matrix.py 文件源码

def preprocess_matrix(matrix, num_bcs=None, use_bcs=None, use_genes=None, force_cells=None):
        if force_cells is not None:
            bc_counts = matrix.get_reads_per_bc()
            bc_indices, _, _ = cr_stats.filter_cellular_barcodes_fixed_cutoff(bc_counts, force_cells)
            matrix = matrix.select_barcodes(bc_indices)
        elif use_bcs is not None:
            bc_seqs = cr_utils.load_csv_rownames(use_bcs)
            bc_indices = matrix.bcs_to_ints(bc_seqs)
            matrix = matrix.select_barcodes(bc_indices)
        elif num_bcs is not None and num_bcs < matrix.bcs_dim:
            bc_indices = np.sort(np.random.choice(np.arange(matrix.bcs_dim), size=num_bcs, replace=False))
            matrix = matrix.select_barcodes(bc_indices)

        if use_genes is not None:
            gene_ids = cr_utils.load_csv_rownames(use_genes)
            gene_indices = matrix.gene_ids_to_ints(gene_ids)
            matrix = matrix.select_genes(gene_indices)

        matrix, _, _ = matrix.select_nonzero_axes()
        return matrix