From 9dfd97e301335093806df014f5d21339d0ba42fb Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Sun, 15 Oct 2023 17:18:24 +1000
Subject: [PATCH 01/20] group_split by column

---
 R/dplyr_methods.R                   |  29 ++++++++++++++++++++++++++++
 tests/testthat/Rplots.pdf           | Bin 0 -> 5794 bytes
 tests/testthat/test-dplyr_methods.R |   7 +++++++
 3 files changed, 36 insertions(+)
 create mode 100644 tests/testthat/Rplots.pdf

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index db079f9..9418d5a 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -875,3 +875,32 @@ pull.SingleCellExperiment <- function(.data, var=-1, name=NULL, ...) {
         as_tibble() %>%
         dplyr::pull(var=!!var, name=!!name, ...)
 }
+
+#' @name group_split
+#' @rdname group_split
+#' @inherit dplyr::group_split
+#'
+#' @param .data 
+#'
+#' @return
+#' @export
+#'
+#' @examples
+#' data(pbmc_small)
+#' pbmc_small |> group_split(pbmc_small, groups)
+group_split.SingleCellExperiment <- function(.data, var) {
+    var <- enquo(var)
+    
+    var_list <- .data |> 
+        as_tibble() |> 
+        select(!!var) |> 
+        unlist(use.names = FALSE)
+    
+    groups <- unique(var_list)
+    
+    v <- vector(mode = "list", length = length(groups))
+    
+    for (n in seq_along(groups)) { v[[n]] <- .data[, var_list == groups[[n]]] }
+    
+    v
+}
diff --git a/tests/testthat/Rplots.pdf b/tests/testthat/Rplots.pdf
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diff --git a/tests/testthat/test-dplyr_methods.R b/tests/testthat/test-dplyr_methods.R
index 9e01f96..4b5c7de 100755
--- a/tests/testthat/test-dplyr_methods.R
+++ b/tests/testthat/test-dplyr_methods.R
@@ -318,3 +318,10 @@ test_that("rowwise()", {
     expect_equal(dim(fd), c(ncol(df), 1))
     expect_identical(fd[[1]], sapply(df$lys, sum))
 })
+
+test_that("group_split()", {
+    fd <- df |> 
+    group_split("groups")
+    expect_equal(length(fd), length(unique(df$groups)))
+})
+

From b87b8dc87c40e1c72ddce917a9e260d8409eaad9 Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Sun, 15 Oct 2023 17:18:24 +1000
Subject: [PATCH 02/20] group_split by column

issue #35975561
---
 R/dplyr_methods.R                   |  29 ++++++++++++++++++++++++++++
 tests/testthat/Rplots.pdf           | Bin 0 -> 5794 bytes
 tests/testthat/test-dplyr_methods.R |   7 +++++++
 3 files changed, 36 insertions(+)
 create mode 100644 tests/testthat/Rplots.pdf

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index db079f9..9418d5a 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -875,3 +875,32 @@ pull.SingleCellExperiment <- function(.data, var=-1, name=NULL, ...) {
         as_tibble() %>%
         dplyr::pull(var=!!var, name=!!name, ...)
 }
+
+#' @name group_split
+#' @rdname group_split
+#' @inherit dplyr::group_split
+#'
+#' @param .data 
+#'
+#' @return
+#' @export
+#'
+#' @examples
+#' data(pbmc_small)
+#' pbmc_small |> group_split(pbmc_small, groups)
+group_split.SingleCellExperiment <- function(.data, var) {
+    var <- enquo(var)
+    
+    var_list <- .data |> 
+        as_tibble() |> 
+        select(!!var) |> 
+        unlist(use.names = FALSE)
+    
+    groups <- unique(var_list)
+    
+    v <- vector(mode = "list", length = length(groups))
+    
+    for (n in seq_along(groups)) { v[[n]] <- .data[, var_list == groups[[n]]] }
+    
+    v
+}
diff --git a/tests/testthat/Rplots.pdf b/tests/testthat/Rplots.pdf
new file mode 100644
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HcmV?d00001

diff --git a/tests/testthat/test-dplyr_methods.R b/tests/testthat/test-dplyr_methods.R
index 9e01f96..4b5c7de 100755
--- a/tests/testthat/test-dplyr_methods.R
+++ b/tests/testthat/test-dplyr_methods.R
@@ -318,3 +318,10 @@ test_that("rowwise()", {
     expect_equal(dim(fd), c(ncol(df), 1))
     expect_identical(fd[[1]], sapply(df$lys, sum))
 })
+
+test_that("group_split()", {
+    fd <- df |> 
+    group_split("groups")
+    expect_equal(length(fd), length(unique(df$groups)))
+})
+

From ea644372420f88ef624450c9c112286d5d7d053d Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Sun, 15 Oct 2023 19:04:22 +1000
Subject: [PATCH 03/20] split groups row data

---
 R/dplyr_methods.R                   |  41 ++++++++++++++++++++--------
 tests/testthat/Rplots.pdf           | Bin 5794 -> 5789 bytes
 tests/testthat/test-dplyr_methods.R |   8 ++++++
 3 files changed, 37 insertions(+), 12 deletions(-)

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index 9418d5a..789eb97 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -889,18 +889,35 @@ pull.SingleCellExperiment <- function(.data, var=-1, name=NULL, ...) {
 #' data(pbmc_small)
 #' pbmc_small |> group_split(pbmc_small, groups)
 group_split.SingleCellExperiment <- function(.data, var) {
-    var <- enquo(var)
-    
-    var_list <- .data |> 
-        as_tibble() |> 
-        select(!!var) |> 
-        unlist(use.names = FALSE)
-    
-    groups <- unique(var_list)
     
-    v <- vector(mode = "list", length = length(groups))
-    
-    for (n in seq_along(groups)) { v[[n]] <- .data[, var_list == groups[[n]]] }
+  
+    if(any(paste(substitute(var)) == names(colData(.data)))) {
+        var <- enquo(var)
+        var_list <- .data |> 
+            as_tibble() |> 
+            select(!!var) |> 
+            unlist(use.names = FALSE)
+        
+        groups <- unique(var_list)
+        
+        v <- vector(mode = "list", length = length(groups))
+        
+        for (n in seq_along(groups)) {
+            v[[n]] <- .data[, var_list == groups[[n]]] 
+            }
+        
+        return(v)
+    }
     
-    v
+    if(any(paste(substitute(var)) == names(rowData(.data)))) {
+      var <- enquo(var)
+        var_list <- .data |> 
+            rowData() |>
+            as_tibble() |> 
+            select(!!var) |> 
+            unlist(use.names = FALSE)
+      
+        split(.data, var_list) |> 
+            as.list()
+    }
 }
diff --git a/tests/testthat/Rplots.pdf b/tests/testthat/Rplots.pdf
index 73b7057a8fa17bcb60fff62d6a7dc05ba57d1d47..5b3a1bf157b9a28919010bcdc0f1d8947aabcb0b 100644
GIT binary patch
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diff --git a/tests/testthat/test-dplyr_methods.R b/tests/testthat/test-dplyr_methods.R
index 4b5c7de..f8c1923 100755
--- a/tests/testthat/test-dplyr_methods.R
+++ b/tests/testthat/test-dplyr_methods.R
@@ -323,5 +323,13 @@ test_that("group_split()", {
     fd <- df |> 
     group_split("groups")
     expect_equal(length(fd), length(unique(df$groups)))
+    
+    fd <- df |> 
+    group_split("vst.variable")
+    expect_equal(length(fd), length(unique(rowData(df)$vst.variable)))
+    
+    fd <- df |> 
+      group_split(vst.variable)
+    expect_equal(length(fd), length(unique(rowData(df)$vst.variable)))
 })
 

From 2da015c351e2f821e1949dc995e3dfd6e01d9eee Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Sun, 15 Oct 2023 19:04:22 +1000
Subject: [PATCH 04/20] split groups row data

Issue #35975561
---
 R/dplyr_methods.R                   |  41 ++++++++++++++++++++--------
 tests/testthat/Rplots.pdf           | Bin 5794 -> 5789 bytes
 tests/testthat/test-dplyr_methods.R |   8 ++++++
 3 files changed, 37 insertions(+), 12 deletions(-)

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index 9418d5a..789eb97 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -889,18 +889,35 @@ pull.SingleCellExperiment <- function(.data, var=-1, name=NULL, ...) {
 #' data(pbmc_small)
 #' pbmc_small |> group_split(pbmc_small, groups)
 group_split.SingleCellExperiment <- function(.data, var) {
-    var <- enquo(var)
-    
-    var_list <- .data |> 
-        as_tibble() |> 
-        select(!!var) |> 
-        unlist(use.names = FALSE)
-    
-    groups <- unique(var_list)
     
-    v <- vector(mode = "list", length = length(groups))
-    
-    for (n in seq_along(groups)) { v[[n]] <- .data[, var_list == groups[[n]]] }
+  
+    if(any(paste(substitute(var)) == names(colData(.data)))) {
+        var <- enquo(var)
+        var_list <- .data |> 
+            as_tibble() |> 
+            select(!!var) |> 
+            unlist(use.names = FALSE)
+        
+        groups <- unique(var_list)
+        
+        v <- vector(mode = "list", length = length(groups))
+        
+        for (n in seq_along(groups)) {
+            v[[n]] <- .data[, var_list == groups[[n]]] 
+            }
+        
+        return(v)
+    }
     
-    v
+    if(any(paste(substitute(var)) == names(rowData(.data)))) {
+      var <- enquo(var)
+        var_list <- .data |> 
+            rowData() |>
+            as_tibble() |> 
+            select(!!var) |> 
+            unlist(use.names = FALSE)
+      
+        split(.data, var_list) |> 
+            as.list()
+    }
 }
diff --git a/tests/testthat/Rplots.pdf b/tests/testthat/Rplots.pdf
index 73b7057a8fa17bcb60fff62d6a7dc05ba57d1d47..5b3a1bf157b9a28919010bcdc0f1d8947aabcb0b 100644
GIT binary patch
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diff --git a/tests/testthat/test-dplyr_methods.R b/tests/testthat/test-dplyr_methods.R
index 4b5c7de..f8c1923 100755
--- a/tests/testthat/test-dplyr_methods.R
+++ b/tests/testthat/test-dplyr_methods.R
@@ -323,5 +323,13 @@ test_that("group_split()", {
     fd <- df |> 
     group_split("groups")
     expect_equal(length(fd), length(unique(df$groups)))
+    
+    fd <- df |> 
+    group_split("vst.variable")
+    expect_equal(length(fd), length(unique(rowData(df)$vst.variable)))
+    
+    fd <- df |> 
+      group_split(vst.variable)
+    expect_equal(length(fd), length(unique(rowData(df)$vst.variable)))
 })
 

From 1ac4299e25b4d73bd65ec4eda84bf1e270292331 Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Sat, 21 Oct 2023 13:34:02 +1000
Subject: [PATCH 05/20] tidy up code and docs

---
 NAMESPACE          |  1 +
 R/dplyr_methods.R  |  2 --
 man/group_split.Rd | 58 ++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 59 insertions(+), 2 deletions(-)
 create mode 100644 man/group_split.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 26adeae..535ebe6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -13,6 +13,7 @@ S3method(full_join,SingleCellExperiment)
 S3method(ggplot,SingleCellExperiment)
 S3method(glimpse,tidySingleCellExperiment)
 S3method(group_by,SingleCellExperiment)
+S3method(group_split,SingleCellExperiment)
 S3method(inner_join,SingleCellExperiment)
 S3method(join_transcripts,Seurat)
 S3method(join_transcripts,default)
diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index 789eb97..b8cfb19 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -882,7 +882,6 @@ pull.SingleCellExperiment <- function(.data, var=-1, name=NULL, ...) {
 #'
 #' @param .data 
 #'
-#' @return
 #' @export
 #'
 #' @examples
@@ -890,7 +889,6 @@ pull.SingleCellExperiment <- function(.data, var=-1, name=NULL, ...) {
 #' pbmc_small |> group_split(pbmc_small, groups)
 group_split.SingleCellExperiment <- function(.data, var) {
     
-  
     if(any(paste(substitute(var)) == names(colData(.data)))) {
         var <- enquo(var)
         var_list <- .data |> 
diff --git a/man/group_split.Rd b/man/group_split.Rd
new file mode 100644
index 0000000..1ffd177
--- /dev/null
+++ b/man/group_split.Rd
@@ -0,0 +1,58 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/dplyr_methods.R
+\name{group_split}
+\alias{group_split}
+\alias{group_split.SingleCellExperiment}
+\title{Split data frame by groups}
+\usage{
+\method{group_split}{SingleCellExperiment}(.data, var)
+}
+\arguments{
+\item{.data}{}
+}
+\value{
+A list of tibbles. Each tibble contains the rows of \code{.tbl} for the
+associated group and all the columns, including the grouping variables.
+Note that this returns a \link[vctrs:list_of]{list_of} which is slightly
+stricter than a simple list but is useful for representing lists where
+every element has the same type.
+}
+\description{
+\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
+
+\code{\link[dplyr:group_split]{group_split()}} works like \code{\link[base:split]{base::split()}} but:
+\itemize{
+\item It uses the grouping structure from \code{\link[dplyr:group_by]{group_by()}} and therefore is subject
+to the data mask
+\item It does not name the elements of the list based on the grouping as this
+only works well for a single character grouping variable. Instead,
+use \code{\link[dplyr:group_keys]{group_keys()}} to access a data frame that defines the groups.
+}
+
+\code{group_split()} is primarily designed to work with grouped data frames.
+You can pass \code{...} to group and split an ungrouped data frame, but this
+is generally not very useful as you want have easy access to the group
+metadata.
+}
+\section{Lifecycle}{
+
+
+\code{group_split()} is not stable because you can achieve very similar results by
+manipulating the nested column returned from
+\code{\link[tidyr:nest]{tidyr::nest(.by =)}}. That also retains the group keys all
+within a single data structure. \code{group_split()} may be deprecated in the
+future.
+
+}
+
+\examples{
+data(pbmc_small)
+pbmc_small |> group_split(pbmc_small, groups)
+}
+\seealso{
+Other grouping functions: 
+\code{\link[dplyr]{group_by}()},
+\code{\link[dplyr]{group_map}()},
+\code{\link[dplyr]{group_nest}()},
+\code{\link[dplyr]{group_trim}()}
+}

From 3c9648b1a72e40eea7d6ecebd58ebb9094f09302 Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Sat, 21 Oct 2023 19:54:41 +1000
Subject: [PATCH 06/20] refactor group_split

Issue #97
---
 R/dplyr_methods.R                   | 55 +++++++++++++----------------
 tests/testthat/test-dplyr_methods.R |  9 ++---
 2 files changed, 29 insertions(+), 35 deletions(-)

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index b8cfb19..abb3673 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -887,35 +887,28 @@ pull.SingleCellExperiment <- function(.data, var=-1, name=NULL, ...) {
 #' @examples
 #' data(pbmc_small)
 #' pbmc_small |> group_split(pbmc_small, groups)
-group_split.SingleCellExperiment <- function(.data, var) {
-    
-    if(any(paste(substitute(var)) == names(colData(.data)))) {
-        var <- enquo(var)
-        var_list <- .data |> 
-            as_tibble() |> 
-            select(!!var) |> 
-            unlist(use.names = FALSE)
-        
-        groups <- unique(var_list)
-        
-        v <- vector(mode = "list", length = length(groups))
-        
-        for (n in seq_along(groups)) {
-            v[[n]] <- .data[, var_list == groups[[n]]] 
-            }
-        
-        return(v)
-    }
-    
-    if(any(paste(substitute(var)) == names(rowData(.data)))) {
-      var <- enquo(var)
-        var_list <- .data |> 
-            rowData() |>
-            as_tibble() |> 
-            select(!!var) |> 
-            unlist(use.names = FALSE)
-      
-        split(.data, var_list) |> 
-            as.list()
-    }
+group_split.SingleCellExperiment <- function(.data, ...) {
+  
+  var_list <- enquos(...)
+  
+  .data <- .data |> 
+      unite("group_col", !!!var_list, remove = FALSE)
+  
+  group_list <- .data |> 
+      as_tibble() |> 
+      select(group_col) |> 
+      unlist() |> 
+      unique()
+  
+  v <- vector(mode = "list", length = length(group_list))
+  
+  for (i in seq_along(v)) {
+      v[[i]] <- .data |> 
+        filter(group_col == group_list[[i]]) |> 
+        select(!group_col)
+  }
+  
+  v
+  
 }
+
diff --git a/tests/testthat/test-dplyr_methods.R b/tests/testthat/test-dplyr_methods.R
index f8c1923..7a00291 100755
--- a/tests/testthat/test-dplyr_methods.R
+++ b/tests/testthat/test-dplyr_methods.R
@@ -325,11 +325,12 @@ test_that("group_split()", {
     expect_equal(length(fd), length(unique(df$groups)))
     
     fd <- df |> 
-    group_split("vst.variable")
-    expect_equal(length(fd), length(unique(rowData(df)$vst.variable)))
+    group_split("groups")
+    expect_equal(length(fd), length(unique(df$groups)))
     
     fd <- df |> 
-      group_split(vst.variable)
-    expect_equal(length(fd), length(unique(rowData(df)$vst.variable)))
+      group_split(groups, ident)
+    expect_equal(length(fd), length(unique(df$groups)) *
+                   length(unique(df$ident)))
 })
 

From c12ec7af86b9a90ce3fd003a94e1689fbbc5b9a3 Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Sun, 22 Oct 2023 11:30:40 +1000
Subject: [PATCH 07/20] docs

---
 R/dplyr_methods.R  |  5 +++--
 man/group_split.Rd | 20 ++++----------------
 2 files changed, 7 insertions(+), 18 deletions(-)

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index abb3673..374e023 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -878,9 +878,10 @@ pull.SingleCellExperiment <- function(.data, var=-1, name=NULL, ...) {
 
 #' @name group_split
 #' @rdname group_split
-#' @inherit dplyr::group_split
+#' @inherit dplyr::group_split title description details sections source
 #'
-#' @param .data 
+#' @param .data A `tidySingleCellExperiment` object
+#' @param ... The grouping variables by which to split the object
 #'
 #' @export
 #'
diff --git a/man/group_split.Rd b/man/group_split.Rd
index 1ffd177..b954a30 100644
--- a/man/group_split.Rd
+++ b/man/group_split.Rd
@@ -5,17 +5,12 @@
 \alias{group_split.SingleCellExperiment}
 \title{Split data frame by groups}
 \usage{
-\method{group_split}{SingleCellExperiment}(.data, var)
+\method{group_split}{SingleCellExperiment}(.data, ...)
 }
 \arguments{
-\item{.data}{}
-}
-\value{
-A list of tibbles. Each tibble contains the rows of \code{.tbl} for the
-associated group and all the columns, including the grouping variables.
-Note that this returns a \link[vctrs:list_of]{list_of} which is slightly
-stricter than a simple list but is useful for representing lists where
-every element has the same type.
+\item{.data}{A `tidySingleCellExperiment` object}
+
+\item{...}{The grouping variables by which to split the object}
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
@@ -49,10 +44,3 @@ future.
 data(pbmc_small)
 pbmc_small |> group_split(pbmc_small, groups)
 }
-\seealso{
-Other grouping functions: 
-\code{\link[dplyr]{group_by}()},
-\code{\link[dplyr]{group_map}()},
-\code{\link[dplyr]{group_nest}()},
-\code{\link[dplyr]{group_trim}()}
-}

From 9f22be8208e413d30d8b18b0f5ca0df86d12a9fe Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Sun, 22 Oct 2023 12:32:38 +1000
Subject: [PATCH 08/20] fix warning, error persists

I seem to be doing something that the SCE version of unite doesn't like. Maybe could avoiding adding a column in the first place.
---
 R/dplyr_methods.R | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index 374e023..3d227ba 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -893,11 +893,12 @@ group_split.SingleCellExperiment <- function(.data, ...) {
   var_list <- enquos(...)
   
   .data <- .data |> 
-      unite("group_col", !!!var_list, remove = FALSE)
+      unite.SingleCellExperiment("group_col", !!!var_list, remove = FALSE)
   
-  group_list <- .data |> 
-      as_tibble() |> 
-      select(group_col) |> 
+  group_df <- .data |> 
+      as_tibble()
+  
+  group_list <- group_df$group_col |> 
       unlist() |> 
       unique()
   
@@ -905,8 +906,9 @@ group_split.SingleCellExperiment <- function(.data, ...) {
   
   for (i in seq_along(v)) {
       v[[i]] <- .data |> 
-        filter(group_col == group_list[[i]]) |> 
-        select(!group_col)
+        filter(group_col == group_list[[i]], )
+      
+      v[[i]] <- select(v[[i]], !group_col)
   }
   
   v

From dee22e5f0b95f94297b4271385f5886426b5ec46 Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Sun, 22 Oct 2023 15:06:05 +1000
Subject: [PATCH 09/20] should fix error but doesn't

---
 R/dplyr_methods.R | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index 3d227ba..3fa40dd 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -892,23 +892,21 @@ group_split.SingleCellExperiment <- function(.data, ...) {
   
   var_list <- enquos(...)
   
-  .data <- .data |> 
-      unite.SingleCellExperiment("group_col", !!!var_list, remove = FALSE)
-  
   group_df <- .data |> 
       as_tibble()
   
-  group_list <- group_df$group_col |> 
-      unlist() |> 
+  group_df <- group_df |> 
+      unite("group_col", !!!var_list, remove = FALSE)
+    
+  group_list <- group_df$group_col
+  
+  groups <- group_list |> 
       unique()
   
-  v <- vector(mode = "list", length = length(group_list))
+  v <- vector(mode = "list", length = length(groups))
   
   for (i in seq_along(v)) {
-      v[[i]] <- .data |> 
-        filter(group_col == group_list[[i]], )
-      
-      v[[i]] <- select(v[[i]], !group_col)
+      v[[i]] <- .data[,group_list == groups[[i]]]
   }
   
   v

From 4b7565ed0a637ab691827c199887c2c49c23528f Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Thu, 7 Dec 2023 18:22:42 +1000
Subject: [PATCH 10/20] group_column___

---
 R/dplyr_methods.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index 3fa40dd..77b4c67 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -896,9 +896,9 @@ group_split.SingleCellExperiment <- function(.data, ...) {
       as_tibble()
   
   group_df <- group_df |> 
-      unite("group_col", !!!var_list, remove = FALSE)
+      unite("group_column___", !!!var_list, remove = FALSE)
     
-  group_list <- group_df$group_col
+  group_list <- group_df$group_column___
   
   groups <- group_list |> 
       unique()

From 5a55e7a2490c4443bde5d29213f7935629abc963 Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Thu, 7 Dec 2023 18:35:02 +1000
Subject: [PATCH 11/20] consistency with dplyr

---
 R/dplyr_methods.R  | 15 ++++++++-------
 man/group_split.Rd | 23 ++++++++++++++++++++---
 2 files changed, 28 insertions(+), 10 deletions(-)

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index 77b4c67..d1d95b6 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -878,21 +878,18 @@ pull.SingleCellExperiment <- function(.data, var=-1, name=NULL, ...) {
 
 #' @name group_split
 #' @rdname group_split
-#' @inherit dplyr::group_split title description details sections source
-#'
-#' @param .data A `tidySingleCellExperiment` object
-#' @param ... The grouping variables by which to split the object
+#' @inherit dplyr::group_split
 #'
 #' @export
 #'
 #' @examples
 #' data(pbmc_small)
 #' pbmc_small |> group_split(pbmc_small, groups)
-group_split.SingleCellExperiment <- function(.data, ...) {
+group_split.SingleCellExperiment <- function(.tbl, ..., .keep = TRUE) {
   
   var_list <- enquos(...)
   
-  group_df <- .data |> 
+  group_df <- .tbl |> 
       as_tibble()
   
   group_df <- group_df |> 
@@ -906,7 +903,11 @@ group_split.SingleCellExperiment <- function(.data, ...) {
   v <- vector(mode = "list", length = length(groups))
   
   for (i in seq_along(v)) {
-      v[[i]] <- .data[,group_list == groups[[i]]]
+      v[[i]] <- .tbl[,group_list == groups[[i]]]
+      
+      if(.keep == FALSE) {
+        v[[i]] <- select(v[[i]], !!!var_list)
+      }
   }
   
   v
diff --git a/man/group_split.Rd b/man/group_split.Rd
index b954a30..e921cc7 100644
--- a/man/group_split.Rd
+++ b/man/group_split.Rd
@@ -5,12 +5,22 @@
 \alias{group_split.SingleCellExperiment}
 \title{Split data frame by groups}
 \usage{
-\method{group_split}{SingleCellExperiment}(.data, ...)
+\method{group_split}{SingleCellExperiment}(.tbl, ..., .keep = TRUE)
 }
 \arguments{
-\item{.data}{A `tidySingleCellExperiment` object}
+\item{.tbl}{A tbl.}
 
-\item{...}{The grouping variables by which to split the object}
+\item{...}{If \code{.tbl} is an ungrouped data frame, a grouping specification,
+forwarded to \code{\link[dplyr:group_by]{group_by()}}.}
+
+\item{.keep}{Should the grouping columns be kept?}
+}
+\value{
+A list of tibbles. Each tibble contains the rows of \code{.tbl} for the
+associated group and all the columns, including the grouping variables.
+Note that this returns a \link[vctrs:list_of]{list_of} which is slightly
+stricter than a simple list but is useful for representing lists where
+every element has the same type.
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
@@ -44,3 +54,10 @@ future.
 data(pbmc_small)
 pbmc_small |> group_split(pbmc_small, groups)
 }
+\seealso{
+Other grouping functions: 
+\code{\link[dplyr]{group_by}()},
+\code{\link[dplyr]{group_map}()},
+\code{\link[dplyr]{group_nest}()},
+\code{\link[dplyr]{group_trim}()}
+}

From 1de8c85ac1416c80aa8e8eeb95c4bb3c9a8eebdc Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Thu, 7 Dec 2023 18:44:37 +1000
Subject: [PATCH 12/20] simplify

---
 R/dplyr_methods.R | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index d1d95b6..d513f25 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -889,13 +889,10 @@ group_split.SingleCellExperiment <- function(.tbl, ..., .keep = TRUE) {
   
   var_list <- enquos(...)
   
-  group_df <- .tbl |> 
-      as_tibble()
-  
-  group_df <- group_df |> 
-      unite("group_column___", !!!var_list, remove = FALSE)
-    
-  group_list <- group_df$group_column___
+  group_list <- .tbl |> 
+      as_tibble() |> 
+      unite("group_column___", !!!var_list, remove = FALSE) |> 
+      pull(group_column___)
   
   groups <- group_list |> 
       unique()

From 9c1cbeb9a5a29b9c76ef33b0da093f72761cdde8 Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Thu, 7 Dec 2023 18:58:10 +1000
Subject: [PATCH 13/20] quotes to fix global binding issue

---
 R/dplyr_methods.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index 37ce936..38e944c 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -837,7 +837,7 @@ group_split.SingleCellExperiment <- function(.tbl, ..., .keep = TRUE) {
   group_list <- .tbl |> 
       as_tibble() |> 
       unite("group_column___", !!!var_list, remove = FALSE) |> 
-      pull(group_column___)
+      pull("group_column___")
   
   groups <- group_list |> 
       unique()

From 1ea58298e060414af7678390212dec52e78146ce Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Thu, 7 Dec 2023 19:01:21 +1000
Subject: [PATCH 14/20] fix .keep

Think I accidentally reverted this
---
 R/dplyr_methods.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index 38e944c..ac10afc 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -848,7 +848,7 @@ group_split.SingleCellExperiment <- function(.tbl, ..., .keep = TRUE) {
       v[[i]] <- .tbl[,group_list == groups[[i]]]
       
       if(.keep == FALSE) {
-        v[[i]] <- select(v[[i]], !!!var_list)
+        v[[i]] <- select(v[[i]], !(!!!var_list))
       }
   }
   

From c7585e3276b44e35babbc205d885587672eb6563 Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Thu, 7 Dec 2023 19:06:37 +1000
Subject: [PATCH 15/20] check dots

---
 R/dplyr_methods.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index ac10afc..9b46a32 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -825,6 +825,7 @@ pull.SingleCellExperiment <- function(.data, var=-1, name=NULL, ...) {
 #' @rdname group_split
 #' @inherit dplyr::group_split
 #'
+#' @importFrom ellipsis check_dots_used
 #' @export
 #'
 #' @examples

From 2d52d9930e810de341e0fd5463ffe65aadc64d77 Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Thu, 7 Dec 2023 19:35:44 +1000
Subject: [PATCH 16/20] fix example code

---
 R/dplyr_methods.R  | 11 ++++++-----
 man/group_split.Rd |  3 ++-
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index 9b46a32..d081285 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -824,13 +824,14 @@ pull.SingleCellExperiment <- function(.data, var=-1, name=NULL, ...) {
 #' @name group_split
 #' @rdname group_split
 #' @inherit dplyr::group_split
-#'
-#' @importFrom ellipsis check_dots_used
-#' @export
-#'
+#' 
 #' @examples
 #' data(pbmc_small)
-#' pbmc_small |> group_split(pbmc_small, groups)
+#' group_split(pbmc_small, groups)
+#' 
+#' @importFrom ellipsis check_dots_used
+#' @importFrom dplyr group_split
+#' @export
 group_split.SingleCellExperiment <- function(.tbl, ..., .keep = TRUE) {
   
   var_list <- enquos(...)
diff --git a/man/group_split.Rd b/man/group_split.Rd
index e921cc7..1cf3fa3 100644
--- a/man/group_split.Rd
+++ b/man/group_split.Rd
@@ -52,7 +52,8 @@ future.
 
 \examples{
 data(pbmc_small)
-pbmc_small |> group_split(pbmc_small, groups)
+group_split(pbmc_small, groups)
+
 }
 \seealso{
 Other grouping functions: 

From 9347b5d2259d84cbadbf885b5a37214b665da4bc Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Thu, 7 Dec 2023 19:41:36 +1000
Subject: [PATCH 17/20] consistency

---
 R/dplyr_methods.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index d081285..be4db25 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -827,10 +827,9 @@ pull.SingleCellExperiment <- function(.data, var=-1, name=NULL, ...) {
 #' 
 #' @examples
 #' data(pbmc_small)
-#' group_split(pbmc_small, groups)
+#' pbmc_small |> group_split(groups)
 #' 
 #' @importFrom ellipsis check_dots_used
-#' @importFrom dplyr group_split
 #' @export
 group_split.SingleCellExperiment <- function(.tbl, ..., .keep = TRUE) {
   

From 332e30e83cb0934812220b98777b596066d5a357 Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Sat, 9 Dec 2023 19:04:33 +1000
Subject: [PATCH 18/20] drop tests with qoutes

---
 tests/testthat/test-dplyr_methods.R | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/tests/testthat/test-dplyr_methods.R b/tests/testthat/test-dplyr_methods.R
index 948c2f8..2dc4135 100755
--- a/tests/testthat/test-dplyr_methods.R
+++ b/tests/testthat/test-dplyr_methods.R
@@ -378,14 +378,6 @@ test_that("rowwise()", {
 })
 
 test_that("group_split()", {
-    fd <- df |> 
-    group_split("groups")
-    expect_equal(length(fd), length(unique(df$groups)))
-    
-    fd <- df |> 
-    group_split("groups")
-    expect_equal(length(fd), length(unique(df$groups)))
-    
     fd <- df |> 
       group_split(groups, ident)
     expect_equal(length(fd), length(unique(df$groups)) *

From 0fb669aea1c374327d899ef3ef36dede23d6f348 Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Sat, 9 Dec 2023 19:05:25 +1000
Subject: [PATCH 19/20] use dplyr functions

---
 NAMESPACE          | 1 +
 R/dplyr_methods.R  | 9 +++++----
 man/group_split.Rd | 2 +-
 3 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 17170d6..45635a7 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -74,6 +74,7 @@ importFrom(dplyr,filter)
 importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
 importFrom(dplyr,group_by_drop_default)
+importFrom(dplyr,group_rows)
 importFrom(dplyr,group_split)
 importFrom(dplyr,inner_join)
 importFrom(dplyr,left_join)
diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index be4db25..8a18f54 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -830,6 +830,8 @@ pull.SingleCellExperiment <- function(.data, var=-1, name=NULL, ...) {
 #' pbmc_small |> group_split(groups)
 #' 
 #' @importFrom ellipsis check_dots_used
+#' @importFrom dplyr group_by
+#' @importFrom dplyr group_rows
 #' @export
 group_split.SingleCellExperiment <- function(.tbl, ..., .keep = TRUE) {
   
@@ -837,16 +839,15 @@ group_split.SingleCellExperiment <- function(.tbl, ..., .keep = TRUE) {
   
   group_list <- .tbl |> 
       as_tibble() |> 
-      unite("group_column___", !!!var_list, remove = FALSE) |> 
-      pull("group_column___")
+      dplyr::group_by(!!!var_list)
   
   groups <- group_list |> 
-      unique()
+      dplyr::group_rows()
   
   v <- vector(mode = "list", length = length(groups))
   
   for (i in seq_along(v)) {
-      v[[i]] <- .tbl[,group_list == groups[[i]]]
+      v[[i]] <- .tbl[,groups[[i]]]
       
       if(.keep == FALSE) {
         v[[i]] <- select(v[[i]], !(!!!var_list))
diff --git a/man/group_split.Rd b/man/group_split.Rd
index 1cf3fa3..11e2394 100644
--- a/man/group_split.Rd
+++ b/man/group_split.Rd
@@ -52,7 +52,7 @@ future.
 
 \examples{
 data(pbmc_small)
-group_split(pbmc_small, groups)
+pbmc_small |> group_split(groups)
 
 }
 \seealso{

From b2a7e3db2830b3f0386f23f62b713b991e3a7ca8 Mon Sep 17 00:00:00 2001
From: Boyd Tarlinton <tarlintb@qut.edu.au>
Date: Sun, 10 Dec 2023 15:14:36 +1000
Subject: [PATCH 20/20] tests

---
 tests/testthat/test-dplyr_methods.R | 24 +++++++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-dplyr_methods.R b/tests/testthat/test-dplyr_methods.R
index 2dc4135..93f0541 100755
--- a/tests/testthat/test-dplyr_methods.R
+++ b/tests/testthat/test-dplyr_methods.R
@@ -377,10 +377,32 @@ test_that("rowwise()", {
     expect_identical(fd[[1]], sapply(df$lys, sum))
 })
 
-test_that("group_split()", {
+test_that("group_split() works for one variable", {
+  fd <- df |> 
+    group_split(groups)
+  expect_equal(length(fd), length(unique(df$groups)))
+})
+
+test_that("group_split() works for combination of variables", {
     fd <- df |> 
       group_split(groups, ident)
     expect_equal(length(fd), length(unique(df$groups)) *
                    length(unique(df$ident)))
 })
 
+test_that("group_split() works for one logical statement", {
+  fd_log <- df |> 
+    group_split(groups=="g1")
+  fd_var <- df |> 
+    group_split(groups=="g1")
+  expect_equal(lapply(fd_var, count), lapply(fd_log, count))
+})
+
+test_that("group_split() works for two logical statements", {
+  fd <- df |>
+    group_split(PC_1>0 & groups=="g1")
+  fd_counts <- lapply(fd, count)
+  expect_equal(c(fd_counts[[1]], fd_counts[[2]], use.names = FALSE), 
+               list(75, 5))
+})
+