Function run_differential_expression

src/memory/processing/diffexp/mod.rs:445–509

(
    adata: &IMAnnData,
    csr_matrix: &CsrMatrix<T>,
    groups_to_test: &[String],
    reference_group: &Option<String>,
    groupby: &str,
    method: TestMethod,
    correction_method: Correctio

#[allow(clippy::too_many_arguments)]
fn run_differential_expression<T>(
    adata: &IMAnnData,
    csr_matrix: &CsrMatrix<T>,
    groups_to_test: &[String],
    reference_group: &Option<String>,
    groupby: &str,
    method: TestMethod,
    correction_method: CorrectionMethod,
    compute_lfc: bool,
    pseudocount: f64,
    n_genes: usize,
    var_names: &[String],
) -> anyhow::Result<DifferentialExpressionResults>
where
    T: FloatOpsTS,
    CsrMatrix<T>: MatrixStatTests<T>,
{
    let mut scores_map: HashMap<String, Vec<f64>> = HashMap::new();
    let mut pvals_map: HashMap<String, Vec<f64>> = HashMap::new();
    let mut pvals_adj_map: HashMap<String, Vec<f64>> = HashMap::new();
    let mut logfoldchanges_map: HashMap<String, Vec<f64>> = HashMap::new();
    let mut gene_names_map: HashMap<String, Vec<String>> = HashMap::new();

    for group in groups_to_test {
        let group_indices = get_group_indices(adata, groupby, group)?;
        let reference_indices = match reference_group {
            None => {
                let mut all_indices: Vec<usize> = (0..adata.n_obs()).collect();
                all_indices.retain(|&idx| !group_indices.contains(&idx));

                if all_indices.is_empty() {
                    return Err(anyhow::anyhow!("No cells found in reference group: rest"));
                }
                all_indices
            }
            Some(reference_group) => get_group_indices(adata, groupby, reference_group)?,
        };

        let group_results = run_tests_for_group(
            csr_matrix,
            &group_indices,
            &reference_indices,
            method,
            correction_method.clone(),
            compute_lfc,
            pseudocount,
            n_genes,
            var_names,
        )?;

        scores_map.insert(group.clone(), group_results.scores);
        pvals_map.insert(group.clone(), group_results.pvals);
        pvals_adj_map.insert(group.clone(), group_results.pvals_adj);
        logfoldchanges_map.insert(group.clone(), group_results.logfoldchanges);
        gene_names_map.insert(group.clone(), group_results.gene_names);
    }

    Ok(DifferentialExpressionResults {