Merge pull request #115 from tidyomics/change-default-to-wide-for-join_features

Change default shape parameter in join_features() and join_transcript…

Author: stemangiola

DESCRIPTION

@@ -71,6 +71,6 @@ biocViews:
     AssayDomain, Infrastructure, RNASeq, DifferentialExpression, SingleCell,
     GeneExpression, Normalization, Clustering, QualityControl, Sequencing
 Encoding: UTF-8
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 URL: https://github.com/stemangiola/tidySingleCellExperiment
 BugReports: https://github.com/stemangiola/tidySingleCellExperiment/issues

NAMESPACE

@@ -83,6 +83,7 @@ importFrom(dplyr,group_split)
 importFrom(dplyr,inner_join)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
+importFrom(dplyr,n)
 importFrom(dplyr,pull)
 importFrom(dplyr,rename)
 importFrom(dplyr,right_join)

R/dplyr_methods.R

@@ -198,7 +198,7 @@ filter.SingleCellExperiment <- function(.data, ..., .preserve=FALSE) {
 #' @name group_by
 #' @rdname group_by
 #' @inherit dplyr::group_by
-#' @seealso \code{}
+#' @seealso \code{\link[dplyr]{group_by}}
 #'
 #' @examples
 #' data(pbmc_small)

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
@@ -157,7 +157,7 @@ tidy.SingleCellExperiment <- function(object) {
 #' @importFrom dplyr mutate
 #' @importFrom dplyr pull
 #' @importFrom dplyr left_join
-#' @importFrom dplyr unnest
+#' @importFrom tidyr unnest
 #' @importFrom S4Vectors DataFrame
 #' @importFrom methods as
 #'
@@ -170,6 +170,9 @@ setMethod("aggregate_cells", "SingleCellExperiment", function(.data,
 
     # Fix NOTEs
     feature <- NULL
+    .feature <- NULL
+    my_id_to_split_by___ <- NULL
+    assay_name <- NULL
     .sample <- enquo(.sample)
 
     # Subset only wanted assays

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()", 

R/tidyr_methods.R

@@ -93,6 +93,7 @@ unnest_single_cell_experiment  <-  function(data, cols, ...,
 #' @importFrom tidyr nest
 #' @importFrom rlang enquos
 #' @importFrom rlang :=
+#' @importFrom dplyr n
 #' @export
 nest.SingleCellExperiment <- function(.data, ..., .names_sep = NULL) {
 

inst/NEWS.rd

@@ -23,3 +23,10 @@
     \item Use .cell for cell column name to avoid errors when cell column is defined by the user
 }}
 
+\section{Changes in version 1.19.2, 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"}.
+}}
+