feat(tests): Added function to produce synthetic AnnData.

Signed-off-by: Alexander Aivazidis <alexander.aivazidis@sanger.ac.uk>

src/pyrovelocity/tests/synthetic_AnnData.py

@@ -0,0 +1,62 @@
+"""Producing synthetic AnnData for tests."""
+
+import numpy as np
+import pandas as pd
+import anndata as ad
+
+def synthetic_AnnData(
+    n_cell_types: int = 3,
+    n_genes: int = 10,
+    cells_per_type: int = 20,
+    seed: int = 42
+    ):
+
+    """
+    Produces a simple synthetic AnnData object.
+
+    Args:
+        n_cell_types (int): Number of cell types.
+        n_genes (int): Number of genes.
+        cells_per_type (int): Number of cells per cell type.
+        seed (int): Random seed.
+    Returns:
+        AnnData: Synthetic AnnData object.
+
+    Examples:
+        >>> synthetic_AnnData()
+    """
+
+    # Number of genes, cells, and cell types
+    n_genes = 10
+    n_cells = cells_per_type * n_cell_types
+
+    # Create synthetic gene expression data
+    # Each cell type will have slightly different expression profiles
+    np.random.seed(seed)  # For reproducibility
+
+    cells_per_type = int(n_cells/n_cell_types)
+    # Generate data with different means for different cell types
+    expression_data = np.vstack([
+        np.random.normal(loc=i, scale=0.5, size=(cells_per_type, n_genes))
+        for i in range(n_cell_types)
+    ])
+
+    # Create an AnnData object
+    adata = ad.AnnData(X=expression_data)
+
+    # Add cell type annotations
+    cell_types = []
+    for i in range(n_cell_types):
+        cell_types += ['Type ' + str(i)] * cells_per_type
+    adata.obs['cell_type'] = pd.Categorical(cell_types)
+
+    # Add gene names (e.g., Gene1, Gene2, ..., Gene20)
+    gene_names = [f'Gene{i+1}' for i in range(n_genes)]
+    adata.var['gene_names'] = gene_names
+
+    # Add cell names (e.g., Cell1, Cell2, ..., Cell30)
+    cell_names = [f'Cell{i+1}' for i in range(n_cells)]
+    adata.obs_names = cell_names
+    adata.var_names = gene_names
+
+    return adata