From bf36acf6c66039ab6df7d68104b2883ee7a26270 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Thu, 10 Jul 2025 16:12:14 +0930
Subject: [PATCH 01/10] 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.

---
 DESCRIPTION                   |  2 +-
 R/methods.R                   |  2 +-
 R/methods_DEPRECATED.R        |  6 +++---
 inst/NEWS.rd                  |  7 +++++++
 man/join_features.Rd          |  2 +-
 man/join_transcripts.Rd       |  2 +-
 tests/testthat/test-methods.R | 14 +++++++-------
 7 files changed, 21 insertions(+), 14 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e108588..57f69ab 100644
--- a/DESCRIPTION
+++ b/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="mangiolastefano@gmail.com",
diff --git a/R/methods.R b/R/methods.R
index 9d2c679..efee955 100755
--- a/R/methods.R
+++ b/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
diff --git a/R/methods_DEPRECATED.R b/R/methods_DEPRECATED.R
index b832e7f..38a6019 100644
--- a/R/methods_DEPRECATED.R
+++ b/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()", 
diff --git a/inst/NEWS.rd b/inst/NEWS.rd
index c4c99f7..0eb6dde 100644
--- a/inst/NEWS.rd
+++ b/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"}.
+}}
+
diff --git a/man/join_features.Rd b/man/join_features.Rd
index fad2c8c..62f2dc0 100644
--- a/man/join_features.Rd
+++ b/man/join_features.Rd
@@ -10,7 +10,7 @@
   features = NULL,
   all = FALSE,
   exclude_zeros = FALSE,
-  shape = "long",
+  shape = "wide",
   ...
 )
 }
diff --git a/man/join_transcripts.Rd b/man/join_transcripts.Rd
index c4dfa6a..13337d7 100644
--- a/man/join_transcripts.Rd
+++ b/man/join_transcripts.Rd
@@ -9,7 +9,7 @@ join_transcripts(
   transcripts = NULL,
   all = FALSE,
   exclude_zeros = FALSE,
-  shape = "long",
+  shape = "wide",
   ...
 )
 }
diff --git a/tests/testthat/test-methods.R b/tests/testthat/test-methods.R
index b42540e..2d8e52e 100644
--- a/tests/testthat/test-methods.R
+++ b/tests/testthat/test-methods.R
@@ -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()", {

From d3abb3cc93d5681a7c0c941e4afe2d69e1f74def Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Thu, 10 Jul 2025 16:13:31 +0930
Subject: [PATCH 02/10] Update NEWS.rd

---
 inst/NEWS.rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/NEWS.rd b/inst/NEWS.rd
index 0eb6dde..69b4396 100644
--- a/inst/NEWS.rd
+++ b/inst/NEWS.rd
@@ -15,7 +15,7 @@
     \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}{
+\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. 

From 2c9526a373c6ddf0d53a0c4c5fad78532073bf07 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Thu, 10 Jul 2025 21:01:55 +0930
Subject: [PATCH 03/10] Update version to 1.19.2, introduce 'append_samples()'
 method for combining SingleCellExperiment objects, and deprecate
 'bind_rows()' in favor of the new method. Update documentation and examples
 accordingly.

---
 DESCRIPTION                         |  2 +-
 NAMESPACE                           |  2 +
 R/dplyr_methods.R                   | 55 ++++++++++++++++++----
 README.Rmd                          |  2 +-
 README.md                           |  6 +--
 inst/NEWS.rd                        |  8 ++++
 man/append_samples.Rd               | 28 +++++++++++
 man/bind_rows.Rd                    | 72 -----------------------------
 tests/testthat/test-dplyr_methods.R |  4 +-
 vignettes/introduction.Rmd          | 20 +++++++-
 10 files changed, 109 insertions(+), 90 deletions(-)
 create mode 100644 man/append_samples.Rd
 delete mode 100644 man/bind_rows.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index e108588..57f69ab 100644
--- a/DESCRIPTION
+++ b/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="mangiolastefano@gmail.com",
diff --git a/NAMESPACE b/NAMESPACE
index c8e6f8e..a84701d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,6 +2,7 @@
 
 S3method(add_count,SingleCellExperiment)
 S3method(anti_join,SingleCellExperiment)
+S3method(append_samples,SingleCellExperiment)
 S3method(arrange,SingleCellExperiment)
 S3method(as_tibble,SingleCellExperiment)
 S3method(bind_cols,SingleCellExperiment)
@@ -158,6 +159,7 @@ importFrom(tidyr,unnest)
 importFrom(tidyselect,all_of)
 importFrom(tidyselect,eval_select)
 importFrom(ttservice,aggregate_cells)
+importFrom(ttservice,append_samples)
 importFrom(ttservice,bind_cols)
 importFrom(ttservice,bind_rows)
 importFrom(ttservice,join_features)
diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index baec5fc..f8500d1 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -29,14 +29,7 @@ arrange.SingleCellExperiment <- function(.data, ..., .by_group=FALSE) {
 #' @name bind_rows
 #' @rdname bind_rows
 #' @inherit ttservice::bind_rows
-#' 
-#' @examples
-#' data(pbmc_small)
-#' tt <- pbmc_small
-#' bind_rows(tt, tt)
-#'
-#' tt_bind <- tt |> select(nCount_RNA, nFeature_RNA)
-#' tt |> bind_cols(tt_bind)
+#' @noRd
 #' 
 #' @references
 #' Hutchison, W.J., Keyes, T.J., The tidyomics Consortium. et al. The tidyomics ecosystem: enhancing omic data analyses. Nat Methods 21, 1166–1170 (2024). https://doi.org/10.1038/s41592-024-02299-2
@@ -48,6 +41,13 @@ arrange.SingleCellExperiment <- function(.data, ..., .by_group=FALSE) {
 #' @importFrom SingleCellExperiment cbind
 #' @export
 bind_rows.SingleCellExperiment <- function(..., .id=NULL, add.cell.ids=NULL) {
+    lifecycle::deprecate_warn(
+        when = "1.19.2",
+        what = "bind_rows()",
+        with = "append_samples()",
+        details = "bind_rows is not a generic method in dplyr and may cause conflicts. Use append_samples."
+    )
+    
     tts <- flatten_if(dots_values(...), is_spliced)
     
     new_obj <- SingleCellExperiment::cbind(tts[[1]], tts[[2]])
@@ -62,6 +62,45 @@ bind_rows.SingleCellExperiment <- function(..., .id=NULL, add.cell.ids=NULL) {
     new_obj
 }
 
+#' @name append_samples
+#' @rdname append_samples
+#' @title Append samples from multiple SingleCellExperiment objects
+#' 
+#' @description
+#' Append samples from multiple SingleCellExperiment objects by column-binding them.
+#' This function is equivalent to `cbind` but provides a tidyverse-like interface.
+#' 
+#' @param x First SingleCellExperiment object to combine
+#' @param ... Additional SingleCellExperiment objects to combine by samples
+#' @param .id Object identifier (currently not used)
+#' 
+#' @return A combined SingleCellExperiment object
+#' 
+#' @examples
+#' data(pbmc_small)
+#' append_samples(pbmc_small, pbmc_small)
+#' 
+#' @importFrom ttservice append_samples
+#' @importFrom rlang flatten_if
+#' @importFrom rlang is_spliced
+#' @importFrom SingleCellExperiment cbind
+#' @export
+append_samples.SingleCellExperiment <- function(x, ..., .id = NULL) {
+    # Combine all arguments into a list
+    tts <- flatten_if(list(x, ...), is_spliced)
+    new_obj <- do.call(cbind, tts)
+
+    # If duplicated cell names
+    if (any(duplicated(colnames(new_obj)))) {
+        warning("tidySingleCellExperiment says:",
+                " you have duplicated cell names, they will be made unique.")
+        unique_colnames <- make.unique(colnames(new_obj), sep = "_")
+        colnames(new_obj) <- unique_colnames
+    }
+
+    new_obj
+}
+
 #' @importFrom rlang flatten_if
 #' @importFrom rlang is_spliced
 #' @importFrom rlang dots_values
diff --git a/README.Rmd b/README.Rmd
index c3d990f..228cdf0 100755
--- a/README.Rmd
+++ b/README.Rmd
@@ -461,7 +461,7 @@ pbmc_small_nested_interactions <-
             cell_signaling(genes=rownames(data), cluster=cluster) |>
             inter_network(data=data, signal=_, genes=rownames(data), cluster=cluster) %$%
             `individual-networks` |>
-            map_dfr(~ bind_rows(as_tibble(.x)))
+            map_dfr(~ append_samples(as_tibble(.x)))
     }))
 
 pbmc_small_nested_interactions |>
diff --git a/README.md b/README.md
index 9edd55f..b766b72 100755
--- a/README.md
+++ b/README.md
@@ -314,10 +314,6 @@ pbmc_small_pca <-
     ## TRUE, : You're computing too large a percentage of total singular values, use a
     ## standard svd instead.
 
-    ## Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth =
-    ## TRUE, : did not converge--results might be invalid!; try increasing work or
-    ## maxit
-
 ``` r
 pbmc_small_pca
 ```
@@ -742,7 +738,7 @@ pbmc_small_nested_interactions <-
             cell_signaling(genes=rownames(data), cluster=cluster) |>
             inter_network(data=data, signal=_, genes=rownames(data), cluster=cluster) %$%
             `individual-networks` |>
-            map_dfr(~ bind_rows(as_tibble(.x)))
+            map_dfr(~ append_samples(as_tibble(.x)))
     }))
 
 pbmc_small_nested_interactions |>
diff --git a/inst/NEWS.rd b/inst/NEWS.rd
index c4c99f7..cce925b 100644
--- a/inst/NEWS.rd
+++ b/inst/NEWS.rd
@@ -1,6 +1,14 @@
 \name{NEWS}
 \title{News for Package \pkg{tidySingleCellExperiment}}
 
+\section{Changes in version 1.19.2, Bioconductor 3.22 Release}{
+\itemize{
+    \item Soft deprecated \code{bind_rows()} in favor of \code{append_samples()} from ttservice.
+    \item Added \code{append_samples()} method for SingleCellExperiment objects.
+    \item \code{bind_rows()} is not a generic method in dplyr and may cause conflicts.
+    \item Users are encouraged to use \code{append_samples()} instead.
+}}
+
 \section{Changes in version 1.4.0, Bioconductor 3.14 Release}{
 \itemize{
     \item Improved sample_n, and sample_frac functions.
diff --git a/man/append_samples.Rd b/man/append_samples.Rd
new file mode 100644
index 0000000..dc54941
--- /dev/null
+++ b/man/append_samples.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/dplyr_methods.R
+\name{append_samples}
+\alias{append_samples}
+\alias{append_samples.SingleCellExperiment}
+\title{Append samples from multiple SingleCellExperiment objects}
+\usage{
+\method{append_samples}{SingleCellExperiment}(x, ..., .id = NULL)
+}
+\arguments{
+\item{x}{First SingleCellExperiment object to combine}
+
+\item{...}{Additional SingleCellExperiment objects to combine by samples}
+
+\item{.id}{Object identifier (currently not used)}
+}
+\value{
+A combined SingleCellExperiment object
+}
+\description{
+Append samples from multiple SingleCellExperiment objects by column-binding them.
+This function is equivalent to `cbind` but provides a tidyverse-like interface.
+}
+\examples{
+data(pbmc_small)
+append_samples(pbmc_small, pbmc_small)
+
+}
diff --git a/man/bind_rows.Rd b/man/bind_rows.Rd
deleted file mode 100644
index ed34bb5..0000000
--- a/man/bind_rows.Rd
+++ /dev/null
@@ -1,72 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/dplyr_methods.R
-\name{bind_rows}
-\alias{bind_rows}
-\alias{bind_rows.SingleCellExperiment}
-\alias{bind_cols.SingleCellExperiment}
-\alias{bind_cols}
-\title{Efficiently bind multiple data frames by row and column}
-\usage{
-\method{bind_rows}{SingleCellExperiment}(..., .id = NULL, add.cell.ids = NULL)
-
-\method{bind_cols}{SingleCellExperiment}(..., .id = NULL)
-}
-\arguments{
-\item{...}{Data frames to combine.
-
-  Each argument can either be a data frame, a list that could be a data
-  frame, or a list of data frames.
-
-  When row-binding, columns are matched by name, and any missing
-  columns will be filled with NA.
-
-  When column-binding, rows are matched by position, so all data
-  frames must have the same number of rows. To match by value, not
-  position, see mutate-joins.}
-
-\item{.id}{Data frame identifier.
-
-  When `.id` is supplied, a new column of identifiers is
-  created to link each row to its original data frame. The labels
-  are taken from the named arguments to `bind_rows()`. When a
-  list of data frames is supplied, the labels are taken from the
-  names of the list. If no names are found a numeric sequence is
-  used instead.}
-
-\item{add.cell.ids}{from Seurat 3.0 A character vector of length(x = c(x, y)). Appends the corresponding values to the start of each objects' cell names.}
-}
-\value{
-`bind_rows()` and `bind_cols()` return the same type as
-  the first input, either a data frame, `tbl_df`, or `grouped_df`.
-
-`bind_rows()` and `bind_cols()` return the same type as
-  the first input, either a data frame, `tbl_df`, or `grouped_df`.
-}
-\description{
-This is an efficient implementation of the common pattern of
-`do.call(rbind, dfs)` or `do.call(cbind, dfs)` for binding many
-data frames into one.
-
-This is an efficient implementation of the common pattern of
-`do.call(rbind, dfs)` or `do.call(cbind, dfs)` for binding many
-data frames into one.
-}
-\details{
-The output of `bind_rows()` will contain a column if that column
-appears in any of the inputs.
-
-The output of `bind_rows()` will contain a column if that column
-appears in any of the inputs.
-}
-\examples{
-data(pbmc_small)
-tt <- pbmc_small
-bind_rows(tt, tt)
-
-tt_bind <- tt |> select(nCount_RNA, nFeature_RNA)
-tt |> bind_cols(tt_bind)
-
-}
-\references{
-Hutchison, W.J., Keyes, T.J., The tidyomics Consortium. et al. The tidyomics ecosystem: enhancing omic data analyses. Nat Methods 21, 1166–1170 (2024). https://doi.org/10.1038/s41592-024-02299-2
-}
diff --git a/tests/testthat/test-dplyr_methods.R b/tests/testthat/test-dplyr_methods.R
index 46cb83f..755b475 100755
--- a/tests/testthat/test-dplyr_methods.R
+++ b/tests/testthat/test-dplyr_methods.R
@@ -24,9 +24,9 @@ df$factor <- sample(
 #     expect_identical(fd, df)
 # })
 
-test_that("bind_rows()", {
+test_that("append_samples()", {
     # warn about duplicated cells names
-    expect_warning(fd <- bind_rows(df, df))
+    expect_warning(fd <- append_samples(df, df))
     # cell names should be unique after binding
     expect_true(!any(duplicated(pull(fd, .cell))))
 })
diff --git a/vignettes/introduction.Rmd b/vignettes/introduction.Rmd
index 53230ce..d35c039 100755
--- a/vignettes/introduction.Rmd
+++ b/vignettes/introduction.Rmd
@@ -273,6 +273,24 @@ pbmc_small_cluster %>%
         .value=.abundance_counts, scale="column")
 ```
 
+# Combining datasets
+
+We can use `append_samples()` to combine multiple SingleCellExperiment objects by samples.
+This is useful when you have multiple datasets that you want to analyze together.
+
+```{r}
+# Create two subsets of the data
+pbmc_subset1 <- pbmc_small_cluster %>%
+    filter(groups == "g1")
+
+pbmc_subset2 <- pbmc_small_cluster %>%
+    filter(groups == "g2")
+
+# Combine them using append_samples
+combined_data <- append_samples(pbmc_subset1, pbmc_subset2)
+combined_data
+```
+
 # Reduce dimensions
 
 We can calculate the first 3 UMAP dimensions using `r BiocStyle::Biocpkg("scater")`.
@@ -454,7 +472,7 @@ pbmc_small_nested_interactions <-
             cell_signaling(genes=rownames(data), cluster=cluster) %>%
             inter_network(data=data, signal=., genes=rownames(data), cluster=cluster) %$%
             `individual-networks` %>%
-            map_dfr(~ bind_rows(as_tibble(.x)))
+            map_dfr(~ append_samples(as_tibble(.x)))
     }))
 
 pbmc_small_nested_interactions %>%

From f42ad3ace57fa26b6b777809b800541072f5bac4 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Fri, 11 Jul 2025 13:19:29 +0930
Subject: [PATCH 04/10] Update vignette formatting to use prettydoc with new
 options for improved presentation, including table of contents and section
 numbering.

---
 vignettes/introduction.Rmd | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/vignettes/introduction.Rmd b/vignettes/introduction.Rmd
index 53230ce..68c68b1 100755
--- a/vignettes/introduction.Rmd
+++ b/vignettes/introduction.Rmd
@@ -3,8 +3,13 @@ title: "Overview of the tidySingleCellExperiment package"
 package: "`r BiocStyle::pkg_ver('tidySingleCellExperiment')`"
 author: "Stefano Mangiola"
 output:
-  BiocStyle::html_document:
-    toc_float: true
+  prettydoc::html_pretty:
+    theme: cayman
+    toc: yes
+    toc_depth: 2
+    number_sections: yes
+    fig_caption: yes
+    df_print: paged
 bibliography: tidySingleCellExperiment.bib
 vignette: >
   %\VignetteIndexEntry{Overview of the tidySingleCellExperiment package}

From 2db3d0db14c2f0cab210a736089a372cf7d83244 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Fri, 11 Jul 2025 13:33:03 +0930
Subject: [PATCH 05/10] Update vignette formatting options in introduction.Rmd
 to enable table of contents, section numbering, and figure captions for
 enhanced readability.

---
 vignettes/introduction.Rmd | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/vignettes/introduction.Rmd b/vignettes/introduction.Rmd
index 68c68b1..10b7b32 100755
--- a/vignettes/introduction.Rmd
+++ b/vignettes/introduction.Rmd
@@ -5,10 +5,10 @@ author: "Stefano Mangiola"
 output:
   prettydoc::html_pretty:
     theme: cayman
-    toc: yes
+    toc: true
     toc_depth: 2
-    number_sections: yes
-    fig_caption: yes
+    number_sections: true
+    fig_caption: true
     df_print: paged
 bibliography: tidySingleCellExperiment.bib
 vignette: >

From 63bb13a1d619fba2134f8fa99deb5f22e5e0c089 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Fri, 11 Jul 2025 13:48:36 +0930
Subject: [PATCH 06/10] add prettydoc

---
 DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e108588..b9dcb56 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -60,7 +60,8 @@ Suggests:
     celldex,
     dittoSeq,
     plotly,
-    rbibutils
+    rbibutils,
+    prettydoc
 VignetteBuilder: 
     knitr
 RdMacros:

From 94fc42859ab306243623bc774a9dfd8f15fd9024 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Thu, 10 Jul 2025 16:12:14 +0930
Subject: [PATCH 07/10] 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.

---
 R/methods.R                   |  2 +-
 R/methods_DEPRECATED.R        |  6 +++---
 inst/NEWS.rd                  |  7 +++++++
 man/join_features.Rd          |  2 +-
 man/join_transcripts.Rd       |  2 +-
 tests/testthat/test-methods.R | 14 +++++++-------
 6 files changed, 20 insertions(+), 13 deletions(-)

diff --git a/R/methods.R b/R/methods.R
index 9d2c679..efee955 100755
--- a/R/methods.R
+++ b/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
diff --git a/R/methods_DEPRECATED.R b/R/methods_DEPRECATED.R
index b832e7f..38a6019 100644
--- a/R/methods_DEPRECATED.R
+++ b/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()", 
diff --git a/inst/NEWS.rd b/inst/NEWS.rd
index cce925b..c60bfb8 100644
--- a/inst/NEWS.rd
+++ b/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 1.5.2, 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"}.
+}}
+
diff --git a/man/join_features.Rd b/man/join_features.Rd
index fad2c8c..62f2dc0 100644
--- a/man/join_features.Rd
+++ b/man/join_features.Rd
@@ -10,7 +10,7 @@
   features = NULL,
   all = FALSE,
   exclude_zeros = FALSE,
-  shape = "long",
+  shape = "wide",
   ...
 )
 }
diff --git a/man/join_transcripts.Rd b/man/join_transcripts.Rd
index c4dfa6a..13337d7 100644
--- a/man/join_transcripts.Rd
+++ b/man/join_transcripts.Rd
@@ -9,7 +9,7 @@ join_transcripts(
   transcripts = NULL,
   all = FALSE,
   exclude_zeros = FALSE,
-  shape = "long",
+  shape = "wide",
   ...
 )
 }
diff --git a/tests/testthat/test-methods.R b/tests/testthat/test-methods.R
index b42540e..2d8e52e 100644
--- a/tests/testthat/test-methods.R
+++ b/tests/testthat/test-methods.R
@@ -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()", {

From b1f0192269b62184c030f807aa2da4cb18e9fbe2 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Thu, 10 Jul 2025 16:13:31 +0930
Subject: [PATCH 08/10] Update NEWS.rd

---
 inst/NEWS.rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/NEWS.rd b/inst/NEWS.rd
index c60bfb8..23d1858 100644
--- a/inst/NEWS.rd
+++ b/inst/NEWS.rd
@@ -23,7 +23,7 @@
     \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}{
+\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. 

From 195a24b33ffd5c9ae2f508d91666256558ce4a76 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Thu, 23 Oct 2025 22:03:29 +1030
Subject: [PATCH 09/10] Modify import statements for dplyr and tidyr, enhance
 documentation links, and refine example code in the introduction vignette for
 clarity and uniqueness.

---
 DESCRIPTION                | 4 ++--
 NAMESPACE                  | 1 +
 R/dplyr_methods.R          | 2 +-
 R/methods.R                | 5 ++++-
 R/tidyr_methods.R          | 1 +
 man/group_by.Rd            | 2 +-
 vignettes/introduction.Rmd | 7 ++++---
 7 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 09dfc7e..247b189 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: tidySingleCellExperiment
 Title: Brings SingleCellExperiment to the Tidyverse 
-Version: 1.19.2
+Version: 1.19.3
 Authors@R: c(person("Stefano", "Mangiola", 
     comment=c(ORCID="0000-0001-7474-836X"),
     email="mangiolastefano@gmail.com",
@@ -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
diff --git a/NAMESPACE b/NAMESPACE
index a84701d..423ce68 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index f8500d1..8b77667 100755
--- a/R/dplyr_methods.R
+++ b/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)
diff --git a/R/methods.R b/R/methods.R
index efee955..8c2b7f2 100755
--- a/R/methods.R
+++ b/R/methods.R
@@ -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
diff --git a/R/tidyr_methods.R b/R/tidyr_methods.R
index c2af43e..da6e406 100755
--- a/R/tidyr_methods.R
+++ b/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) {
 
diff --git a/man/group_by.Rd b/man/group_by.Rd
index b88b8a3..35cbbc3 100644
--- a/man/group_by.Rd
+++ b/man/group_by.Rd
@@ -101,5 +101,5 @@ Hutchison, W.J., Keyes, T.J., The tidyomics Consortium. et al. The tidyomics eco
 Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, et al. Welcome to the tidyverse. Journal of Open Source Software. 2019;4(43):1686. https://doi.org/10.21105/joss.01686
 }
 \seealso{
-\code{}
+\code{\link[dplyr]{group_by}}
 }
diff --git a/vignettes/introduction.Rmd b/vignettes/introduction.Rmd
index fc79f5f..5213f27 100755
--- a/vignettes/introduction.Rmd
+++ b/vignettes/introduction.Rmd
@@ -184,7 +184,7 @@ Here we plot abundance of two features for each group.
 
 ```{r}
 pbmc_small_polished %>%
-    join_features(features=c("HLA-DRA", "LYZ")) %>%
+    join_features(features=c("HLA-DRA", "LYZ"), shape="long") %>%
     ggplot(aes(groups, .abundance_counts + 1, fill=groups)) +
     geom_boxplot(outlier.shape=NA) +
     geom_jitter(aes(size=nCount_RNA), alpha=0.5, width=0.2) +
@@ -267,11 +267,12 @@ marker_genes <-
     map(~ .x %>%
         head(10) %>%
         rownames()) %>%
-    unlist()
+    unlist() %>%
+    unique()
 
 # Plot heatmap
 pbmc_small_cluster %>%
-    join_features(features=marker_genes) %>%
+    join_features(features=marker_genes, shape="long") %>%
     group_by(label) %>%
     heatmap(
         .row=.feature, .column=.cell, 

From cd7ce8aeaa1fd1dffebdd15b7679db3e071ea466 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Thu, 23 Oct 2025 22:19:56 +1030
Subject: [PATCH 10/10] Update package version to 1.19.2

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 247b189..f0d7439 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: tidySingleCellExperiment
 Title: Brings SingleCellExperiment to the Tidyverse 
-Version: 1.19.3
+Version: 1.19.2
 Authors@R: c(person("Stefano", "Mangiola", 
     comment=c(ORCID="0000-0001-7474-836X"),
     email="mangiolastefano@gmail.com",