[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2
+    rev: v0.4.3.9015
     hooks:
       - id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style]
@@ -12,12 +12,12 @@ repos:
       - id: no-debug-statement
       - id: deps-in-desc
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v6.0.0
     hooks:
       - id: end-of-file-fixer
         exclude: '\.Rd'
   - repo: https://github.com/pre-commit-ci/pre-commit-ci-config
-    rev: v1.5.1
+    rev: v1.6.1
     hooks:
       # Only reuiqred when https://pre-commit.ci is used for config validation
       - id: check-pre-commit-ci-config
@@ -31,7 +31,7 @@ repos:
         exclude: "inst/extdata/.*"
         # `exclude: <regex>` to allow committing specific files
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v2.7.1
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
 

DESCRIPTION

@@ -14,7 +14,7 @@ Description: SimBu can be used to simulate bulk RNA-seq datasets with known cell
 License: GPL-3 + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE) 
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.3
 Imports: 
     basilisk,
     BiocParallel,

R/basilisk.R

@@ -1,4 +1,3 @@
-
 # dependencies for sfaira and anndata0.7.6 (taken from zellkonverter package)
 SimBu_env <- basilisk::BasiliskEnvironment(
   envname = "SimBu_env_1_1_1",

R/census.R

@@ -1,4 +1,3 @@
-
 #' Applies the Census count transformation on a count matrix
 #'
 #' needs a sparse matrix with cells in columns and genes in rows. You can find the detailed explaination here:

R/simulator.R

@@ -74,7 +74,7 @@ simulate_sample <- function(data,
       if (n == 0) {
         n <- 1
       }
-      if(!is.na(seed)){
+      if (!is.na(seed)) {
         # fix seed for random selection of cells
         set.seed(seed)
       }
@@ -437,7 +437,6 @@ simulate_bulk <- function(data,
 
   # sample cells and generate pseudo-bulk profiles
   all_samples <- BiocParallel::bplapply(seq_along(simulation_vector_list), function(i) {
-
     simulation_vector <- simulation_vector_list[[i]]
     sample <- simulate_sample(
       data = data,
@@ -454,22 +453,24 @@ simulate_bulk <- function(data,
     return(sample)
   }, BPPARAM = BPPARAM)
 
-  bulk_counts <- Matrix::Matrix(vapply(
-    X = all_samples,
-    FUN = "[[",
-    ... = 1,
-    FUN.VALUE = double(dim(SummarizedExperiment::assays(data)[["counts"]])[1])
-  ),
-  sparse = TRUE
-  )
-  if ("tpm" %in% names(SummarizedExperiment::assays(data))) {
-    bulk_tpm <- Matrix::Matrix(vapply(
+  bulk_counts <- Matrix::Matrix(
+    vapply(
       X = all_samples,
       FUN = "[[",
-      ... = 2,
-      FUN.VALUE = double(dim(SummarizedExperiment::assays(data)[["tpm"]])[1])
+      ... = 1,
+      FUN.VALUE = double(dim(SummarizedExperiment::assays(data)[["counts"]])[1])
     ),
     sparse = TRUE
+  )
+  if ("tpm" %in% names(SummarizedExperiment::assays(data))) {
+    bulk_tpm <- Matrix::Matrix(
+      vapply(
+        X = all_samples,
+        FUN = "[[",
+        ... = 2,
+        FUN.VALUE = double(dim(SummarizedExperiment::assays(data)[["tpm"]])[1])
+      ),
+      sparse = TRUE
     )
     assays <- list(bulk_counts = bulk_counts, bulk_tpm = bulk_tpm)
   } else {

tests/testthat/test_simulator.R

@@ -48,15 +48,14 @@ test_that("test RNG", {
   seed <- 123
   sim1 <- SimBu::simulate_bulk(data = dataset, scenario = "even", scaling_factor = "NONE", balance_even_mirror_scenario = 0, nsamples = 10, ncells = 100, run_parallel = FALSE, seed = seed)
   sim2 <- SimBu::simulate_bulk(data = dataset, scenario = "even", scaling_factor = "NONE", balance_even_mirror_scenario = 0, nsamples = 10, ncells = 100, run_parallel = FALSE, seed = seed)
-  x1 <- Matrix::rowSums(assays(sim1$bulk)[['bulk_counts']])
-  x2 <- Matrix::rowSums(assays(sim2$bulk)[['bulk_counts']])
-  testthat::expect_equal(x1,x2)
-
-  # test that samples inside one simulation still are different
-  sample1 <- sim1$bulk[,1]
-  sample2 <- sim1$bulk[,2]
-  testthat::expect_false(all(assays(sample1)[['bulk_counts']] == assays(sample2)[['bulk_counts']]))
+  x1 <- Matrix::rowSums(assays(sim1$bulk)[["bulk_counts"]])
+  x2 <- Matrix::rowSums(assays(sim2$bulk)[["bulk_counts"]])
+  testthat::expect_equal(x1, x2)
 
+  # test that samples inside one simulation still are different
+  sample1 <- sim1$bulk[, 1]
+  sample2 <- sim1$bulk[, 2]
+  testthat::expect_false(all(assays(sample1)[["bulk_counts"]] == assays(sample2)[["bulk_counts"]]))
 })
 
 test_that("test different scaling factor calculations + mRNA bias removal from counts", {