bug fix: use reshape2::melt instead of stats::reshape (#329)

stats::reshape would munge values (typically gene names)
waldronlab · May 1, 2024 · 82691c6 · 82691c6
1 parent 1ebad2f
commit 82691c6
Show file tree

Hide file tree

Showing 3 changed files with 32 additions and 22 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -11,11 +11,11 @@ Authors@R: c(
     person("Vincent J", "Carey", , , c("aut", "ctb")),
     person("Levi", "Waldron", , "lwaldron.research@gmail.com", "aut"),
     person("MultiAssay", "SIG", , "biocmultiassay@googlegroups.com", "ctb"))
-Description: MultiAssayExperiment harmonizes data management of multiple
-    experimental assays performed on an overlapping set of specimens.  It
-    provides a familiar Bioconductor user experience by extending concepts
-    from SummarizedExperiment, supporting an open-ended mix of standard
-    data classes for individual assays, and allowing subsetting by genomic
+Description: Harmonize data management of multiple experimental assays
+    performed on an overlapping set of specimens.  It provides a familiar
+    Bioconductor user experience by extending concepts from
+    SummarizedExperiment, supporting an open-ended mix of standard data
+    classes for individual assays, and allowing subsetting by genomic
     ranges or rownames. Facilities are provided for reshaping data into
     wide and long formats for adaptability to graphing and downstream
     analysis.
@@ -33,7 +33,6 @@ Imports:
     IRanges,
     methods,
     S4Vectors (>= 0.23.19),
-    stats,
     tidyr,
     utils
 Suggests:
@@ -43,6 +42,7 @@ Suggests:
     maftools (>= 2.7.10),
     R.rsp,
     RaggedExperiment,
+    reshape2,
     rmarkdown,
     survival,
     survminer,

diff --git a/R/MultiAssayExperiment-helpers.R b/R/MultiAssayExperiment-helpers.R
@@ -340,27 +340,20 @@ setMethod("mergeReplicates", "ANY",
 
 .longFormatANY <- function(object, i) {
     rowNAMES <- rownames(object)
-    nullROWS <- is.null(rowNAMES)
-    if (nullROWS)
-        rowNAMES <- as.character(seq_len(nrow(object)))
+    if (is.null(rowNAMES))
+        rowNames <- as.character(seq_len(nrow(object)))
 
     if (is(object, "ExpressionSet"))
         object <- Biobase::exprs(object)
     if (is(object, "SummarizedExperiment") || is(object, "RaggedExperiment"))
         object <- assay(object, i = i)
-    if (is(object, "matrix"))
-        object <- as.data.frame(object)
-
-    ## use stats::reshape instead of reshape2::melt
-    if (nullROWS)
-        rownames(object) <- rowNAMES
-    object <- stats::reshape(object, idvar = "rowname",
-        ids = rownames(object), times = names(object),
-        timevar = "colname", varying = list(names(object)),
-        direction = "long", v.names = "value")
-    ## Reshape leaves rownames even if new.row.names = NULL
-    rownames(object) <- NULL
-    object[, c("rowname", "colname", "value")]
+
+    if (!requireNamespace("reshape2", quietly = TRUE))
+        stop("Package 'reshape2' is required for 'longFormat()' conversion")
+
+    reshape2::melt(
+        object, varnames = c("rowname", "colname"), value.name = "value"
+    )
 }
 
 .longFormatElist <- function(object, i) {

diff --git a/tests/testthat/test-MultiAssayExperiment-helpers.R b/tests/testthat/test-MultiAssayExperiment-helpers.R
@@ -238,3 +238,20 @@ test_that("renaming helpers work", {
         newaffynames
     )
 })
+
+
+test_that(".longFormatANY works", {
+    denv <- new.env(parent = emptyenv())
+    data("miniACC", package="MultiAssayExperiment", envir = denv)
+    miniACC <- denv[["miniACC"]]
+
+    expect_silent(
+        longdf <- longFormat(miniACC)
+    )
+    expect_true(
+        all(
+            as.character(longdf[["rowname"]]) %in%
+                Reduce(union, rownames(miniACC))
+        )
+    )
+})