[r] removed unused variable

bnprks · Dec 14, 2024 · 6381f74 · 6381f74
1 parent 2f83ae6
commit 6381f74
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Showing 3 changed files with 3 additions and 4 deletions.
diff --git a/r/R/transforms.R b/r/R/transforms.R
@@ -936,10 +936,9 @@ regress_out <- function(mat, latent_data, prediction_axis = c("row", "col")) {
 #'  the log normalization of that element, \eqn{\tilde{x}_{ij}} is calculated as:
 #' \eqn{\tilde{x}_{ij} = \log(\frac{x_{ij} \cdot \text{scaleFactor}}{\text{colSum}_j} + 1)}
 #' @export
-normalize_log <- function(mat, scale_factor = 1e4, add_one = TRUE, threads = 1L) {
+normalize_log <- function(mat, scale_factor = 1e4, threads = 1L) {
   assert_is(mat, "IterableMatrix")
   assert_is_numeric(scale_factor)
-  assert_true(is.logical(add_one))
   assert_greater_than_zero(scale_factor)
   read_depth <- matrix_stats(mat, col_stats = c("mean"), threads = threads)$col_stats["mean", ] * nrow(mat)
   mat <- mat %>% multiply_cols(1 / read_depth)

diff --git a/r/man/normalize_log.Rd b/r/man/normalize_log.Rd
diff --git a/r/tests/testthat/test-matrix_transforms.R b/r/tests/testthat/test-matrix_transforms.R
@@ -365,7 +365,7 @@ test_that("tf-idf normalization works", {
 
 
     res <- normalize_tfidf(m2)
-    expect_equal(res %>% as("dgCMatrix"), res_dgc)
+    expect_equal(res %>% as("dgCMatrix"), res_dgc, tolerance = 1e-6)
     res_with_row_means <- normalize_tfidf(m2, feature_means = row_means)
     expect_identical(res, res_with_row_means)