tidyomics · stemangiola · Jul 10, 2025 · Jul 10, 2025 · Jul 10, 2025 · Jul 11, 2025
diff --git 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",
@@ -60,7 +60,8 @@ Suggests:
     celldex,
     dittoSeq,
     plotly,
-    rbibutils
+    rbibutils,
+    prettydoc
 VignetteBuilder: 
     knitr
 RdMacros:

diff --git 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
@@ -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/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
@@ -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/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
@@ -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
@@ -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.
@@ -15,3 +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"}.
+}}
+
diff --git a/man/append_samples.Rd b/man/append_samples.Rd
diff --git a/man/bind_rows.Rd b/man/bind_rows.Rd
diff --git a/man/join_features.Rd b/man/join_features.Rd
diff --git a/man/join_transcripts.Rd b/man/join_transcripts.Rd
diff --git 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/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()", {