inst/testme/test-futurize-GSVA.R

In futurize: Parallelize Common Functions via One Magic Function

#' @tags skip_on_cran  ## (20s) to limit total check time
if (requireNamespace("GSVA") && requireNamespace("doFuture")) {
library(futurize)
library(GSVA)
print(sessionInfo())

options(future.rng.onMisuse = "error")

plan(multisession)

## Create simple test data
set.seed(42)
n_genes <- 120L    # > 100 for gsva() to parallelize
n_samples <- 120L  # > 100 for gsva() to parallelize
expr <- matrix(rnorm(n_genes * n_samples), nrow = n_genes, ncol = n_samples)
rownames(expr) <- paste0("gene", seq_len(n_genes))
colnames(expr) <- paste0("sample", seq_len(n_samples))

geneSets <- list(
  geneSet1 = paste0("gene", sample(n_genes, 10L)),
  geneSet2 = paste0("gene", sample(n_genes, 15L)),
  geneSet3 = paste0("gene", sample(n_genes, 20L))
)

## gsva() in GSVA (< 2.4) relies on BiocParallel::bpiterate(),
## which does _not_ support DoparParam by design.
if ("gsva" %in% futurize_supported_functions("GSVA")) {
  ## ---------------------------------------------------------
  ## gsva() with gsvaParam()
  ## ---------------------------------------------------------
  param <- gsvaParam(expr, geneSets)
  
  set.seed(42)
  result_truth <- gsva(param, verbose = FALSE)
  str(result_truth)
  
  set.seed(42)
  counters <- plan("backend")[["counters"]]
  result <- gsva(param, verbose = FALSE) |> futurize()
  delta <- plan("backend")[["counters"]] - counters
  cat(sprintf("Futures created: %d\n", delta[["created"]]))
  stopifnot(delta[["created"]] > 0L)
  str(result)
  stopifnot(all.equal(result, result_truth))
  
  set.seed(42)
  counters <- plan("backend")[["counters"]]
  result2 <- GSVA::gsva(param, verbose = FALSE) |> futurize()
  delta <- plan("backend")[["counters"]] - counters
  cat(sprintf("Futures created: %d\n", delta[["created"]]))
  stopifnot(delta[["created"]] > 0L)
  stopifnot(all.equal(result2, result_truth))


  ## ---------------------------------------------------------
  ## gsva() with ssgseaParam()
  ## ---------------------------------------------------------
  param_ssgsea <- ssgseaParam(expr, geneSets)
  
  set.seed(42)
  result_truth <- gsva(param_ssgsea, verbose = FALSE)
  str(result_truth)
  
  set.seed(42)
  counters <- plan("backend")[["counters"]]
  result <- gsva(param_ssgsea, verbose = FALSE) |> futurize()
  delta <- plan("backend")[["counters"]] - counters
  cat(sprintf("Futures created: %d\n", delta[["created"]]))
  stopifnot(delta[["created"]] > 0L)
  str(result)
  stopifnot(all.equal(result, result_truth))
  
  
  ## ---------------------------------------------------------
  ## gsva() with plageParam()
  ## ---------------------------------------------------------
  param_plage <- plageParam(expr, geneSets)
  
  set.seed(42)
  result_truth <- gsva(param_plage, verbose = FALSE)
  str(result_truth)
  
  set.seed(42)
  counters <- plan("backend")[["counters"]]
  result <- gsva(param_plage, verbose = FALSE) |> futurize()
  delta <- plan("backend")[["counters"]] - counters
  cat(sprintf("Futures created: %d\n", delta[["created"]]))
  stopifnot(delta[["created"]] > 0L)
  str(result)
  stopifnot(all.equal(result, result_truth))
} ## if ("gsva" %in% futurize_supported_functions("GSVA"))  

plan(sequential)
} ## if (requireNamespace("GSVA") && ...)