diff --git a/src/metrics/coranking/config.vsh.yaml b/src/metrics/coranking/config.vsh.yaml index a269ca6..6984492 100644 --- a/src/metrics/coranking/config.vsh.yaml +++ b/src/metrics/coranking/config.vsh.yaml @@ -103,8 +103,9 @@ engines: - type: r cran: - coRanking + - Rfast runners: - type: executable - type: nextflow directives: - label: [hightime, lowmem, lowcpu] + label: [hightime, midmem, lowcpu] diff --git a/src/metrics/coranking/script.R b/src/metrics/coranking/script.R index a835bdb..170e6e3 100644 --- a/src/metrics/coranking/script.R +++ b/src/metrics/coranking/script.R @@ -30,8 +30,8 @@ if (any(is.na(X_emb))) { # TODO: computing a square distance matrix is problematic for large datasets! # TODO: should we use a different distance metric for the high_dim? # TODO: or should we subset to the HVG? - dist_highdim <- coRanking:::euclidean(as.matrix(high_dim)) - dist_emb <- coRanking:::euclidean(as.matrix(X_emb)) + dist_highdim <- Rfast::Dist(as.matrix(high_dim)) + dist_emb <- Rfast::Dist(as.matrix(X_emb)) message("Compute ranking matrices") rmat_highdim <- rankmatrix(dist_highdim, input = "dist")