fix mean-based CoNGAfy

add specific Matrix:: to function and testthat for mean values
ncborcherding · Apr 12, 2024 · e62c250 · e62c250
1 parent 9384510
commit e62c250
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Showing 4 changed files with 16 additions and 3 deletions.
diff --git a/R/CoNGAfy.R b/R/CoNGAfy.R
@@ -117,7 +117,7 @@ CoNGA.dist <- function(sc, features, assay) {
 }
 # Adapted from the AverageExpression() function in Seurat
 #' @importFrom rlang %||%
-#' @importFrom Matrix sparse.model.matrix
+#' @importFrom Matrix sparse.model.matrix colSums
 #' @importFrom SummarizedExperiment assay
 #' @importFrom stats as.formula
 CoNGA.mean <- function(sc, features, assay) {
@@ -152,7 +152,7 @@ CoNGA.mean <- function(sc, features, assay) {
             )
         )
     ))
-    colsums <- colSums(x = category.matrix)
+    colsums <- Matrix::colSums(x = category.matrix)
     category.matrix <- category.matrix[, colsums > 0]
     colsums <- colsums[colsums > 0]
 

diff --git a/tests/testthat/test-CoNGAfy.R b/tests/testthat/test-CoNGAfy.R
@@ -4,7 +4,6 @@ test_that("CoNGAfy works", {
 
   data("ibex_example")
 
-
   conga_reduction <- CoNGAfy(ibex_example)
 
   expect_equal(
@@ -17,4 +16,18 @@ test_that("CoNGAfy works", {
     getdata("CoNGAfy", "CoNGAfy_counts"),
     tolerance=1e-2
   )
+
+  conga_mean_reduction <- CoNGAfy(ibex_example,
+                                  method = "mean")
+
+  expect_equal(
+    conga_mean_reduction@meta.data,
+    getdata("CoNGAfy", "CoNGAfy_mean_meta.data")
+  )
+
+  expect_equal(
+    conga_mean_reduction@assays$RNA@layers$counts,
+    getdata("CoNGAfy", "CoNGAfy_mean_counts"),
+    tolerance=1e-2
+  )
 })
diff --git a/tests/testthat/testdata/CoNGAfy/CoNGAfy_mean_counts.rds b/tests/testthat/testdata/CoNGAfy/CoNGAfy_mean_counts.rds
diff --git a/tests/testthat/testdata/CoNGAfy/CoNGAfy_mean_meta.data.rds b/tests/testthat/testdata/CoNGAfy/CoNGAfy_mean_meta.data.rds