Update plotExpression.R (#211)

* Update plotExpression.R Ensure `log2_values` actually does what it's supposed to * Add unit test * Bump version --------- Co-authored-by: Alan O'Callaghan <[email protected]>
alanocallaghan · Jul 18, 2024 · d14427e · d14427e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -12,8 +12,8 @@ Authors@R: c(
         person("Leo", "Lahti", role=c("ctb"), email="[email protected]", comment = c(ORCID = "0000-0001-5537-637X")),
         person("Tuomas", "Borman", role = c("ctb"), comment = c(ORCID = "0000-0002-8563-8884"))
     )
-Version: 1.33.3
-Date: 2024-07-16
+Version: 1.33.4
+Date: 2024-07-18
 License: GPL-3
 Title: Single-Cell Analysis Toolkit for Gene Expression Data in R
 Description: A collection of tools for doing various analyses of

diff --git a/R/plotExpression.R b/R/plotExpression.R
@@ -142,7 +142,7 @@ plotExpression <- function(object, features, x = NULL,
     nfeatures <- length(features)
 
     if (log2_values) {
-        exprs_val <- lapply(exprs_vals, function(x) log2(x + 1))
+        exprs_vals <- lapply(exprs_vals, function(x) log2(x + 1))
         ylab <- paste0("Expression (", assay.type, "; log2-scale)")
     } else {
         ylab <- paste0("Expression (", assay.type, ")")

diff --git a/tests/testthat/test-plot-exprs.R b/tests/testthat/test-plot-exprs.R
@@ -84,3 +84,10 @@ test_that("plotExpression with binning", {
                                  bins = 10, colour_by = "Gene_0002", hex = TRUE,
                                  summary_fun = "mean"))
 })
+
+
+test_that("log2_values works as expected", {
+    g1 <- plotExpression(example_sce, features=rownames(example_sce)[1:10], assay.type="counts", log2_values=FALSE)
+    g2 <- plotExpression(example_sce, features=rownames(example_sce)[1:10], assay.type="counts", log2_values=TRUE)
+    expect_false(isTRUE(all.equal(g1$data$Y, g2$data$Y)))
+})