From 425911936c2a78008bf39439b77610df20be8ccf Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Tue, 12 Oct 2021 16:43:22 +1100
Subject: [PATCH 01/17] fix filter for objects with missing cell names

---
 NAMESPACE         |  1 +
 R/dplyr_methods.R | 13 ++++++++++---
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 249bbf8..56f3a05 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -77,6 +77,7 @@ export(summarise)
 export(tidy)
 export(unite)
 export(unnest)
+export(unnest_single_cell_experiment)
 importFrom(S4Vectors,DataFrame)
 importFrom(SingleCellExperiment,cbind)
 importFrom(SingleCellExperiment,counts)
diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index ac49cc5..eca5238 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -297,10 +297,17 @@ filter.SingleCellExperiment <- function(.data, ..., .preserve=FALSE) {
     new_meta <- .data %>%
         as_tibble() %>%
         dplyr::filter(..., .preserve=.preserve) # %>% as_meta_data(.data)
-    new_obj <- .data[, new_meta$cell]
-    # colData(new_obj)=new_meta
 
-    new_obj
+    # Try to solve missing colnames
+    if(colnames(.data) %>% is.null()){
+      message("tidySingleCellExperiment says: the input object does not have cell names (colnames(...)). \n Therefore, the cell column in the filtered tibble abstraction will still include an incremental integer vector.")
+      new_meta$cell = as.integer(new_meta$cell)
+
+    }
+
+
+    .data[, new_meta$cell]
+
 }
 
 

From 465c1813fa3c01af7928df866c1e6093eb121e99 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Sat, 23 Oct 2021 19:35:20 +1100
Subject: [PATCH 02/17] use ttservice

---
 DESCRIPTION          |   1 +
 NAMESPACE            |  57 +++++++++++-----------
 R/methods.R          | 113 ++++++++++++++++++++-----------------------
 man/join_features.Rd |  26 +++++-----
 4 files changed, 95 insertions(+), 102 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index c26f942..7024be9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,6 +9,7 @@ Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCe
 License: GPL-3
 Depends:
     R (>= 4.0.0),
+    ttservice,
     SingleCellExperiment
 Imports:
     SummarizedExperiment,
diff --git a/NAMESPACE b/NAMESPACE
index 56f3a05..20ba739 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,81 +2,79 @@
 
 S3method(add_count,SingleCellExperiment)
 S3method(add_count,default)
-S3method(arrange,SingleCellExperiment)
-S3method(as_tibble,SingleCellExperiment)
 S3method(bind_cols,SingleCellExperiment)
 S3method(bind_cols,default)
 S3method(bind_rows,SingleCellExperiment)
 S3method(bind_rows,default)
 S3method(count,SingleCellExperiment)
 S3method(count,default)
-S3method(distinct,SingleCellExperiment)
-S3method(extract,SingleCellExperiment)
-S3method(filter,SingleCellExperiment)
-S3method(full_join,SingleCellExperiment)
-S3method(ggplot,SingleCellExperiment)
-S3method(glimpse,tidySingleCellExperiment)
-S3method(group_by,SingleCellExperiment)
-S3method(inner_join,SingleCellExperiment)
-S3method(join_features,SingleCellExperiment)
-S3method(join_features,default)
 S3method(join_transcripts,Seurat)
 S3method(join_transcripts,default)
-S3method(left_join,SingleCellExperiment)
-S3method(mutate,SingleCellExperiment)
-S3method(nest,SingleCellExperiment)
-S3method(pivot_longer,SingleCellExperiment)
 S3method(plot_ly,SingleCellExperiment)
 S3method(plot_ly,default)
 S3method(print,SingleCellExperiment)
-S3method(pull,SingleCellExperiment)
-S3method(rename,SingleCellExperiment)
-S3method(right_join,SingleCellExperiment)
-S3method(rowwise,SingleCellExperiment)
-S3method(sample_frac,SingleCellExperiment)
-S3method(sample_n,SingleCellExperiment)
-S3method(select,SingleCellExperiment)
-S3method(separate,SingleCellExperiment)
-S3method(slice,SingleCellExperiment)
-S3method(summarise,SingleCellExperiment)
 S3method(tidy,SingleCellExperiment)
-S3method(unite,SingleCellExperiment)
-S3method(unnest,tidySingleCellExperiment_nested)
 export("%>%")
 export(add_count)
 export(arrange)
+export(arrange.SingleCellExperiment)
 export(as_tibble)
+export(as_tibble.SingleCellExperiment)
 export(bind_cols)
 export(bind_rows)
 export(count)
 export(distinct)
+export(distinct.SingleCellExperiment)
 export(extract)
+export(extract.SingleCellExperiment)
 export(filter)
+export(filter.SingleCellExperiment)
 export(full_join)
+export(full_join.SingleCellExperiment)
 export(ggplot)
+export(ggplot.SingleCellExperiment)
 export(glimpse)
+export(glimpse.tidySingleCellExperiment)
 export(group_by)
+export(group_by.SingleCellExperiment)
 export(inner_join)
+export(inner_join.SingleCellExperiment)
 export(join_features)
 export(join_transcripts)
 export(left_join)
+export(left_join.SingleCellExperiment)
 export(mutate)
+export(mutate.SingleCellExperiment)
 export(nest)
+export(nest.SingleCellExperiment)
 export(pivot_longer)
+export(pivot_longer.SingleCellExperiment)
 export(plot_ly)
 export(pull)
+export(pull.SingleCellExperiment)
 export(rename)
+export(rename.SingleCellExperiment)
 export(right_join)
+export(right_join.SingleCellExperiment)
 export(rowwise)
+export(rowwise.SingleCellExperiment)
 export(sample_frac)
+export(sample_frac.SingleCellExperiment)
 export(sample_n)
+export(sample_n.SingleCellExperiment)
 export(select)
+export(select.SingleCellExperiment)
 export(separate)
+export(separate.SingleCellExperiment)
 export(slice)
+export(slice.SingleCellExperiment)
 export(summarise)
+export(summarise.SingleCellExperiment)
 export(tidy)
 export(unite)
+export(unite.SingleCellExperiment)
 export(unnest)
+export(unnest.tidySingleCellExperiment_nested)
 export(unnest_single_cell_experiment)
 importFrom(S4Vectors,DataFrame)
 importFrom(SingleCellExperiment,cbind)
@@ -147,7 +145,6 @@ importFrom(tidyr,separate)
 importFrom(tidyr,spread)
 importFrom(tidyr,unite)
 importFrom(tidyr,unnest)
-importFrom(tidyselect,contains)
 importFrom(tidyselect,eval_select)
-importFrom(tidyselect,everything)
+importFrom(ttservice,join_features)
 importFrom(utils,tail)
diff --git a/R/methods.R b/R/methods.R
index b1d35c1..c0ecfb8 100755
--- a/R/methods.R
+++ b/R/methods.R
@@ -52,89 +52,82 @@ setMethod(
     }
 )
 
-#' Add differential featureion information to a tbl using edgeR.
+#' Extract and join information for features.
 #'
-#' \lifecycle{experimental}
 #'
-#' @description join_features() extracts and joins information for specific
-#'   features
+#' @description join_features() extracts and joins information for specified features
 #'
 #' @importFrom rlang enquo
 #' @importFrom magrittr "%>%"
+#' @importFrom ttservice join_features
 #'
 #' @name join_features
 #' @rdname join_features
 #'
-#' @param .data A tidy SingleCellExperiment object
+#' @param .data A SingleCellExperiment object
 #' @param features A vector of feature identifiers to join
 #' @param all If TRUE return all
 #' @param exclude_zeros If TRUE exclude zero values
 #' @param shape Format of the returned table "long" or "wide"
 #' @param ... Parameters to pass to join wide, i.e. assay name to extract feature abundance from and gene prefix, for shape="wide"
 #'
-#' @details This function extracts information for specified features and
-#'   returns the information in either long or wide format.
+#' @details This function extracts information for specified features and returns the information in either long or wide format.
 #'
-#' @return A `tbl` containing the information.for the specified features
+#' @return An object containing the information.for the specified features
 #'
 #' @examples
 #'
-#' tidySingleCellExperiment::pbmc_small %>%
+#' data("pbmc_small")
+#' pbmc_small %>%
+#' join_features(features = c("HLA-DRA", "LYZ"))
 #'
-#'     join_features(features=c("HLA-DRA", "LYZ"))
-#' @export
 #'
-join_features <- function(.data,
-                             features = NULL,
-                             all = FALSE,
-                             exclude_zeros = FALSE,
-                             shape = "long", ...) {
-    UseMethod("join_features", .data)
-}
-#' @export
-join_features.default <-
-    function(.data,
-             features = NULL,
-             all = FALSE,
-             exclude_zeros = FALSE,
-             shape = "long", ...) {
-        print("This function cannot be applied to this object")
-    }
-#' @importFrom tidyselect contains
-#' @importFrom tidyselect everything
 #' @export
-join_features.SingleCellExperiment <-
-    function(.data,
-             features = NULL,
-             all = FALSE,
-             exclude_zeros = FALSE,
-             shape = "long", ...) {
+#'
+NULL
+
+#' join_features
+#'
+#' @docType methods
+#' @rdname join_features
+#'
+#' @return An object containing the information.for the specified features
+#'
+setMethod("join_features", "SingleCellExperiment",  function(.data,
+                                               features = NULL,
+                                               all = FALSE,
+                                               exclude_zeros = FALSE,
+                                               shape = "long", ...)
+{
 
-        # CRAN Note
-        cell = NULL
-        feature= NULL
+  # CRAN Note
+  cell = NULL
+  feature= NULL
+
+  # Shape is long
+  if (shape == "long")
+    .data %>%
+    left_join(
+      get_abundance_sc_long(
+        .data = .data,
+        features = features,
+        all = all,
+        exclude_zeros = exclude_zeros
+      ),
+      by = "cell"
+    ) %>%
+    select(cell, feature, contains("abundance"), everything())
+
+  # Shape if wide
+  else
+    .data  %>% left_join(get_abundance_sc_wide(
+      .data = .data,
+      features = features,
+      all = all, ...
+    ),
+    by = "cell")
+
+})
 
-        # Shape is long
-        if (shape == "long")
-          .data %>%
-            left_join(
-                get_abundance_sc_long(
-                    .data = .data,
-                    features = features,
-                    all = all,
-                    exclude_zeros = exclude_zeros
-                ),
-                by = "cell"
-            ) %>%
-            select(cell, feature, contains("abundance"), everything())
 
-        # Shape if wide
-        else
-          .data  %>% left_join(get_abundance_sc_wide(
-                .data = .data,
-                features = features,
-                all = all, ...
-            ),
-            by = "cell")
 
-    }
diff --git a/man/join_features.Rd b/man/join_features.Rd
index c1c4fb3..3463178 100644
--- a/man/join_features.Rd
+++ b/man/join_features.Rd
@@ -1,10 +1,12 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/methods.R
+\docType{methods}
 \name{join_features}
 \alias{join_features}
-\title{Add differential featureion information to a tbl using edgeR.}
+\alias{join_features,SingleCellExperiment-method}
+\title{Extract and join information for features.}
 \usage{
-join_features(
+\S4method{join_features}{SingleCellExperiment}(
   .data,
   features = NULL,
   all = FALSE,
@@ -14,7 +16,7 @@ join_features(
 )
 }
 \arguments{
-\item{.data}{A tidy SingleCellExperiment object}
+\item{.data}{A SingleCellExperiment object}
 
 \item{features}{A vector of feature identifiers to join}
 
@@ -27,21 +29,21 @@ join_features(
 \item{...}{Parameters to pass to join wide, i.e. assay name to extract feature abundance from and gene prefix, for shape="wide"}
 }
 \value{
-A \code{tbl} containing the information.for the specified features
+An object containing the information.for the specified features
+
+An object containing the information.for the specified features
 }
 \description{
-join_features() extracts and joins information for specific
-features
+join_features() extracts and joins information for specified features
 }
 \details{
-\lifecycle{experimental}
-
-This function extracts information for specified features and
-returns the information in either long or wide format.
+This function extracts information for specified features and returns the information in either long or wide format.
 }
 \examples{
 
-tidySingleCellExperiment::pbmc_small \%>\%
+data("pbmc_small")
+pbmc_small \%>\%
+join_features(features = c("HLA-DRA", "LYZ"))
+
 
-    join_features(features=c("HLA-DRA", "LYZ"))
 }

From 762784ddcc5b607af4a0c05bafde3f6ae8b55ec3 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Sat, 23 Oct 2021 20:00:36 +1100
Subject: [PATCH 03/17] update NAMESPACE

---
 NAMESPACE | 52 ++++++++++++++++++++++++++--------------------------
 1 file changed, 26 insertions(+), 26 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 20ba739..b65a854 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,79 +2,79 @@
 
 S3method(add_count,SingleCellExperiment)
 S3method(add_count,default)
+S3method(arrange,SingleCellExperiment)
+S3method(as_tibble,SingleCellExperiment)
 S3method(bind_cols,SingleCellExperiment)
 S3method(bind_cols,default)
 S3method(bind_rows,SingleCellExperiment)
 S3method(bind_rows,default)
 S3method(count,SingleCellExperiment)
 S3method(count,default)
+S3method(distinct,SingleCellExperiment)
+S3method(extract,SingleCellExperiment)
+S3method(filter,SingleCellExperiment)
+S3method(full_join,SingleCellExperiment)
+S3method(ggplot,SingleCellExperiment)
+S3method(glimpse,tidySingleCellExperiment)
+S3method(group_by,SingleCellExperiment)
+S3method(inner_join,SingleCellExperiment)
 S3method(join_transcripts,Seurat)
 S3method(join_transcripts,default)
+S3method(left_join,SingleCellExperiment)
+S3method(mutate,SingleCellExperiment)
+S3method(nest,SingleCellExperiment)
+S3method(pivot_longer,SingleCellExperiment)
 S3method(plot_ly,SingleCellExperiment)
 S3method(plot_ly,default)
 S3method(print,SingleCellExperiment)
+S3method(pull,SingleCellExperiment)
+S3method(rename,SingleCellExperiment)
+S3method(right_join,SingleCellExperiment)
+S3method(rowwise,SingleCellExperiment)
+S3method(sample_frac,SingleCellExperiment)
+S3method(sample_n,SingleCellExperiment)
+S3method(select,SingleCellExperiment)
+S3method(separate,SingleCellExperiment)
+S3method(slice,SingleCellExperiment)
+S3method(summarise,SingleCellExperiment)
 S3method(tidy,SingleCellExperiment)
+S3method(unite,SingleCellExperiment)
+S3method(unnest,tidySingleCellExperiment_nested)
 export("%>%")
 export(add_count)
 export(arrange)
-export(arrange.SingleCellExperiment)
 export(as_tibble)
-export(as_tibble.SingleCellExperiment)
 export(bind_cols)
 export(bind_rows)
 export(count)
 export(distinct)
-export(distinct.SingleCellExperiment)
 export(extract)
-export(extract.SingleCellExperiment)
 export(filter)
-export(filter.SingleCellExperiment)
 export(full_join)
-export(full_join.SingleCellExperiment)
 export(ggplot)
-export(ggplot.SingleCellExperiment)
 export(glimpse)
-export(glimpse.tidySingleCellExperiment)
 export(group_by)
-export(group_by.SingleCellExperiment)
 export(inner_join)
-export(inner_join.SingleCellExperiment)
 export(join_features)
 export(join_transcripts)
 export(left_join)
-export(left_join.SingleCellExperiment)
 export(mutate)
-export(mutate.SingleCellExperiment)
 export(nest)
-export(nest.SingleCellExperiment)
 export(pivot_longer)
-export(pivot_longer.SingleCellExperiment)
 export(plot_ly)
 export(pull)
-export(pull.SingleCellExperiment)
 export(rename)
-export(rename.SingleCellExperiment)
 export(right_join)
-export(right_join.SingleCellExperiment)
 export(rowwise)
-export(rowwise.SingleCellExperiment)
 export(sample_frac)
-export(sample_frac.SingleCellExperiment)
 export(sample_n)
-export(sample_n.SingleCellExperiment)
 export(select)
-export(select.SingleCellExperiment)
 export(separate)
-export(separate.SingleCellExperiment)
 export(slice)
-export(slice.SingleCellExperiment)
 export(summarise)
-export(summarise.SingleCellExperiment)
 export(tidy)
 export(unite)
-export(unite.SingleCellExperiment)
 export(unnest)
-export(unnest.tidySingleCellExperiment_nested)
 export(unnest_single_cell_experiment)
 importFrom(S4Vectors,DataFrame)
 importFrom(SingleCellExperiment,cbind)

From 42ee280bdfeb0c4b90ac5714c8d5b816dd29e0d2 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Tue, 12 Oct 2021 16:43:22 +1100
Subject: [PATCH 04/17] fix filter for objects with missing cell names

---
 R/dplyr_methods.R | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index ac49cc5..eca5238 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -297,10 +297,17 @@ filter.SingleCellExperiment <- function(.data, ..., .preserve=FALSE) {
     new_meta <- .data %>%
         as_tibble() %>%
         dplyr::filter(..., .preserve=.preserve) # %>% as_meta_data(.data)
-    new_obj <- .data[, new_meta$cell]
-    # colData(new_obj)=new_meta
 
-    new_obj
+    # Try to solve missing colnames
+    if(colnames(.data) %>% is.null()){
+      message("tidySingleCellExperiment says: the input object does not have cell names (colnames(...)). \n Therefore, the cell column in the filtered tibble abstraction will still include an incremental integer vector.")
+      new_meta$cell = as.integer(new_meta$cell)
+
+    }
+
+
+    .data[, new_meta$cell]
+
 }
 
 

From 0de9a1f7be112c1cedc7d34330ac8a57a13bddf4 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Wed, 24 Nov 2021 10:28:17 +1100
Subject: [PATCH 05/17] deprecate cell column

---
 NAMESPACE               |   4 ++
 R/dplyr_methods.R       | 143 +++++++++++++++++++++++++++++++++-------
 R/ggplot2_methods.R     |  11 +++-
 R/methods.R             |   6 +-
 R/methods_DEPRECATED.R  |   6 +-
 R/tibble_methods.R      |   2 +-
 R/tidyr_methods.R       |  53 +++++++++++++--
 R/utilities.R           |  68 ++++++++++++++++---
 man/ggplot2-methods.Rd  |   2 +-
 man/join_transcripts.Rd |   2 +-
 man/print.Rd            |  27 --------
 11 files changed, 249 insertions(+), 75 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 56f3a05..9848486 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -78,7 +78,9 @@ export(tidy)
 export(unite)
 export(unnest)
 export(unnest_single_cell_experiment)
+importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,DataFrame)
+importFrom(S4Vectors,metadata)
 importFrom(SingleCellExperiment,cbind)
 importFrom(SingleCellExperiment,counts)
 importFrom(SummarizedExperiment,"colData<-")
@@ -135,6 +137,8 @@ importFrom(rlang,is_spliced)
 importFrom(rlang,names2)
 importFrom(rlang,quo_name)
 importFrom(rlang,quo_squash)
+importFrom(stringr,regex)
+importFrom(stringr,str_detect)
 importFrom(stringr,str_replace)
 importFrom(tibble,as_tibble)
 importFrom(tibble,enframe)
diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index eca5238..e74a4fb 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -63,7 +63,7 @@ arrange.SingleCellExperiment <- function(.data, ..., .by_group=FALSE) {
         as_tibble() %>%
         dplyr::arrange(..., .by_group=.by_group)
 
-    .data[, new_metadata$cell]
+    .data[, pull(new_metadata, !!c_(.data)$symbol)]
 
 }
 
@@ -215,6 +215,14 @@ NULL
 distinct.SingleCellExperiment <- function(.data, ..., .keep_all=FALSE) {
     message(data_frame_returned_message)
 
+  distinct_columns =
+    (enquos(..., .ignore_empty = "all") %>% map(~ quo_name(.x)) %>% unlist)
+
+  # Deprecation of special column names
+  if(is_sample_feature_deprecated_used(.data, distinct_columns)){
+    .data= ping_old_special_column_into_metadata(.data)
+  }
+
     .data %>%
         as_tibble() %>%
         dplyr::distinct(..., .keep_all=.keep_all)
@@ -294,19 +302,28 @@ NULL
 #'
 #' @export
 filter.SingleCellExperiment <- function(.data, ..., .preserve=FALSE) {
-    new_meta <- .data %>%
+
+  # Deprecation of special column names
+  if(is_sample_feature_deprecated_used(
+    .data,
+    (enquos(..., .ignore_empty = "all") %>% map(~ quo_name(.x)) %>% unlist)
+  )){
+    .data= ping_old_special_column_into_metadata(.data)
+  }
+
+  new_meta <- .data %>%
         as_tibble() %>%
         dplyr::filter(..., .preserve=.preserve) # %>% as_meta_data(.data)
 
     # Try to solve missing colnames
     if(colnames(.data) %>% is.null()){
       message("tidySingleCellExperiment says: the input object does not have cell names (colnames(...)). \n Therefore, the cell column in the filtered tibble abstraction will still include an incremental integer vector.")
-      new_meta$cell = as.integer(new_meta$cell)
+      new_meta = mew_meta %>% mutate(!!c_(.data)$symbol := as.integer(!!c_(.data)$symbol))
 
     }
 
 
-    .data[, new_meta$cell]
+    .data[, pull(new_meta, !!c_(.data)$symbol)]
 
 }
 
@@ -361,6 +378,14 @@ NULL
 group_by.SingleCellExperiment <- function(.data, ..., .add=FALSE, .drop=group_by_drop_default(.data)) {
     message(data_frame_returned_message)
 
+  # Deprecation of special column names
+  if(is_sample_feature_deprecated_used(
+    .data,
+    (enquos(..., .ignore_empty = "all") %>% map(~ quo_name(.x)) %>% unlist)
+  )){
+    .data= ping_old_special_column_into_metadata(.data)
+  }
+
     .data %>%
         as_tibble() %>%
         dplyr::group_by(..., .add=.add, .drop=.drop)
@@ -447,6 +472,13 @@ NULL
 summarise.SingleCellExperiment <- function(.data, ...) {
     message(data_frame_returned_message)
 
+  # Deprecation of special column names
+  if(is_sample_feature_deprecated_used(
+    .data,
+    (enquos(..., .ignore_empty = "all") %>% map(~ quo_name(.x)) %>% unlist)
+  )){
+    .data= ping_old_special_column_into_metadata(.data)
+  }
 
     .data %>%
         as_tibble() %>%
@@ -554,12 +586,20 @@ mutate.SingleCellExperiment <- function(.data, ...) {
     # Check that we are not modifying a key column
     cols <- enquos(...) %>% names()
 
+    # Deprecation of special column names
+    if(is_sample_feature_deprecated_used(
+      .data,
+      (enquos(..., .ignore_empty = "all") %>% map(~ quo_name(.x)) %>% unlist)
+    )){
+      .data= ping_old_special_column_into_metadata(.data)
+    }
+
     tst <-
         intersect(
             cols %>%
                 names(),
             get_special_columns(.data) %>%
-                c(get_needed_columns())
+                c(get_needed_columns(.data))
         ) %>%
         length() %>%
         gt(0)
@@ -642,7 +682,7 @@ rename.SingleCellExperiment <- function(.data, ...) {
             cols %>%
                 names(),
             get_special_columns(.data) %>%
-                c(get_needed_columns())
+                c(get_needed_columns(.data))
         ) %>%
         length() %>%
         gt(0)
@@ -650,7 +690,7 @@ rename.SingleCellExperiment <- function(.data, ...) {
     if (tst) {
         columns =
             get_special_columns(.data) %>%
-            c(get_needed_columns()) %>%
+            c(get_needed_columns(.data)) %>%
             paste(collapse=", ")
         stop(
             "tidySingleCellExperiment says: you are trying to rename a column that is view only",
@@ -742,13 +782,19 @@ NULL
 #' @export
 left_join.SingleCellExperiment <- function(x, y, by=NULL, copy=FALSE, suffix=c(".x", ".y"),
     ...) {
+
+  # Deprecation of special column names
+  if(is_sample_feature_deprecated_used( x, when(by, !is.null(.) ~ by, ~ colnames(y)))){
+    x= ping_old_special_column_into_metadata(x)
+  }
+
     x %>%
         as_tibble() %>%
         dplyr::left_join(y, by=by, copy=copy, suffix=suffix, ...) %>%
         when(
 
             # If duplicated cells returns tibble
-            dplyr::count(., cell) %>%
+            dplyr::count(., !!c_(x)$symbol) %>%
                 filter(n > 1) %>%
                 nrow() %>%
                 gt(0) ~ {
@@ -793,13 +839,19 @@ NULL
 #' @importFrom SummarizedExperiment colData
 #' @export
 inner_join.SingleCellExperiment <- function(x, y, by=NULL, copy=FALSE, suffix=c(".x", ".y"), ...) {
+
+  # Deprecation of special column names
+  if(is_sample_feature_deprecated_used( x, when(by, !is.null(.) ~ by, ~ colnames(y)))){
+    x= ping_old_special_column_into_metadata(x)
+  }
+
     x %>%
         as_tibble() %>%
         dplyr::inner_join(y, by=by, copy=copy, suffix=suffix, ...) %>%
         when(
 
             # If duplicated cells returns tibble
-            count(., cell) %>%
+            count(., !!c_(x)$symbol) %>%
                 filter(n > 1) %>%
                 nrow() %>%
                 gt(0) ~ {
@@ -809,7 +861,7 @@ inner_join.SingleCellExperiment <- function(x, y, by=NULL, copy=FALSE, suffix=c(
 
             # Otherwise return updated tidySingleCellExperiment
             ~ {
-                new_obj <- x[, .$cell]
+                new_obj <- x[, pull(., c_(x)$name)]
                 colData(new_obj) <- (.) %>% as_meta_data(new_obj)
                 new_obj
             }
@@ -849,13 +901,19 @@ NULL
 #' @export
 right_join.SingleCellExperiment <- function(x, y, by=NULL, copy=FALSE, suffix=c(".x", ".y"),
     ...) {
+
+  # Deprecation of special column names
+  if(is_sample_feature_deprecated_used( x, when(by, !is.null(.) ~ by, ~ colnames(y)))){
+    x= ping_old_special_column_into_metadata(x)
+  }
+
     x %>%
         as_tibble() %>%
         dplyr::right_join(y, by=by, copy=copy, suffix=suffix, ...) %>%
         when(
 
             # If duplicated cells returns tibble
-            count(., cell) %>%
+            count(., !!c_(x)$symbol) %>%
                 filter(n > 1) %>%
                 nrow() %>%
                 gt(0) ~ {
@@ -865,7 +923,7 @@ right_join.SingleCellExperiment <- function(x, y, by=NULL, copy=FALSE, suffix=c(
 
             # Otherwise return updated tidySingleCellExperiment
             ~ {
-                new_obj <- x[, .$cell]
+                new_obj <- x[, pull(., c_(x)$name)]
                 colData(new_obj) <- (.) %>% as_meta_data(new_obj)
                 new_obj
             }
@@ -905,13 +963,19 @@ NULL
 #' @export
 full_join.SingleCellExperiment <- function(x, y, by=NULL, copy=FALSE, suffix=c(".x", ".y"),
     ...) {
+
+  # Deprecation of special column names
+  if(is_sample_feature_deprecated_used( x, when(by, !is.null(.) ~ by, ~ colnames(y)))){
+    x= ping_old_special_column_into_metadata(x)
+  }
+
     x %>%
         as_tibble() %>%
         dplyr::full_join(y, by=by, copy=copy, suffix=suffix, ...) %>%
         when(
 
             # If duplicated cells returns tibble
-            count(., cell) %>%
+            count(., !!c_(x)$symbol) %>%
                 filter(n > 1) %>%
                 nrow() %>%
                 gt(0) ~ {
@@ -921,7 +985,7 @@ full_join.SingleCellExperiment <- function(x, y, by=NULL, copy=FALSE, suffix=c("
 
             # Otherwise return updated tidySingleCellExperiment
             ~ {
-                new_obj <- x[, .$cell]
+                new_obj <- x[, pull(., c_(x)$name)]
                 colData(new_obj) <- (.) %>% as_meta_data(x)
                 new_obj
             }
@@ -1065,13 +1129,22 @@ NULL
 #' @importFrom SummarizedExperiment colData
 #' @export
 select.SingleCellExperiment <- function(.data, ...) {
+
+  # Deprecation of special column names
+  if(is_sample_feature_deprecated_used(
+    .data,
+    (enquos(..., .ignore_empty = "all") %>% map(~ quo_name(.x)) %>% unlist)
+  )){
+    .data= ping_old_special_column_into_metadata(.data)
+  }
+
     .data %>%
         as_tibble() %>%
         select_helper(...) %>%
         when(
 
             # If key columns are missing
-            (get_needed_columns() %in% colnames(.)) %>%
+            (get_needed_columns(.data) %in% colnames(.)) %>%
                 all() %>%
                 `!`() ~ {
                 message("tidySingleCellExperiment says: Key columns are missing. A data frame is returned for independent data analysis.")
@@ -1148,19 +1221,19 @@ sample_n.SingleCellExperiment <- function(tbl, size, replace=FALSE,
 
     new_meta = colData(tbl) %>%
         as.data.frame() %>%
-        as_tibble(rownames = "cell") %>%
+        as_tibble(rownames = c_(tbl)$name) %>%
         dplyr::sample_n( size, replace = replace, weight = weight, .env = .env, ...)
 
-    count_cells = new_meta %>% select(cell) %>% count(cell)
+    count_cells = new_meta %>% select(!!c_(tbl)$symbol) %>% count(!!c_(tbl)$symbol)
 
     # If repeted cells
     if(count_cells$n %>% max() %>% gt(1)){
         message("tidySingleCellExperiment says: When sampling with replacement a data frame is returned for independent data analysis.")
         tbl %>%
             as_tibble() %>%
-            right_join(new_meta %>% select(cell),  by = "cell")
+            right_join(new_meta %>% select(!!c_(tbl)$symbol),  by = c_(tbl)$name)
     }  else{
-        new_obj = tbl[,  new_meta %>% pull(cell)]
+        new_obj = tbl[,  new_meta %>% pull(!!c_(tbl)$symbol)]
         new_obj
     }
 }
@@ -1185,19 +1258,19 @@ sample_frac.SingleCellExperiment <- function(tbl, size=1, replace=FALSE,
 
     new_meta = colData(tbl) %>%
         as.data.frame() %>%
-        as_tibble(rownames = "cell") %>%
+        as_tibble(rownames = c_(tbl)$name) %>%
         dplyr::sample_frac( size, replace = replace, weight = weight, .env = .env, ...)
 
-    count_cells = new_meta %>% select(cell) %>% count(cell)
+    count_cells = new_meta %>% select(!!c_(tbl)$symbol) %>% count(!!c_(tbl)$symbol)
 
     # If repeted cells
     if(count_cells$n %>% max() %>% gt(1)){
         message("tidySingleCellExperiment says: When sampling with replacement a data frame is returned for independent data analysis.")
         tbl %>%
             as_tibble() %>%
-            right_join(new_meta %>% select(cell),  by = "cell")
+            right_join(new_meta %>% select(!!c_(tbl)$symbol),  by = c_(tbl)$name)
     }  else{
-        new_obj = tbl[,  new_meta %>% pull(cell)]
+        new_obj = tbl[,  new_meta %>% pull(!!c_(tbl)$symbol)]
         new_obj
     }
 }
@@ -1266,6 +1339,14 @@ count.default <- function(x, ..., wt=NULL, sort=FALSE, name=NULL, .drop=group_by
 count.SingleCellExperiment <- function(x, ..., wt=NULL, sort=FALSE, name=NULL, .drop=group_by_drop_default(x)) {
     message(data_frame_returned_message)
 
+  # Deprecation of special column names
+  if(is_sample_feature_deprecated_used(
+    x,
+    (enquos(..., .ignore_empty = "all") %>% map(~ quo_name(.x)) %>% unlist)
+  )){
+    x= ping_old_special_column_into_metadata(x)
+  }
+
     x %>%
         as_tibble() %>%
         dplyr::count(..., wt=!!enquo(wt), sort=sort, name=name, .drop=.drop)
@@ -1289,6 +1370,14 @@ add_count.default <- function(x, ..., wt = NULL, sort = FALSE, name = NULL, .dro
 #' @rdname count
 add_count.SingleCellExperiment <- function(x, ..., wt = NULL, sort = FALSE, name = NULL, .drop = group_by_drop_default(x)) {
 
+  # Deprecation of special column names
+  if(is_sample_feature_deprecated_used(
+    x,
+    (enquos(..., .ignore_empty = "all") %>% map(~ quo_name(.x)) %>% unlist)
+  )){
+    x= ping_old_special_column_into_metadata(x)
+  }
+
     colData(x) =
         x %>%
         as_tibble %>%
@@ -1342,6 +1431,14 @@ pull.SingleCellExperiment <- function(.data, var=-1, name=NULL, ...) {
     var <- enquo(var)
     name <- enquo(name)
 
+    # Deprecation of special column names
+    if(is_sample_feature_deprecated_used(
+      .data,
+      quo_name(var)
+    )){
+      .data= ping_old_special_column_into_metadata(.data)
+    }
+
     .data %>%
         as_tibble() %>%
         dplyr::pull(var=!!var, name=!!name, ...)
diff --git a/R/ggplot2_methods.R b/R/ggplot2_methods.R
index 217a4d5..c6bb225 100755
--- a/R/ggplot2_methods.R
+++ b/R/ggplot2_methods.R
@@ -47,13 +47,22 @@
 #' library(ggplot2)
 #'
 #' tidySingleCellExperiment::pbmc_small %>%
-#'     
+#'
 #'     tidySingleCellExperiment::ggplot(aes(groups, nCount_RNA)) +
 #'     geom_boxplot()
 NULL
 
 #' @export
 ggplot.SingleCellExperiment <- function(data=NULL, mapping=aes(), ..., environment=parent.frame()) {
+
+  # Deprecation of special column names
+  if(is_sample_feature_deprecated_used(
+    data,
+    mapping %>% unlist() %>% map(~ quo_name(.x)) %>% unlist() %>% as.character()
+  )){
+    data= ping_old_special_column_into_metadata(data)
+  }
+
     data %>%
         as_tibble() %>%
         ggplot2::ggplot(mapping=mapping)
diff --git a/R/methods.R b/R/methods.R
index b1d35c1..e08e812 100755
--- a/R/methods.R
+++ b/R/methods.R
@@ -124,9 +124,9 @@ join_features.SingleCellExperiment <-
                     all = all,
                     exclude_zeros = exclude_zeros
                 ),
-                by = "cell"
+                by = c_(.data)$name
             ) %>%
-            select(cell, feature, contains("abundance"), everything())
+            select(!!c_(.data)$symbol, feature, contains("abundance"), everything())
 
         # Shape if wide
         else
@@ -135,6 +135,6 @@ join_features.SingleCellExperiment <-
                 features = features,
                 all = all, ...
             ),
-            by = "cell")
+            by = c_(.data)$name)
 
     }
diff --git a/R/methods_DEPRECATED.R b/R/methods_DEPRECATED.R
index d53a983..7fd8d6e 100644
--- a/R/methods_DEPRECATED.R
+++ b/R/methods_DEPRECATED.R
@@ -9,7 +9,7 @@
 #' @name join_transcripts
 #' @rdname join_transcripts
 #'
-#' @param .data A tidyseurat object
+#' @param .data A tidySingleCellExperiment object
 #' @param transcripts A vector of transcript identifiers to join
 #' @param all If TRUE return all
 #' @param exclude_zeros If TRUE exclude zero values
@@ -42,7 +42,7 @@ join_transcripts.default <-
            exclude_zeros = FALSE,
            shape = "long", ...)
   {
-    print("tidyseurat says: This function cannot be applied to this object")
+    print("tidySingleCellExperiment says: This function cannot be applied to this object")
   }
 #' @export
 join_transcripts.Seurat <-
@@ -53,7 +53,7 @@ join_transcripts.Seurat <-
            shape = "long", ...)
   {
 
-    deprecate_warn("1.1.2", "join_transcripts()", "tidyseurat::join_features()")
+    deprecate_warn("1.1.2", "join_transcripts()", "tidySingleCellExperiment::join_features()")
 
 
     .data %>%
diff --git a/R/tibble_methods.R b/R/tibble_methods.R
index 2dcb500..d8fbafb 100755
--- a/R/tibble_methods.R
+++ b/R/tibble_methods.R
@@ -74,7 +74,7 @@ as_tibble.SingleCellExperiment <- function(x, ...,
     rownames=pkgconfig::get_config("tibble::rownames", NULL)) {
     colData(x) %>%
         as.data.frame() %>%
-        tibble::as_tibble(rownames="cell") %>%
+        tibble::as_tibble(rownames=c_(x)$name) %>%
 
 
         # Attach reduced dimensions
diff --git a/R/tidyr_methods.R b/R/tidyr_methods.R
index c4db48d..b3024c5 100755
--- a/R/tidyr_methods.R
+++ b/R/tidyr_methods.R
@@ -185,10 +185,19 @@ NULL
 #'
 #' @export
 nest.SingleCellExperiment <- function(.data, ..., .names_sep = NULL) {
-    my_data__ <- .data
     cols <- enquos(...)
     col_name_data <- names(cols)
 
+    # Deprecation of special column names
+    if(is_sample_feature_deprecated_used(
+      .data,
+      (enquos(..., .ignore_empty = "all") %>% map(~ quo_name(.x)) %>% unlist)
+    )){
+      .data= ping_old_special_column_into_metadata(.data)
+    }
+
+    my_data__ = .data
+
     my_data__ %>%
 
         # This is needed otherwise nest goes into loop and fails
@@ -200,7 +209,7 @@ nest.SingleCellExperiment <- function(.data, ..., .names_sep = NULL) {
                 ~ my_data__ %>%
 
                     # Subset cells
-                    filter(cell %in% .x$cell) %>%
+                  filter(!!c_(my_data__)$symbol %in% pull(.x, !!c_(my_data__)$symbol)) %>%
 
                     # Subset columns
                     select(colnames(.x))
@@ -266,6 +275,14 @@ extract.SingleCellExperiment <- function(data, col, into, regex="([[:alnum:]]+)"
     convert=FALSE, ...) {
     col <- enquo(col)
 
+    # Deprecation of special column names
+    if(is_sample_feature_deprecated_used(
+      data,
+      c(quo_name(col), into)
+    )){
+      data= ping_old_special_column_into_metadata(data)
+    }
+
     colData(data) <-
         data %>%
         as_tibble() %>%
@@ -387,6 +404,14 @@ pivot_longer.SingleCellExperiment <- function(data,
 
     message(data_frame_returned_message)
 
+    # Deprecation of special column names
+    if(is_sample_feature_deprecated_used(
+      data,
+      c(quo_names(cols))
+    )){
+      data= ping_old_special_column_into_metadata(data)
+    }
+
     data %>%
         as_tibble() %>%
         tidyr::pivot_longer(!!cols,
@@ -449,10 +474,18 @@ unite.SingleCellExperiment <- function(data, col, ..., sep="_", remove=TRUE, na.
     # Check that we are not modifying a key column
     cols <- enquo(col)
 
+    # Deprecation of special column names
+    if(is_sample_feature_deprecated_used(
+      data,
+      (enquos(..., .ignore_empty = "all") %>% map(~ quo_name(.x)) %>% unlist)
+    )){
+      data= ping_old_special_column_into_metadata(data)
+    }
+
     tst <-
         intersect(
             cols %>% quo_names(),
-            get_special_columns(data) %>% c(get_needed_columns())
+            get_special_columns(data) %>% c(get_needed_columns(data))
         ) %>%
         length() %>%
         gt(0) &
@@ -461,7 +494,7 @@ unite.SingleCellExperiment <- function(data, col, ..., sep="_", remove=TRUE, na.
     if (tst) {
         columns =
             get_special_columns(data) %>%
-            c(get_needed_columns()) %>%
+            c(get_needed_columns(data)) %>%
             paste(collapse=", ")
         stop(
             "tidySingleCellExperiment says: you are trying to rename a column that is view only",
@@ -538,10 +571,18 @@ separate.SingleCellExperiment <- function(data, col, into, sep="[^[:alnum:]]+",
     # Check that we are not modifying a key column
     cols <- enquo(col)
 
+    # Deprecation of special column names
+    if(is_sample_feature_deprecated_used(
+      data,
+      c(quo_names(cols))
+    )){
+      data= ping_old_special_column_into_metadata(data)
+    }
+
     tst <-
         intersect(
             cols %>% quo_names(),
-            get_special_columns(data) %>% c(get_needed_columns())
+            get_special_columns(data) %>% c(get_needed_columns(data))
         ) %>%
         length() %>%
         gt(0) &
@@ -550,7 +591,7 @@ separate.SingleCellExperiment <- function(data, col, into, sep="[^[:alnum:]]+",
     if (tst) {
         columns =
             get_special_columns(data) %>%
-            c(get_needed_columns()) %>%
+            c(get_needed_columns(data)) %>%
             paste(collapse=", ")
         stop(
             "tidySingleCellExperiment says: you are trying to rename a column that is view only",
diff --git a/R/utilities.R b/R/utilities.R
index b8f2616..496e0fe 100755
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -9,7 +9,7 @@
 to_tib <- function(.data) {
     colData(.data) %>%
         as.data.frame() %>%
-        as_tibble(rownames="cell")
+        as_tibble(rownames=c_(.data)$name)
 }
 
 # Greater than
@@ -142,10 +142,10 @@ get_abundance_sc_wide <- function(.data, features=NULL, all=FALSE, assay = assay
         ) %>%
         as.matrix() %>%
         t() %>%
-        as_tibble(rownames="cell") %>%
+        as_tibble(rownames=c_(.data)$name) %>%
 
         # Add prefix
-        setNames(c("cell", sprintf("%s%s", prefix, colnames(.)[-1])))
+        setNames(c(c_(.data)$name, sprintf("%s%s", prefix, colnames(.)[-1])))
 }
 
 #' get abundance long
@@ -237,14 +237,14 @@ get_abundance_sc_long <- function(.data, features=NULL, all=FALSE, exclude_zeros
                 as_tibble(rownames="feature") %>%
                 tidyr::pivot_longer(
                     cols=-feature,
-                    names_to="cell",
+                    names_to=c_(.data)$name,
                     values_to="abundance" %>% paste(.y, sep="_"),
                     values_drop_na=TRUE
                 )
             # %>%
             # mutate_if(is.character, as.factor) %>%
         ) %>%
-        Reduce(function(...) full_join(..., by=c("feature", "cell")), .)
+        Reduce(function(...) full_join(..., by=c("feature", c_(.data)$name)), .)
 }
 
 #' @importFrom dplyr select_if
@@ -266,7 +266,7 @@ as_meta_data <- function(.data, SingleCellExperiment_object) {
     .data %>%
         select_if(!colnames(.) %in% col_to_exclude) %>%
         # select(-one_of(col_to_exclude)) %>%
-        data.frame(row.names="cell") %>%
+        data.frame(row.names=c_(SingleCellExperiment_object)$name) %>%
         DataFrame()
 }
 
@@ -298,9 +298,9 @@ get_special_datasets <- function(SingleCellExperiment_object, n_dimensions_to_re
     })
 }
 
-get_needed_columns <- function() {
-    # c("cell",  "orig.ident", "nCount_RNA", "nFeature_RNA")
-    c("cell")
+get_needed_columns <- function(.data) {
+
+  c(c_(.data)$name)
 }
 
 #' Convert array of quosure (e.g. c(col_a, col_b)) into character vector
@@ -333,3 +333,53 @@ select_helper <- function(.data, ...) {
 data_frame_returned_message = "tidySingleCellExperiment says: A data frame is returned for independent data analysis."
 duplicated_cell_names = "tidySingleCellExperiment says: This operation lead to duplicated cell names. A data frame is returned for independent data analysis."
 
+# This function is used for the change of special sample column to .sample
+# Check if "sample" is included in the query and is not part of any other existing annotation
+#' @importFrom stringr str_detect
+#' @importFrom stringr regex
+is_sample_feature_deprecated_used = function(.data, user_columns, use_old_special_names = FALSE){
+
+  old_standard_is_used_for_cell =
+    (
+      ( any(str_detect(user_columns  , regex("\\bcell\\b"))) & !any(str_detect(user_columns  , regex("\\W*(\\.cell)\\W*")))  ) |
+        "cell" %in% user_columns
+    ) &
+    !"cell" %in% colnames(colData(.data))
+
+  old_standard_is_used = old_standard_is_used_for_cell
+
+  if(old_standard_is_used){
+    warning("tidySingleCellExperiment says: from version 1.3.1, the special columns including cell id (colnames(se)) has changed to \".cell\". This dataset is returned with the old-style vocabulary (feature), however we suggest to update your workflow to reflect the new vocabulary (.cell)")
+
+    use_old_special_names = TRUE
+  }
+
+  use_old_special_names
+}
+
+get_special_column_name_symbol = function(name){
+  list(name = name, symbol = as.symbol(name))
+}
+
+# Key column names
+#' @importFrom S4Vectors metadata
+#' @importFrom S4Vectors metadata<-
+ping_old_special_column_into_metadata = function(.data){
+
+  metadata(.data)$cell__ = get_special_column_name_symbol("cell")
+
+  .data
+}
+
+get_special_column_name_cell = function(name){
+  list(name = name, symbol = as.symbol(name))
+}
+
+cell__ = get_special_column_name_symbol(".cell")
+
+#' @importFrom S4Vectors metadata
+c_ =  function(x){
+  # Check if old deprecated columns are used
+  if("cell__" %in% names(metadata(x))) cell__ = metadata(x)$cell__
+  return(cell__)
+}
diff --git a/man/ggplot2-methods.Rd b/man/ggplot2-methods.Rd
index 05328f6..171dd34 100644
--- a/man/ggplot2-methods.Rd
+++ b/man/ggplot2-methods.Rd
@@ -47,7 +47,7 @@ is often the case in complex graphics.
 library(ggplot2)
 
 tidySingleCellExperiment::pbmc_small \%>\%
-    
+
     tidySingleCellExperiment::ggplot(aes(groups, nCount_RNA)) +
     geom_boxplot()
 }
diff --git a/man/join_transcripts.Rd b/man/join_transcripts.Rd
index 498dd40..2954e36 100644
--- a/man/join_transcripts.Rd
+++ b/man/join_transcripts.Rd
@@ -14,7 +14,7 @@ join_transcripts(
 )
 }
 \arguments{
-\item{.data}{A tidyseurat object}
+\item{.data}{A tidySingleCellExperiment object}
 
 \item{transcripts}{A vector of transcript identifiers to join}
 
diff --git a/man/print.Rd b/man/print.Rd
index 85ea70f..53d4817 100644
--- a/man/print.Rd
+++ b/man/print.Rd
@@ -62,33 +62,6 @@ exceeded. Default: 10.
 \item \code{tibble.max_extra_cols}: Number of extra columns printed in reduced form.
 Default: 100.
 }
-
-
-
-\itemize{
-\item \code{pillar.bold}: Use bold font, e.g. for column headers? This currently
-defaults to \code{FALSE}, because many terminal fonts have poor support for
-bold fonts.
-\item \code{pillar.subtle}: Use subtle style, e.g. for row numbers and data types?
-Default: \code{TRUE}.
-\item \code{pillar.subtle_num}: Use subtle style for insignificant digits? Default:
-\code{FALSE}, is also affected by the \code{pillar.subtle} option.
-\item \code{pillar.neg}: Highlight negative numbers? Default: \code{TRUE}.
-\item \code{pillar.sigfig}: The number of significant digits that will be printed and
-highlighted, default: \code{3}. Set the \code{pillar.subtle} option to \code{FALSE} to
-turn off highlighting of significant digits.
-\item \code{pillar.min_title_chars}: The minimum number of characters for the column
-title, default: \code{15}.  Column titles may be truncated up to that width to
-save horizontal space. Set to \code{Inf} to turn off truncation of column
-titles.
-\item \code{pillar.min_chars}: The minimum number of characters wide to
-display character columns, default: \code{0}.  Character columns may be
-truncated up to that width to save horizontal space. Set to \code{Inf} to
-turn off truncation of character columns.
-\item \code{pillar.max_dec_width}: The maximum allowed width for decimal notation,
-default 13.
-}
-
 }
 
 \examples{

From 3c4deb807b951438303c5083fc7ef26a94ad29a9 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Wed, 24 Nov 2021 13:05:32 +1100
Subject: [PATCH 06/17] fix vignette

---
 vignettes/introduction.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vignettes/introduction.Rmd b/vignettes/introduction.Rmd
index 6f6cb46..73413d1 100755
--- a/vignettes/introduction.Rmd
+++ b/vignettes/introduction.Rmd
@@ -250,7 +250,7 @@ marker_genes <-
 pbmc_small_cluster %>%
     join_features(features=marker_genes) %>%
     group_by(label) %>%
-    heatmap(feature, cell, abundance_counts, .scale="column")
+    heatmap(feature, .cell, abundance_counts, .scale="column")
 ```
 
 # Reduce dimensions

From 80732516fd9a0e33fad87ac26556a6a0872b0d1c Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Wed, 24 Nov 2021 13:39:19 +1100
Subject: [PATCH 07/17] change abundance and fix docs

---
 R/methods.R                |  6 +++---
 R/tidyr_methods.R          |  2 +-
 R/utilities.R              | 10 +++++-----
 README.Rmd                 |  4 ++--
 README.md                  |  4 ++--
 man/tidyr-methods.Rd       |  2 ++
 vignettes/introduction.Rmd |  4 ++--
 7 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/R/methods.R b/R/methods.R
index e08e812..a12a8ca 100755
--- a/R/methods.R
+++ b/R/methods.R
@@ -111,8 +111,8 @@ join_features.SingleCellExperiment <-
              shape = "long", ...) {
 
         # CRAN Note
-        cell = NULL
-        feature= NULL
+        .cell = NULL
+        .feature= NULL
 
         # Shape is long
         if (shape == "long")
@@ -126,7 +126,7 @@ join_features.SingleCellExperiment <-
                 ),
                 by = c_(.data)$name
             ) %>%
-            select(!!c_(.data)$symbol, feature, contains("abundance"), everything())
+            select(!!c_(.data)$symbol, .feature, contains(".abundance"), everything())
 
         # Shape if wide
         else
diff --git a/R/tidyr_methods.R b/R/tidyr_methods.R
index b3024c5..d3f5499 100755
--- a/R/tidyr_methods.R
+++ b/R/tidyr_methods.R
@@ -92,7 +92,7 @@ NULL
 #' @param ptype See tidyr::unnest
 #' @param .drop See tidyr::unnest
 #' @param .id tidyr::unnest
-#' @param sep tidyr::unnest
+#' @param .sep tidyr::unnest
 #' @param .preserve See tidyr::unnest
 #'
 #' @return A tidySingleCellExperiment objector a tibble depending on input
diff --git a/R/utilities.R b/R/utilities.R
index 496e0fe..64e717a 100755
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -234,17 +234,17 @@ get_abundance_sc_long <- function(.data, features=NULL, all=FALSE, exclude_zeros
                 }, ~ (.)) %>%
                 as.matrix() %>%
                 data.frame(check.names = FALSE) %>%
-                as_tibble(rownames="feature") %>%
+                as_tibble(rownames=".feature") %>%
                 tidyr::pivot_longer(
-                    cols=-feature,
+                    cols=- .feature,
                     names_to=c_(.data)$name,
-                    values_to="abundance" %>% paste(.y, sep="_"),
+                    values_to=".abundance" %>% paste(.y, sep="_"),
                     values_drop_na=TRUE
                 )
             # %>%
             # mutate_if(is.character, as.factor) %>%
         ) %>%
-        Reduce(function(...) full_join(..., by=c("feature", c_(.data)$name)), .)
+        Reduce(function(...) full_join(..., by=c(".feature", c_(.data)$name)), .)
 }
 
 #' @importFrom dplyr select_if
@@ -349,7 +349,7 @@ is_sample_feature_deprecated_used = function(.data, user_columns, use_old_specia
   old_standard_is_used = old_standard_is_used_for_cell
 
   if(old_standard_is_used){
-    warning("tidySingleCellExperiment says: from version 1.3.1, the special columns including cell id (colnames(se)) has changed to \".cell\". This dataset is returned with the old-style vocabulary (feature), however we suggest to update your workflow to reflect the new vocabulary (.cell)")
+    warning("tidySingleCellExperiment says: from version 1.3.1, the special columns including cell id (colnames(se)) has changed to \".cell\". This dataset is returned with the old-style vocabulary (cell), however we suggest to update your workflow to reflect the new vocabulary (.cell)")
 
     use_old_special_names = TRUE
   }
diff --git a/README.Rmd b/README.Rmd
index 392cb05..481d775 100755
--- a/README.Rmd
+++ b/README.Rmd
@@ -180,7 +180,7 @@ Here we plot abundance of two features for each group.
 ```{r}
 pbmc_small_polished %>%
     join_features(features=c("HLA-DRA", "LYZ")) %>%
-    ggplot(aes(groups, abundance_counts + 1, fill=groups)) +
+    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) +
     scale_y_log10() +
@@ -317,7 +317,7 @@ marker_genes <-
 pbmc_small_cluster %>%
     join_features(features=marker_genes) %>%
     group_by(label) %>%
-    heatmap(feature, cell, abundance_counts, .scale="column")
+    heatmap(.feature, .cell, .abundance_counts, .scale="column")
 ```
 
 # Reduce dimensions
diff --git a/README.md b/README.md
index 6896b6f..f8b517f 100755
--- a/README.md
+++ b/README.md
@@ -224,7 +224,7 @@ Here we plot abundance of two features for each group.
 
     pbmc_small_polished %>%
         join_features(features=c("HLA-DRA", "LYZ")) %>%
-        ggplot(aes(groups, abundance_counts + 1, fill=groups)) +
+        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) +
         scale_y_log10() +
@@ -371,7 +371,7 @@ SingleCellExperiment, tidyverse functions and tidyHeatmap
     pbmc_small_cluster %>%
         join_features(features=marker_genes) %>%
         group_by(label) %>%
-        heatmap(feature, cell, abundance_counts, .scale="column")
+        heatmap(.feature, .cell, .abundance_counts, .scale="column")
 
     ## tidySingleCellExperiment says: A data frame is returned for independent data analysis.
 
diff --git a/man/tidyr-methods.Rd b/man/tidyr-methods.Rd
index 35c5a89..e167177 100644
--- a/man/tidyr-methods.Rd
+++ b/man/tidyr-methods.Rd
@@ -51,6 +51,8 @@ stripped. This makes \code{names_sep} roughly symmetric between nesting and unne
 
 \item{.id}{tidyr::unnest}
 
+\item{.sep}{tidyr::unnest}
+
 \item{.preserve}{See tidyr::unnest}
 
 \item{sep}{tidyr::unnest}
diff --git a/vignettes/introduction.Rmd b/vignettes/introduction.Rmd
index 73413d1..5bb9d53 100755
--- a/vignettes/introduction.Rmd
+++ b/vignettes/introduction.Rmd
@@ -169,7 +169,7 @@ Here we plot abundance of two features for each group.
 ```{r}
 pbmc_small_polished %>%
     join_features(features=c("HLA-DRA", "LYZ")) %>%
-    ggplot(aes(groups, abundance_counts + 1, fill=groups)) +
+    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) +
     scale_y_log10() +
@@ -250,7 +250,7 @@ marker_genes <-
 pbmc_small_cluster %>%
     join_features(features=marker_genes) %>%
     group_by(label) %>%
-    heatmap(feature, .cell, abundance_counts, .scale="column")
+    heatmap(.feature, .cell, .abundance_counts, .scale="column")
 ```
 
 # Reduce dimensions

From a8357cb90695d69a6a19136a26427f6cc1ddc323 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Wed, 24 Nov 2021 14:36:16 +1100
Subject: [PATCH 08/17] fix docs

---
 R/tidyr_methods.R    | 19 +++++++++++++------
 man/tidyr-methods.Rd | 15 +++++++++++++++
 2 files changed, 28 insertions(+), 6 deletions(-)

diff --git a/R/tidyr_methods.R b/R/tidyr_methods.R
index d3f5499..1d86b87 100755
--- a/R/tidyr_methods.R
+++ b/R/tidyr_methods.R
@@ -54,6 +54,19 @@
 #' @export
 NULL
 
+
+#' @rdname tidyr-methods
+#' @name unnest
+#'
+#' @export
+unnest.tidySingleCellExperiment_nested <- function(data, cols, ..., keep_empty=FALSE, ptype=NULL,
+                                                   names_sep=NULL, names_repair="check_unique", .drop, .id, .sep, .preserve) {
+  unnest_single_cell_experiment(data, cols, ..., keep_empty=keep_empty, ptype=ptype,
+                                        names_sep=names_sep, names_repair=names_repair, .drop, .id, .sep, .preserve)
+  }
+
+
+
 #' unnest_single_cell_experiment
 #'
 #' @importFrom tidyr unnest
@@ -148,12 +161,6 @@ unnest_single_cell_experiment  <-  function(data, cols, ..., keep_empty=FALSE, p
         )
 }
 
-#' @importFrom rlang quo_name
-#' @importFrom purrr imap
-#'
-#'
-#' @export
-unnest.tidySingleCellExperiment_nested <- unnest_single_cell_experiment
 
 
 
diff --git a/man/tidyr-methods.Rd b/man/tidyr-methods.Rd
index e167177..65448eb 100644
--- a/man/tidyr-methods.Rd
+++ b/man/tidyr-methods.Rd
@@ -2,11 +2,26 @@
 % Please edit documentation in R/tidyr_methods.R
 \name{unnest}
 \alias{unnest}
+\alias{unnest.tidySingleCellExperiment_nested}
 \alias{unnest_single_cell_experiment}
 \alias{nest}
 \alias{extract}
 \title{unnest}
 \usage{
+\method{unnest}{tidySingleCellExperiment_nested}(
+  data,
+  cols,
+  ...,
+  keep_empty = FALSE,
+  ptype = NULL,
+  names_sep = NULL,
+  names_repair = "check_unique",
+  .drop,
+  .id,
+  .sep,
+  .preserve
+)
+
 unnest_single_cell_experiment(
   data,
   cols,

From d58a6873272b3d078e23ae11f20b69b5af42ded9 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Wed, 24 Nov 2021 16:13:37 +1100
Subject: [PATCH 09/17] fix unnest

---
 R/tidyr_methods.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/R/tidyr_methods.R b/R/tidyr_methods.R
index 1d86b87..57acdcb 100755
--- a/R/tidyr_methods.R
+++ b/R/tidyr_methods.R
@@ -61,7 +61,10 @@ NULL
 #' @export
 unnest.tidySingleCellExperiment_nested <- function(data, cols, ..., keep_empty=FALSE, ptype=NULL,
                                                    names_sep=NULL, names_repair="check_unique", .drop, .id, .sep, .preserve) {
-  unnest_single_cell_experiment(data, cols, ..., keep_empty=keep_empty, ptype=ptype,
+
+  cols <- enquo(cols)
+
+  unnest_single_cell_experiment(data, !!cols, ..., keep_empty=keep_empty, ptype=ptype,
                                         names_sep=names_sep, names_repair=names_repair, .drop, .id, .sep, .preserve)
   }
 

From 9bc512630faf83cb4cc658b3c9b6a3dafb17499b Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Wed, 24 Nov 2021 16:21:01 +1100
Subject: [PATCH 10/17] fix arguments unnest

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

diff --git a/R/tidyr_methods.R b/R/tidyr_methods.R
index 57acdcb..354e4a1 100755
--- a/R/tidyr_methods.R
+++ b/R/tidyr_methods.R
@@ -65,7 +65,7 @@ unnest.tidySingleCellExperiment_nested <- function(data, cols, ..., keep_empty=F
   cols <- enquo(cols)
 
   unnest_single_cell_experiment(data, !!cols, ..., keep_empty=keep_empty, ptype=ptype,
-                                        names_sep=names_sep, names_repair=names_repair, .drop, .id, .sep, .preserve)
+                                        names_sep=names_sep, names_repair=names_repair)
   }
 
 

From 507753e2ebba53582e373962994b308677ab1583 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Mon, 20 Dec 2021 19:16:35 +1100
Subject: [PATCH 11/17] update code and fixes

---
 R/dplyr_methods.R                           |  2 +-
 R/tidyr_methods.R                           | 12 ++--
 man/extract-methods.Rd                      | 61 ++++++++++++++++++++
 man/nest-methods.Rd                         | 26 +++++++++
 man/separate-methods.Rd                     | 52 +++++++++++++++++
 man/unite-methods.Rd                        | 43 +-------------
 man/{tidyr-methods.Rd => unnest-methods.Rd} | 64 +++++----------------
 7 files changed, 163 insertions(+), 97 deletions(-)
 create mode 100644 man/extract-methods.Rd
 create mode 100644 man/nest-methods.Rd
 create mode 100644 man/separate-methods.Rd
 rename man/{tidyr-methods.Rd => unnest-methods.Rd} (56%)

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
index e74a4fb..162d1ed 100755
--- a/R/dplyr_methods.R
+++ b/R/dplyr_methods.R
@@ -318,7 +318,7 @@ filter.SingleCellExperiment <- function(.data, ..., .preserve=FALSE) {
     # Try to solve missing colnames
     if(colnames(.data) %>% is.null()){
       message("tidySingleCellExperiment says: the input object does not have cell names (colnames(...)). \n Therefore, the cell column in the filtered tibble abstraction will still include an incremental integer vector.")
-      new_meta = mew_meta %>% mutate(!!c_(.data)$symbol := as.integer(!!c_(.data)$symbol))
+      new_meta = new_meta %>% mutate(!!c_(.data)$symbol := as.integer(!!c_(.data)$symbol))
 
     }
 
diff --git a/R/tidyr_methods.R b/R/tidyr_methods.R
index 354e4a1..e210215 100755
--- a/R/tidyr_methods.R
+++ b/R/tidyr_methods.R
@@ -48,14 +48,14 @@
 #'     nest(data=-groups) %>%
 #'     unnest(data)
 #'
-#' @rdname tidyr-methods
+#' @rdname unnest-methods
 #' @name unnest
 #'
 #' @export
 NULL
 
 
-#' @rdname tidyr-methods
+#' @rdname unnest-methods
 #' @name unnest
 #'
 #' @export
@@ -121,7 +121,7 @@ unnest.tidySingleCellExperiment_nested <- function(data, cols, ..., keep_empty=F
 #'     nest(data=-groups) %>%
 #'     unnest_single_cell_experiment(data)
 #'
-#' @rdname tidyr-methods
+#' @rdname unnest-methods
 #' @name unnest_single_cell_experiment
 #'
 #'
@@ -184,7 +184,7 @@ unnest_single_cell_experiment  <-  function(data, cols, ..., keep_empty=FALSE, p
 #'
 #'     nest(data=-groups) %>%
 #'     unnest(data)
-#' @rdname tidyr-methods
+#' @rdname nest-methods
 #' @name nest
 #'
 #' @export
@@ -268,7 +268,7 @@ nest.SingleCellExperiment <- function(.data, ..., .names_sep = NULL) {
 #'
 #' @importFrom tidyr extract
 #'
-#' @rdname tidyr-methods
+#' @rdname extract-methods
 #' @name extract
 #'
 #' @export
@@ -559,7 +559,7 @@ unite.SingleCellExperiment <- function(data, col, ..., sep="_", remove=TRUE, na.
 #'
 #' @return A tidySingleCellExperiment objector a tibble depending on input
 #'
-#' @rdname unite-methods
+#' @rdname separate-methods
 #' @name separate
 #'
 #' @export
diff --git a/man/extract-methods.Rd b/man/extract-methods.Rd
new file mode 100644
index 0000000..e496a0a
--- /dev/null
+++ b/man/extract-methods.Rd
@@ -0,0 +1,61 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tidyr_methods.R
+\name{extract}
+\alias{extract}
+\alias{extract.SingleCellExperiment}
+\title{Extract a character column into multiple columns using regular
+expression groups}
+\usage{
+\method{extract}{SingleCellExperiment}(
+  data,
+  col,
+  into,
+  regex = "([[:alnum:]]+)",
+  remove = TRUE,
+  convert = FALSE,
+  ...
+)
+}
+\arguments{
+\item{data}{A tidySingleCellExperiment object}
+
+\item{col}{Column name or position. This is passed to
+\code{\link[tidyselect:vars_pull]{tidyselect::vars_pull()}}.
+
+This argument is passed by expression and supports
+\link[rlang:nse-force]{quasiquotation} (you can unquote column
+names or column positions).}
+
+\item{into}{Names of new variables to create as character vector.
+Use \code{NA} to omit the variable in the output.}
+
+\item{regex}{a regular expression used to extract the desired values.
+There should be one group (defined by \verb{()}) for each element of \code{into}.}
+
+\item{remove}{If \code{TRUE}, remove input column from output data frame.}
+
+\item{convert}{If \code{TRUE}, will run \code{\link[=type.convert]{type.convert()}} with
+\code{as.is=TRUE} on new columns. This is useful if the component
+columns are integer, numeric or logical.
+
+NB: this will cause string \code{"NA"}s to be converted to \code{NA}s.}
+
+\item{...}{Additional arguments passed on to methods.}
+}
+\value{
+A tidySingleCellExperiment objector a tibble depending on input
+}
+\description{
+Given a regular expression with capturing groups, \code{extract()} turns
+each group into a new column. If the groups don't match, or the input
+is NA, the output will be NA.
+}
+\examples{
+
+pbmc_small \%>\%
+
+    extract(groups, into="g", regex="g([0-9])", convert=TRUE)
+}
+\seealso{
+\code{\link[=separate]{separate()}} to split up by a separator.
+}
diff --git a/man/nest-methods.Rd b/man/nest-methods.Rd
new file mode 100644
index 0000000..fb257f9
--- /dev/null
+++ b/man/nest-methods.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tidyr_methods.R
+\name{nest}
+\alias{nest}
+\title{nest}
+\arguments{
+\item{.data}{A tbl. (See tidyr)}
+
+\item{...}{Name-variable pairs of the form new_col=c(col1, col2, col3) (See tidyr)}
+
+\item{.names_sep}{See ?tidyr::nest}
+}
+\value{
+A tidySingleCellExperiment objector a tibble depending on input
+}
+\description{
+nest
+}
+\examples{
+
+library(dplyr)
+pbmc_small \%>\%
+
+    nest(data=-groups) \%>\%
+    unnest(data)
+}
diff --git a/man/separate-methods.Rd b/man/separate-methods.Rd
new file mode 100644
index 0000000..24fd354
--- /dev/null
+++ b/man/separate-methods.Rd
@@ -0,0 +1,52 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tidyr_methods.R
+\name{separate}
+\alias{separate}
+\title{Separate a character column into multiple columns with a regular
+expression or numeric locations}
+\arguments{
+\item{sep}{Separator between columns.
+
+If character, \code{sep} is interpreted as a regular expression. The default
+value is a regular expression that matches any sequence of
+non-alphanumeric values.
+
+If numeric, \code{sep} is interpreted as character positions to split at. Positive
+values start at 1 at the far-left of the string; negative value start at -1 at
+the far-right of the string. The length of \code{sep} should be one less than
+\code{into}.}
+
+\item{extra}{If \code{sep} is a character vector, this controls what
+happens when there are too many pieces. There are three valid options:
+\itemize{
+\item "warn" (the default): emit a warning and drop extra values.
+\item "drop": drop any extra values without a warning.
+\item "merge": only splits at most \code{length(into)} times
+}}
+
+\item{fill}{If \code{sep} is a character vector, this controls what
+happens when there are not enough pieces. There are three valid options:
+\itemize{
+\item "warn" (the default): emit a warning and fill from the right
+\item "right": fill with missing values on the right
+\item "left": fill with missing values on the left
+}}
+}
+\value{
+A tidySingleCellExperiment objector a tibble depending on input
+}
+\description{
+Given either a regular expression or a vector of character positions,
+\code{separate()} turns a single character column into multiple columns.
+}
+\examples{
+
+un <- pbmc_small \%>\%
+
+    unite("new_col", c(orig.ident, groups))
+un \%>\% separate(col=new_col, into=c("orig.ident", "groups"))
+}
+\seealso{
+\code{\link[=unite]{unite()}}, the complement, \code{\link[=extract]{extract()}} which uses regular
+expression capturing groups.
+}
diff --git a/man/unite-methods.Rd b/man/unite-methods.Rd
index 31e9db6..fb19305 100644
--- a/man/unite-methods.Rd
+++ b/man/unite-methods.Rd
@@ -2,7 +2,6 @@
 % Please edit documentation in R/tidyr_methods.R
 \name{unite}
 \alias{unite}
-\alias{separate}
 \title{Unite multiple columns into one by pasting strings together}
 \arguments{
 \item{data}{A data frame.}
@@ -18,63 +17,25 @@ tidyverse; we support it here for backward compatibility).}
 
 \item{...}{<\code{\link[=tidyr_tidy_select]{tidy-select}}> Columns to unite}
 
+\item{sep}{Separator to use between values.}
+
 \item{na.rm}{If \code{TRUE}, missing values will be remove prior to uniting
 each value.}
 
 \item{remove}{If \code{TRUE}, remove input columns from output data frame.}
-
-\item{sep}{Separator between columns.
-
-If character, \code{sep} is interpreted as a regular expression. The default
-value is a regular expression that matches any sequence of
-non-alphanumeric values.
-
-If numeric, \code{sep} is interpreted as character positions to split at. Positive
-values start at 1 at the far-left of the string; negative value start at -1 at
-the far-right of the string. The length of \code{sep} should be one less than
-\code{into}.}
-
-\item{extra}{If \code{sep} is a character vector, this controls what
-happens when there are too many pieces. There are three valid options:
-\itemize{
-\item "warn" (the default): emit a warning and drop extra values.
-\item "drop": drop any extra values without a warning.
-\item "merge": only splits at most \code{length(into)} times
-}}
-
-\item{fill}{If \code{sep} is a character vector, this controls what
-happens when there are not enough pieces. There are three valid options:
-\itemize{
-\item "warn" (the default): emit a warning and fill from the right
-\item "right": fill with missing values on the right
-\item "left": fill with missing values on the left
-}}
 }
 \value{
-A tidySingleCellExperiment objector a tibble depending on input
-
 A tidySingleCellExperiment objector a tibble depending on input
 }
 \description{
 Convenience function to paste together multiple columns into one.
-
-Given either a regular expression or a vector of character positions,
-\code{separate()} turns a single character column into multiple columns.
 }
 \examples{
 
 pbmc_small \%>\%
 
     unite("new_col", c(orig.ident, groups))
-
-un <- pbmc_small \%>\%
-
-    unite("new_col", c(orig.ident, groups))
-un \%>\% separate(col=new_col, into=c("orig.ident", "groups"))
 }
 \seealso{
 \code{\link[=separate]{separate()}}, the complement.
-
-\code{\link[=unite]{unite()}}, the complement, \code{\link[=extract]{extract()}} which uses regular
-expression capturing groups.
 }
diff --git a/man/tidyr-methods.Rd b/man/unnest-methods.Rd
similarity index 56%
rename from man/tidyr-methods.Rd
rename to man/unnest-methods.Rd
index 65448eb..7787fa8 100644
--- a/man/tidyr-methods.Rd
+++ b/man/unnest-methods.Rd
@@ -4,8 +4,6 @@
 \alias{unnest}
 \alias{unnest.tidySingleCellExperiment_nested}
 \alias{unnest_single_cell_experiment}
-\alias{nest}
-\alias{extract}
 \title{unnest}
 \usage{
 \method{unnest}{tidySingleCellExperiment_nested}(
@@ -37,14 +35,24 @@ unnest_single_cell_experiment(
 )
 }
 \arguments{
-\item{data}{A tidySingleCellExperiment object}
+\item{data}{A tbl. (See tidyr)}
 
 \item{cols}{<\code{\link[=tidyr_tidy_select]{tidy-select}}> Columns to unnest.
 If you \code{unnest()} multiple columns, parallel entries must be of
 compatible sizes, i.e. they're either equal or length 1 (following the
 standard tidyverse recycling rules).}
 
-\item{...}{Additional arguments passed on to methods.}
+\item{...}{<\code{\link[=tidyr_tidy_select]{tidy-select}}> Columns to nest, specified
+using name-variable pairs of the form \code{new_col=c(col1, col2, col3)}.
+The right hand side can be any valid tidy select expression.
+
+\Sexpr[results=rd, stage=render]{lifecycle::badge("deprecated")}:
+previously you could write \code{df \%>\% nest(x, y, z)} and \code{df \%>\% unnest(x, y, z)}. Convert to \code{df \%>\% nest(data=c(x, y, z))}.
+and \code{df \%>\% unnest(c(x, y, z))}.
+
+If you previously created new variable in \code{unnest()} you'll now need to
+do it explicitly with \code{mutate()}. Convert \code{df \%>\% unnest(y=fun(x, y, z))}
+to \code{df \%>\% mutate(y=fun(x, y, z)) \%>\% unnest(y)}.}
 
 \item{keep_empty}{See tidyr::unnest}
 
@@ -71,45 +79,16 @@ stripped. This makes \code{names_sep} roughly symmetric between nesting and unne
 \item{.preserve}{See tidyr::unnest}
 
 \item{sep}{tidyr::unnest}
-
-\item{.data}{A tbl. (See tidyr)}
-
-\item{.names_sep}{See ?tidyr::nest}
-
-\item{col}{Column name or position. This is passed to
-\code{\link[tidyselect:vars_pull]{tidyselect::vars_pull()}}.
-
-This argument is passed by expression and supports
-\link[rlang:nse-force]{quasiquotation} (you can unquote column
-names or column positions).}
-
-\item{into}{Names of new variables to create as character vector.
-Use \code{NA} to omit the variable in the output.}
-
-\item{regex}{a regular expression used to extract the desired values.
-There should be one group (defined by \verb{()}) for each element of \code{into}.}
-
-\item{remove}{If \code{TRUE}, remove input column from output data frame.}
-
-\item{convert}{If \code{TRUE}, will run \code{\link[=type.convert]{type.convert()}} with
-\code{as.is=TRUE} on new columns. This is useful if the component
-columns are integer, numeric or logical.
-
-NB: this will cause string \code{"NA"}s to be converted to \code{NA}s.}
 }
 \value{
 A tidySingleCellExperiment objector a tibble depending on input
 
-A tidySingleCellExperiment objector a tibble depending on input
-
-A tidySingleCellExperiment objector a tibble depending on input
-
 A tidySingleCellExperiment objector a tibble depending on input
 }
 \description{
-Given a regular expression with capturing groups, \code{extract()} turns
-each group into a new column. If the groups don't match, or the input
-is NA, the output will be NA.
+unnest
+
+unnest_single_cell_experiment
 }
 \examples{
 
@@ -126,17 +105,4 @@ pbmc_small \%>\%
     nest(data=-groups) \%>\%
     unnest_single_cell_experiment(data)
 
-
-library(dplyr)
-pbmc_small \%>\%
-
-    nest(data=-groups) \%>\%
-    unnest(data)
-
-pbmc_small \%>\%
-
-    extract(groups, into="g", regex="g([0-9])", convert=TRUE)
-}
-\seealso{
-\code{\link[=separate]{separate()}} to split up by a separator.
 }

From 4d2a6488108d1617dba44c470ce94bfc6f781780 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 28 Jan 2022 23:48:38 +1100
Subject: [PATCH 12/17] test

---
 DESCRIPTION                         |  2 +-
 man/print.Rd                        | 27 ---------------------------
 tests/testthat/test-dplyr_methods.R |  2 --
 tests/testthat/test-methods.R       | 15 +++++++++++++++
 4 files changed, 16 insertions(+), 30 deletions(-)
 create mode 100644 tests/testthat/test-methods.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 7024be9..0b88998 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -56,7 +56,7 @@ Biarch: true
 biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression, GeneExpression, Normalization, Clustering, QualityControl, Sequencing, featureion, featureomics
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Roxygen: list(markdown = TRUE)
 URL: https://github.com/stemangiola/tidySingleCellExperiment
 BugReports: https://github.com/stemangiola/tidySingleCellExperiment/issues
diff --git a/man/print.Rd b/man/print.Rd
index 85ea70f..53d4817 100644
--- a/man/print.Rd
+++ b/man/print.Rd
@@ -62,33 +62,6 @@ exceeded. Default: 10.
 \item \code{tibble.max_extra_cols}: Number of extra columns printed in reduced form.
 Default: 100.
 }
-
-
-
-\itemize{
-\item \code{pillar.bold}: Use bold font, e.g. for column headers? This currently
-defaults to \code{FALSE}, because many terminal fonts have poor support for
-bold fonts.
-\item \code{pillar.subtle}: Use subtle style, e.g. for row numbers and data types?
-Default: \code{TRUE}.
-\item \code{pillar.subtle_num}: Use subtle style for insignificant digits? Default:
-\code{FALSE}, is also affected by the \code{pillar.subtle} option.
-\item \code{pillar.neg}: Highlight negative numbers? Default: \code{TRUE}.
-\item \code{pillar.sigfig}: The number of significant digits that will be printed and
-highlighted, default: \code{3}. Set the \code{pillar.subtle} option to \code{FALSE} to
-turn off highlighting of significant digits.
-\item \code{pillar.min_title_chars}: The minimum number of characters for the column
-title, default: \code{15}.  Column titles may be truncated up to that width to
-save horizontal space. Set to \code{Inf} to turn off truncation of column
-titles.
-\item \code{pillar.min_chars}: The minimum number of characters wide to
-display character columns, default: \code{0}.  Character columns may be
-truncated up to that width to save horizontal space. Set to \code{Inf} to
-turn off truncation of character columns.
-\item \code{pillar.max_dec_width}: The maximum allowed width for decimal notation,
-default 13.
-}
-
 }
 
 \examples{
diff --git a/tests/testthat/test-dplyr_methods.R b/tests/testthat/test-dplyr_methods.R
index afdf184..db3204e 100755
--- a/tests/testthat/test-dplyr_methods.R
+++ b/tests/testthat/test-dplyr_methods.R
@@ -2,8 +2,6 @@ context("dplyr test")
 
 library(magrittr)
 
-pbmc_small <- pbmc_small
-
 test_that("arrange", {
     tt_pca_aranged <-
         pbmc_small %>%
diff --git a/tests/testthat/test-methods.R b/tests/testthat/test-methods.R
new file mode 100644
index 0000000..dcc255a
--- /dev/null
+++ b/tests/testthat/test-methods.R
@@ -0,0 +1,15 @@
+context('methods test')
+
+data("pbmc_small")
+
+test_that("join_features",{
+
+
+  pbmc_small |>
+    join_features("CD3D") |>
+    slice(1) |>
+    tidySingleCellExperiment::pull(abundance_counts) |>
+    expect_equal(4, tolerance=0.1)
+
+
+})

From ab6f3d8bbb91dff0f6380b1e8b47ac8355c8b605 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Sat, 23 Oct 2021 19:35:20 +1100
Subject: [PATCH 13/17] use ttservice

---
 DESCRIPTION          |   1 +
 NAMESPACE            |  57 +++++++++++-----------
 R/methods.R          | 113 ++++++++++++++++++++-----------------------
 man/join_features.Rd |  26 +++++-----
 4 files changed, 95 insertions(+), 102 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8223300..febd58f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,6 +9,7 @@ Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCe
 License: GPL-3
 Depends:
     R (>= 4.0.0),
+    ttservice,
     SingleCellExperiment
 Imports:
     SummarizedExperiment,
diff --git a/NAMESPACE b/NAMESPACE
index 56f3a05..20ba739 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,81 +2,79 @@
 
 S3method(add_count,SingleCellExperiment)
 S3method(add_count,default)
-S3method(arrange,SingleCellExperiment)
-S3method(as_tibble,SingleCellExperiment)
 S3method(bind_cols,SingleCellExperiment)
 S3method(bind_cols,default)
 S3method(bind_rows,SingleCellExperiment)
 S3method(bind_rows,default)
 S3method(count,SingleCellExperiment)
 S3method(count,default)
-S3method(distinct,SingleCellExperiment)
-S3method(extract,SingleCellExperiment)
-S3method(filter,SingleCellExperiment)
-S3method(full_join,SingleCellExperiment)
-S3method(ggplot,SingleCellExperiment)
-S3method(glimpse,tidySingleCellExperiment)
-S3method(group_by,SingleCellExperiment)
-S3method(inner_join,SingleCellExperiment)
-S3method(join_features,SingleCellExperiment)
-S3method(join_features,default)
 S3method(join_transcripts,Seurat)
 S3method(join_transcripts,default)
-S3method(left_join,SingleCellExperiment)
-S3method(mutate,SingleCellExperiment)
-S3method(nest,SingleCellExperiment)
-S3method(pivot_longer,SingleCellExperiment)
 S3method(plot_ly,SingleCellExperiment)
 S3method(plot_ly,default)
 S3method(print,SingleCellExperiment)
-S3method(pull,SingleCellExperiment)
-S3method(rename,SingleCellExperiment)
-S3method(right_join,SingleCellExperiment)
-S3method(rowwise,SingleCellExperiment)
-S3method(sample_frac,SingleCellExperiment)
-S3method(sample_n,SingleCellExperiment)
-S3method(select,SingleCellExperiment)
-S3method(separate,SingleCellExperiment)
-S3method(slice,SingleCellExperiment)
-S3method(summarise,SingleCellExperiment)
 S3method(tidy,SingleCellExperiment)
-S3method(unite,SingleCellExperiment)
-S3method(unnest,tidySingleCellExperiment_nested)
 export("%>%")
 export(add_count)
 export(arrange)
+export(arrange.SingleCellExperiment)
 export(as_tibble)
+export(as_tibble.SingleCellExperiment)
 export(bind_cols)
 export(bind_rows)
 export(count)
 export(distinct)
+export(distinct.SingleCellExperiment)
 export(extract)
+export(extract.SingleCellExperiment)
 export(filter)
+export(filter.SingleCellExperiment)
 export(full_join)
+export(full_join.SingleCellExperiment)
 export(ggplot)
+export(ggplot.SingleCellExperiment)
 export(glimpse)
+export(glimpse.tidySingleCellExperiment)
 export(group_by)
+export(group_by.SingleCellExperiment)
 export(inner_join)
+export(inner_join.SingleCellExperiment)
 export(join_features)
 export(join_transcripts)
 export(left_join)
+export(left_join.SingleCellExperiment)
 export(mutate)
+export(mutate.SingleCellExperiment)
 export(nest)
+export(nest.SingleCellExperiment)
 export(pivot_longer)
+export(pivot_longer.SingleCellExperiment)
 export(plot_ly)
 export(pull)
+export(pull.SingleCellExperiment)
 export(rename)
+export(rename.SingleCellExperiment)
 export(right_join)
+export(right_join.SingleCellExperiment)
 export(rowwise)
+export(rowwise.SingleCellExperiment)
 export(sample_frac)
+export(sample_frac.SingleCellExperiment)
 export(sample_n)
+export(sample_n.SingleCellExperiment)
 export(select)
+export(select.SingleCellExperiment)
 export(separate)
+export(separate.SingleCellExperiment)
 export(slice)
+export(slice.SingleCellExperiment)
 export(summarise)
+export(summarise.SingleCellExperiment)
 export(tidy)
 export(unite)
+export(unite.SingleCellExperiment)
 export(unnest)
+export(unnest.tidySingleCellExperiment_nested)
 export(unnest_single_cell_experiment)
 importFrom(S4Vectors,DataFrame)
 importFrom(SingleCellExperiment,cbind)
@@ -147,7 +145,6 @@ importFrom(tidyr,separate)
 importFrom(tidyr,spread)
 importFrom(tidyr,unite)
 importFrom(tidyr,unnest)
-importFrom(tidyselect,contains)
 importFrom(tidyselect,eval_select)
-importFrom(tidyselect,everything)
+importFrom(ttservice,join_features)
 importFrom(utils,tail)
diff --git a/R/methods.R b/R/methods.R
index b1d35c1..c0ecfb8 100755
--- a/R/methods.R
+++ b/R/methods.R
@@ -52,89 +52,82 @@ setMethod(
     }
 )
 
-#' Add differential featureion information to a tbl using edgeR.
+#' Extract and join information for features.
 #'
-#' \lifecycle{experimental}
 #'
-#' @description join_features() extracts and joins information for specific
-#'   features
+#' @description join_features() extracts and joins information for specified features
 #'
 #' @importFrom rlang enquo
 #' @importFrom magrittr "%>%"
+#' @importFrom ttservice join_features
 #'
 #' @name join_features
 #' @rdname join_features
 #'
-#' @param .data A tidy SingleCellExperiment object
+#' @param .data A SingleCellExperiment object
 #' @param features A vector of feature identifiers to join
 #' @param all If TRUE return all
 #' @param exclude_zeros If TRUE exclude zero values
 #' @param shape Format of the returned table "long" or "wide"
 #' @param ... Parameters to pass to join wide, i.e. assay name to extract feature abundance from and gene prefix, for shape="wide"
 #'
-#' @details This function extracts information for specified features and
-#'   returns the information in either long or wide format.
+#' @details This function extracts information for specified features and returns the information in either long or wide format.
 #'
-#' @return A `tbl` containing the information.for the specified features
+#' @return An object containing the information.for the specified features
 #'
 #' @examples
 #'
-#' tidySingleCellExperiment::pbmc_small %>%
+#' data("pbmc_small")
+#' pbmc_small %>%
+#' join_features(features = c("HLA-DRA", "LYZ"))
 #'
-#'     join_features(features=c("HLA-DRA", "LYZ"))
-#' @export
 #'
-join_features <- function(.data,
-                             features = NULL,
-                             all = FALSE,
-                             exclude_zeros = FALSE,
-                             shape = "long", ...) {
-    UseMethod("join_features", .data)
-}
-#' @export
-join_features.default <-
-    function(.data,
-             features = NULL,
-             all = FALSE,
-             exclude_zeros = FALSE,
-             shape = "long", ...) {
-        print("This function cannot be applied to this object")
-    }
-#' @importFrom tidyselect contains
-#' @importFrom tidyselect everything
 #' @export
-join_features.SingleCellExperiment <-
-    function(.data,
-             features = NULL,
-             all = FALSE,
-             exclude_zeros = FALSE,
-             shape = "long", ...) {
+#'
+NULL
+
+#' join_features
+#'
+#' @docType methods
+#' @rdname join_features
+#'
+#' @return An object containing the information.for the specified features
+#'
+setMethod("join_features", "SingleCellExperiment",  function(.data,
+                                               features = NULL,
+                                               all = FALSE,
+                                               exclude_zeros = FALSE,
+                                               shape = "long", ...)
+{
 
-        # CRAN Note
-        cell = NULL
-        feature= NULL
+  # CRAN Note
+  cell = NULL
+  feature= NULL
+
+  # Shape is long
+  if (shape == "long")
+    .data %>%
+    left_join(
+      get_abundance_sc_long(
+        .data = .data,
+        features = features,
+        all = all,
+        exclude_zeros = exclude_zeros
+      ),
+      by = "cell"
+    ) %>%
+    select(cell, feature, contains("abundance"), everything())
+
+  # Shape if wide
+  else
+    .data  %>% left_join(get_abundance_sc_wide(
+      .data = .data,
+      features = features,
+      all = all, ...
+    ),
+    by = "cell")
+
+})
 
-        # Shape is long
-        if (shape == "long")
-          .data %>%
-            left_join(
-                get_abundance_sc_long(
-                    .data = .data,
-                    features = features,
-                    all = all,
-                    exclude_zeros = exclude_zeros
-                ),
-                by = "cell"
-            ) %>%
-            select(cell, feature, contains("abundance"), everything())
 
-        # Shape if wide
-        else
-          .data  %>% left_join(get_abundance_sc_wide(
-                .data = .data,
-                features = features,
-                all = all, ...
-            ),
-            by = "cell")
 
-    }
diff --git a/man/join_features.Rd b/man/join_features.Rd
index c1c4fb3..3463178 100644
--- a/man/join_features.Rd
+++ b/man/join_features.Rd
@@ -1,10 +1,12 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/methods.R
+\docType{methods}
 \name{join_features}
 \alias{join_features}
-\title{Add differential featureion information to a tbl using edgeR.}
+\alias{join_features,SingleCellExperiment-method}
+\title{Extract and join information for features.}
 \usage{
-join_features(
+\S4method{join_features}{SingleCellExperiment}(
   .data,
   features = NULL,
   all = FALSE,
@@ -14,7 +16,7 @@ join_features(
 )
 }
 \arguments{
-\item{.data}{A tidy SingleCellExperiment object}
+\item{.data}{A SingleCellExperiment object}
 
 \item{features}{A vector of feature identifiers to join}
 
@@ -27,21 +29,21 @@ join_features(
 \item{...}{Parameters to pass to join wide, i.e. assay name to extract feature abundance from and gene prefix, for shape="wide"}
 }
 \value{
-A \code{tbl} containing the information.for the specified features
+An object containing the information.for the specified features
+
+An object containing the information.for the specified features
 }
 \description{
-join_features() extracts and joins information for specific
-features
+join_features() extracts and joins information for specified features
 }
 \details{
-\lifecycle{experimental}
-
-This function extracts information for specified features and
-returns the information in either long or wide format.
+This function extracts information for specified features and returns the information in either long or wide format.
 }
 \examples{
 
-tidySingleCellExperiment::pbmc_small \%>\%
+data("pbmc_small")
+pbmc_small \%>\%
+join_features(features = c("HLA-DRA", "LYZ"))
+
 
-    join_features(features=c("HLA-DRA", "LYZ"))
 }

From cc53d23f50ef16f2dd00e885a34407264495f6c1 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Sat, 23 Oct 2021 20:00:36 +1100
Subject: [PATCH 14/17] update NAMESPACE

---
 NAMESPACE | 52 ++++++++++++++++++++++++++--------------------------
 1 file changed, 26 insertions(+), 26 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 20ba739..b65a854 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,79 +2,79 @@
 
 S3method(add_count,SingleCellExperiment)
 S3method(add_count,default)
+S3method(arrange,SingleCellExperiment)
+S3method(as_tibble,SingleCellExperiment)
 S3method(bind_cols,SingleCellExperiment)
 S3method(bind_cols,default)
 S3method(bind_rows,SingleCellExperiment)
 S3method(bind_rows,default)
 S3method(count,SingleCellExperiment)
 S3method(count,default)
+S3method(distinct,SingleCellExperiment)
+S3method(extract,SingleCellExperiment)
+S3method(filter,SingleCellExperiment)
+S3method(full_join,SingleCellExperiment)
+S3method(ggplot,SingleCellExperiment)
+S3method(glimpse,tidySingleCellExperiment)
+S3method(group_by,SingleCellExperiment)
+S3method(inner_join,SingleCellExperiment)
 S3method(join_transcripts,Seurat)
 S3method(join_transcripts,default)
+S3method(left_join,SingleCellExperiment)
+S3method(mutate,SingleCellExperiment)
+S3method(nest,SingleCellExperiment)
+S3method(pivot_longer,SingleCellExperiment)
 S3method(plot_ly,SingleCellExperiment)
 S3method(plot_ly,default)
 S3method(print,SingleCellExperiment)
+S3method(pull,SingleCellExperiment)
+S3method(rename,SingleCellExperiment)
+S3method(right_join,SingleCellExperiment)
+S3method(rowwise,SingleCellExperiment)
+S3method(sample_frac,SingleCellExperiment)
+S3method(sample_n,SingleCellExperiment)
+S3method(select,SingleCellExperiment)
+S3method(separate,SingleCellExperiment)
+S3method(slice,SingleCellExperiment)
+S3method(summarise,SingleCellExperiment)
 S3method(tidy,SingleCellExperiment)
+S3method(unite,SingleCellExperiment)
+S3method(unnest,tidySingleCellExperiment_nested)
 export("%>%")
 export(add_count)
 export(arrange)
-export(arrange.SingleCellExperiment)
 export(as_tibble)
-export(as_tibble.SingleCellExperiment)
 export(bind_cols)
 export(bind_rows)
 export(count)
 export(distinct)
-export(distinct.SingleCellExperiment)
 export(extract)
-export(extract.SingleCellExperiment)
 export(filter)
-export(filter.SingleCellExperiment)
 export(full_join)
-export(full_join.SingleCellExperiment)
 export(ggplot)
-export(ggplot.SingleCellExperiment)
 export(glimpse)
-export(glimpse.tidySingleCellExperiment)
 export(group_by)
-export(group_by.SingleCellExperiment)
 export(inner_join)
-export(inner_join.SingleCellExperiment)
 export(join_features)
 export(join_transcripts)
 export(left_join)
-export(left_join.SingleCellExperiment)
 export(mutate)
-export(mutate.SingleCellExperiment)
 export(nest)
-export(nest.SingleCellExperiment)
 export(pivot_longer)
-export(pivot_longer.SingleCellExperiment)
 export(plot_ly)
 export(pull)
-export(pull.SingleCellExperiment)
 export(rename)
-export(rename.SingleCellExperiment)
 export(right_join)
-export(right_join.SingleCellExperiment)
 export(rowwise)
-export(rowwise.SingleCellExperiment)
 export(sample_frac)
-export(sample_frac.SingleCellExperiment)
 export(sample_n)
-export(sample_n.SingleCellExperiment)
 export(select)
-export(select.SingleCellExperiment)
 export(separate)
-export(separate.SingleCellExperiment)
 export(slice)
-export(slice.SingleCellExperiment)
 export(summarise)
-export(summarise.SingleCellExperiment)
 export(tidy)
 export(unite)
-export(unite.SingleCellExperiment)
 export(unnest)
-export(unnest.tidySingleCellExperiment_nested)
 export(unnest_single_cell_experiment)
 importFrom(S4Vectors,DataFrame)
 importFrom(SingleCellExperiment,cbind)

From 47df266699ffd4d9ca4df709f7fe0f481fabf4cb Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 28 Jan 2022 23:48:38 +1100
Subject: [PATCH 15/17] test

---
 man/print.Rd                        | 27 ---------------------------
 tests/testthat/test-dplyr_methods.R |  2 --
 tests/testthat/test-methods.R       | 15 +++++++++++++++
 3 files changed, 15 insertions(+), 29 deletions(-)
 create mode 100644 tests/testthat/test-methods.R

diff --git a/man/print.Rd b/man/print.Rd
index 85ea70f..53d4817 100644
--- a/man/print.Rd
+++ b/man/print.Rd
@@ -62,33 +62,6 @@ exceeded. Default: 10.
 \item \code{tibble.max_extra_cols}: Number of extra columns printed in reduced form.
 Default: 100.
 }
-
-
-
-\itemize{
-\item \code{pillar.bold}: Use bold font, e.g. for column headers? This currently
-defaults to \code{FALSE}, because many terminal fonts have poor support for
-bold fonts.
-\item \code{pillar.subtle}: Use subtle style, e.g. for row numbers and data types?
-Default: \code{TRUE}.
-\item \code{pillar.subtle_num}: Use subtle style for insignificant digits? Default:
-\code{FALSE}, is also affected by the \code{pillar.subtle} option.
-\item \code{pillar.neg}: Highlight negative numbers? Default: \code{TRUE}.
-\item \code{pillar.sigfig}: The number of significant digits that will be printed and
-highlighted, default: \code{3}. Set the \code{pillar.subtle} option to \code{FALSE} to
-turn off highlighting of significant digits.
-\item \code{pillar.min_title_chars}: The minimum number of characters for the column
-title, default: \code{15}.  Column titles may be truncated up to that width to
-save horizontal space. Set to \code{Inf} to turn off truncation of column
-titles.
-\item \code{pillar.min_chars}: The minimum number of characters wide to
-display character columns, default: \code{0}.  Character columns may be
-truncated up to that width to save horizontal space. Set to \code{Inf} to
-turn off truncation of character columns.
-\item \code{pillar.max_dec_width}: The maximum allowed width for decimal notation,
-default 13.
-}
-
 }
 
 \examples{
diff --git a/tests/testthat/test-dplyr_methods.R b/tests/testthat/test-dplyr_methods.R
index afdf184..db3204e 100755
--- a/tests/testthat/test-dplyr_methods.R
+++ b/tests/testthat/test-dplyr_methods.R
@@ -2,8 +2,6 @@ context("dplyr test")
 
 library(magrittr)
 
-pbmc_small <- pbmc_small
-
 test_that("arrange", {
     tt_pca_aranged <-
         pbmc_small %>%
diff --git a/tests/testthat/test-methods.R b/tests/testthat/test-methods.R
new file mode 100644
index 0000000..dcc255a
--- /dev/null
+++ b/tests/testthat/test-methods.R
@@ -0,0 +1,15 @@
+context('methods test')
+
+data("pbmc_small")
+
+test_that("join_features",{
+
+
+  pbmc_small |>
+    join_features("CD3D") |>
+    slice(1) |>
+    tidySingleCellExperiment::pull(abundance_counts) |>
+    expect_equal(4, tolerance=0.1)
+
+
+})

From 0f816a255a2b357c03606cd50c1849037ac6e4d6 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Sat, 29 Jan 2022 00:09:30 +1100
Subject: [PATCH 16/17] fix |> bug

---
 tests/testthat/test-methods.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/testthat/test-methods.R b/tests/testthat/test-methods.R
index dcc255a..9149341 100644
--- a/tests/testthat/test-methods.R
+++ b/tests/testthat/test-methods.R
@@ -1,14 +1,14 @@
 context('methods test')
 
 data("pbmc_small")
-
+library(dplyr)
 test_that("join_features",{
 
 
-  pbmc_small |>
-    join_features("CD3D") |>
-    slice(1) |>
-    tidySingleCellExperiment::pull(abundance_counts) |>
+  pbmc_small %>%
+    join_features("CD3D") %>%
+    slice(1) %>%
+    tidySingleCellExperiment::pull(abundance_counts) %>%
     expect_equal(4, tolerance=0.1)
 
 

From 5190f6243800d9975e62311b16a27509ea780b73 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Sat, 29 Jan 2022 04:52:23 +1100
Subject: [PATCH 17/17] fix test

---
 tests/testthat/test-methods.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-methods.R b/tests/testthat/test-methods.R
index 9149341..c7fb84a 100644
--- a/tests/testthat/test-methods.R
+++ b/tests/testthat/test-methods.R
@@ -8,7 +8,7 @@ test_that("join_features",{
   pbmc_small %>%
     join_features("CD3D") %>%
     slice(1) %>%
-    tidySingleCellExperiment::pull(abundance_counts) %>%
+    tidySingleCellExperiment::pull(.abundance_counts) %>%
     expect_equal(4, tolerance=0.1)