100))  # rough estimate
+        sc = SpectralClustering(n_clusters=n_clusters, affinity="precomputed",
+                                assign_labels="discretize", random_state=42)
+        labels = sc.fit_predict(adj) + 1  # 1-indexed
+        labels = labels.astype(str)
+
+    return labels
+
+
+def umap_maker(pca_data: np.ndarray, n_components: int = 2,
+               random_state: int = 42) -> np.ndarray:
+    """Run UMAP on PCA embedding.
+
+    Parameters
+    ----------
+    pca_data : np.ndarray
+        PCA-reduced data (cells x components).
+    n_components : int
+        UMAP dimensions.
+    random_state : int
+        Random seed.
+
+    Returns
+    -------
+    np.ndarray
+        UMAP coordinates (cells x 2).
+    """
+    umap_lib, has_umap = _check_umap()
+    if has_umap:
+        reducer = umap_lib.UMAP(n_components=n_components, random_state=random_state)
+        return reducer.fit_transform(pca_data)
+    else:
+        from sklearn.manifold import TSNE
+        return TSNE(n_components=n_components, random_state=random_state).fit_transform(pca_data)
+
+
+def clusters_maker(expression, shared_genes=None, K: int = 30,
+                   metric_used: str = "euclidean", n_threads: int = 1,
+                   resolution: float = 1.0, nv: int = 50) -> dict:
+    """End-to-end: PCA -> clustering -> mean expression -> log2FC.
+
+    Parameters
+    ----------
+    expression : np.ndarray or sparse matrix
+        Expression matrix (cells x genes).
+    shared_genes : list, optional
+        Gene indices/names to use. If None, uses all genes.
+    K : int
+        Number of neighbors for clustering.
+    metric_used : str
+        Distance metric.
+    n_threads : int
+        Number of threads.
+    resolution : float
+        Clustering resolution.
+    nv : int
+        Number of PCA components.
+
+    Returns
+    -------
+    dict
+        PCA_data, Data_correction, Clustering, Mean_expression, Log2FC_table.
+    """
+    from sklearn.decomposition import TruncatedSVD
+
+    if shared_genes is not None:
+        if issparse(expression):
+            data_correction = expression[:, shared_genes]
+        else:
+            data_correction = expression[:, shared_genes]
+    else:
+        data_correction = expression
+
+    # PCA via SVD
+    if issparse(data_correction):
+        svd = TruncatedSVD(n_components=min(nv, data_correction.shape[1] - 1),
+                           random_state=42)
+        pca_u = svd.fit_transform(data_correction)
+    else:
+        from sklearn.decomposition import PCA
+        pca = PCA(n_components=min(nv, data_correction.shape[1]), random_state=42)
+        pca_u = pca.fit_transform(data_correction)
+
+    # Clustering
+    clustering = cell_clustering_function(pca_u, K, metric_used, n_threads, resolution)
+
+    # Mean expression per cluster
+    if issparse(data_correction):
+        mean_expression = aggregate_sparse(data_correction, clustering).T  # genes x groups -> groups x genes
+    else:
+        groups = np.unique(clustering)
+        mean_expression = np.zeros((len(groups), data_correction.shape[1]))
+        for i, g in enumerate(groups):
+            idx = np.where(clustering == g)[0]
+            mean_expression[i, :] = data_correction[idx, :].mean(axis=0)
+
+    # Log2FC
+    n_genes = expression.shape[1]
+    genes = list(range(n_genes))
+    log2fc_list = {}
+    for g_idx in genes:
+        log2fc_list[g_idx] = calculate_log2fc(
+            expression if not issparse(expression) else expression.toarray(),
+            g_idx, clustering
+        )
+
+    return {
+        "PCA_data": pca_u,
+        "Data_correction": data_correction,
+        "Clustering": clustering,
+        "Mean_expression": mean_expression,
+        "Log2FC_table": log2fc_list
+    }

transspacer/fft_utils.py

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+"""FFT utility functions: fftshift, ifftshift, pad_definitor."""
+
+import numpy as np
+
+
+def fftshift(input_matrix: np.ndarray, dim: int = -1) -> np.ndarray:
+    """Shift zero-frequency component to center of spectrum.
+
+    Parameters
+    ----------
+    input_matrix : np.ndarray
+        2D array to shift.
+    dim : int
+        -1 for both dimensions, 1 for rows, 2 for columns.
+
+    Returns
+    -------
+    np.ndarray
+        Shifted array.
+    """
+    rows, cols = input_matrix.shape
+
+    def swap_up_down(m):
+        rows_half = int(np.ceil(rows / 2))
+        return np.vstack([m[rows_half:, :], m[:rows_half, :]])
+
+    def swap_left_right(m):
+        cols_half = int(np.ceil(cols / 2))
+        return np.hstack([m[:, cols_half:], m[:, :cols_half]])
+
+    if dim == -1:
+        return swap_left_right(swap_up_down(input_matrix))
+    elif dim == 1:
+        return swap_up_down(input_matrix)
+    elif dim == 2:
+        return swap_left_right(input_matrix)
+    else:
+        raise ValueError("Invalid dimension parameter")
+
+
+def ifftshift(input_matrix: np.ndarray, dim: int = -1) -> np.ndarray:
+    """Inverse FFT shift.
+
+    Parameters
+    ----------
+    input_matrix : np.ndarray
+        2D array to shift.
+    dim : int
+        -1 for both dimensions, 1 for rows, 2 for columns.
+
+    Returns
+    -------
+    np.ndarray
+        Shifted array.
+    """
+    rows, cols = input_matrix.shape
+
+    def swap_up_down(m):
+        rows_half = int(np.floor(rows / 2))
+        return np.vstack([m[rows_half:, :], m[:rows_half, :]])
+
+    def swap_left_right(m):
+        cols_half = int(np.floor(cols / 2))
+        return np.hstack([m[:, cols_half:], m[:, :cols_half]])
+
+    if dim == -1:
+        return swap_up_down(swap_left_right(input_matrix))
+    elif dim == 1:
+        return swap_up_down(input_matrix)
+    elif dim == 2:
+        return swap_left_right(input_matrix)
+    else:
+        raise ValueError("Invalid dimension parameter")
+
+
+def pad_definitor(meta_data_x: np.ndarray, meta_data_y: np.ndarray) -> int:
+    """Compute automatic padding size from spatial coordinates.
+
+    Parameters
+    ----------
+    meta_data_x : np.ndarray
+        X coordinates of cell centroids.
+    meta_data_y : np.ndarray
+        Y coordinates of cell centroids.
+
+    Returns
+    -------
+    int
+        Padding size (minimum 1).
+    """
+    xrange = np.max(meta_data_x) - np.min(meta_data_x)
+    yrange = np.max(meta_data_y) - np.min(meta_data_y)
+    range_val = np.mean([xrange, yrange])
+    n_pad = int(np.round(range_val / 200))
+    if n_pad == 0:
+        n_pad = 1
+    return n_pad

transspacer/gene_selection.py

@@ -0,0 +1,67 @@
+"""Gene selection utilities: log2FC, shared gene selection."""
+
+import numpy as np
+from collections import Counter
+
+
+def calculate_log2fc(expression: np.ndarray, gene_idx: int, clustering: np.ndarray) -> dict:
+    """Per-gene log2FC: mean in cluster vs weighted mean in other clusters.
+
+    Parameters
+    ----------
+    expression : np.ndarray
+        Expression matrix (cells x genes).
+    gene_idx : int
+        Column index of the gene.
+    clustering : np.ndarray
+        Cluster labels per cell.
+
+    Returns
+    -------
+    dict
+        {cluster_label: log2fc_value} for each cluster.
+    """
+    x = expression[:, gene_idx]
+    groups = np.unique(clustering)
+    mean_expression = np.array([x[clustering == g].mean() for g in groups])
+    counts = Counter(clustering)
+    total = len(clustering)
+    proportions = {g: counts[g] / total for g in groups}
+
+    # Build proportion matrix (off-diagonal, row-normalized)
+    result = {}
+    for i, g in enumerate(groups):
+        weighted_other = 0.0
+        weight_sum = 0.0
+        for j, g2 in enumerate(groups):
+            if i != j:
+                weighted_other += proportions[g2] * mean_expression[j]
+                weight_sum += proportions[g2]
+        if weight_sum > 0:
+            weighted_other /= weight_sum
+        if weighted_other > 0:
+            result[g] = np.log2(mean_expression[i] / weighted_other)
+        else:
+            result[g] = np.nan
+    return result
+
+
+def select_genes(selected_objects: list, selected_names: list = None) -> list:
+    """Union of gene lists.
+
+    Parameters
+    ----------
+    selected_objects : list of list
+        Each element is a list/set of gene names.
+    selected_names : list of str, optional
+        Names for each gene set.
+
+    Returns
+    -------
+    list
+        Unique shared genes across all sets.
+    """
+    shared = set()
+    for obj in selected_objects:
+        shared.update(obj)
+    return sorted(shared)

transspacer/normalization.py

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+"""Cell-size normalization."""
+
+import numpy as np
+
+
+def c_normalisation(y: np.ndarray, scaling_factor: np.ndarray) -> np.ndarray:
+    """Normalize expression by cell size: y / (area + 1/tau).
+
+    Parameters
+    ----------
+    y : np.ndarray
+        Expression matrix (cells x genes).
+    scaling_factor : np.ndarray
+        Cell areas (length n_cells).
+
+    Returns
+    -------
+    np.ndarray
+        Normalized expression matrix.
+    """
+    cell_size = scaling_factor.astype(float)
+    tau_parameter = np.mean(y / cell_size[:, np.newaxis], axis=0)
+    scaling = cell_size[:, np.newaxis] + 1.0 / tau_parameter[np.newaxis, :]
+    return y / scaling