Change default shape parameter in join_features() and join_transcripts() from "long" to "wide", resulting in a return type of SingleCellExperiment by default. Update documentation and tests accordingly.

Author: stemangiola

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidySingleCellExperiment
 Title: Brings SingleCellExperiment to the Tidyverse 
-Version: 1.19.1
+Version: 1.19.2
 Authors@R: c(person("Stefano", "Mangiola", 
     comment=c(ORCID="0000-0001-7474-836X"),
     email="[email protected]",

R/methods.R

@@ -40,7 +40,7 @@ setClass("tidySingleCellExperiment", contains="SingleCellExperiment")
 #' @importFrom stringr str_subset
 #' @export
 setMethod("join_features", "SingleCellExperiment", function(.data,
-    features=NULL, all=FALSE, exclude_zeros=FALSE, shape="long", ...) {
+    features=NULL, all=FALSE, exclude_zeros=FALSE, shape="wide", ...) {
     # CRAN Note
     .cell <- NULL
     .feature <- NULL

R/methods_DEPRECATED.R

@@ -35,7 +35,7 @@ join_transcripts <-
     transcripts=NULL,
     all=FALSE,
     exclude_zeros=FALSE,
-    shape="long", ...)
+    shape="wide", ...)
     {
         UseMethod("join_transcripts", .data)
     }
@@ -45,7 +45,7 @@ join_transcripts.default <-
         transcripts=NULL,
         all=FALSE,
         exclude_zeros=FALSE,
-        shape="long", ...)
+        shape="wide", ...)
     {
         print("tidySingleCellExperiment says:",
             " This function cannot be applied to this object")
@@ -56,7 +56,7 @@ join_transcripts.Seurat <-
         transcripts=NULL,
         all=FALSE,
         exclude_zeros=FALSE,
-        shape="long", ...)
+        shape="wide", ...)
     {
         deprecate_warn(
             "1.1.2", "join_transcripts()", 

inst/NEWS.rd

@@ -15,3 +15,10 @@
     \item Use .cell for cell column name to avoid errors when cell column is defined by the user
 }}
 
+\section{Changes in version 1.5.2, Bioconductor 3.22 Release}{
+\itemize{
+    \item \strong{BREAKING CHANGE}: Changed default shape parameter in \code{join_features()} from "long" to "wide". 
+    This means that \code{join_features()} now returns a SingleCellExperiment object by default instead of a tibble. 
+    To get the old behavior, explicitly specify \code{shape="long"}.
+}}
+

man/join_features.Rd

@@ -12,6 +12,13 @@ test_that("show()", {
 
 test_that("join_features()", {
     gs <- sample(rownames(df), 3)
+    # wide (default)
+    fd <- join_features(df, gs, assay="counts")
+    expect_s4_class(fd, "SingleCellExperiment")
+    expect_null(fd$.feature)
+    expect_identical(
+        unname(t(as.matrix(as_tibble(fd)[, make.names(gs)]))),
+        as.matrix(unname(counts(df)[gs, ])))
     # long
     fd <- join_features(df, gs, shape="long")
     expect_s3_class(fd, "tbl_df")
@@ -20,13 +27,6 @@ test_that("join_features()", {
     expect_identical(
         matrix(fd$.abundance_counts, nrow=length(gs)),
         as.matrix(unname(counts(df)[fd$.feature[seq_along(gs)], ])))
-    # wide
-    fd <- join_features(df, gs, shape="wide", assay="counts")
-    expect_s4_class(fd, "SingleCellExperiment")
-    expect_null(fd$.feature)
-    expect_identical(
-        unname(t(as.matrix(as_tibble(fd)[, make.names(gs)]))),
-        as.matrix(unname(counts(df)[gs, ])))
 })
 
 test_that("as_tibble()", {