From 10d84c2007bf507b8911e3309f1b53c5aa4c8701 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:16:51 +1000
Subject: [PATCH 01/34] use new pillar methods

---
 NAMESPACE              |   8 +-
 R/pillar_utilities.R   |  26 ++++
 R/print_method.R       | 338 +++++++----------------------------------
 R/utilities.R          |  16 ++
 man/extract-methods.Rd |   2 +-
 man/unite-methods.Rd   |   4 +-
 man/unnest-methods.Rd  |   2 -
 7 files changed, 107 insertions(+), 289 deletions(-)
 create mode 100644 R/pillar_utilities.R

diff --git a/NAMESPACE b/NAMESPACE
index a334cf0..f18e25d 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -37,6 +37,7 @@ S3method(select,SingleCellExperiment)
 S3method(separate,SingleCellExperiment)
 S3method(slice,SingleCellExperiment)
 S3method(summarise,SingleCellExperiment)
+S3method(tbl_format_header,tidySingleCellExperiment)
 S3method(tidy,SingleCellExperiment)
 S3method(unite,SingleCellExperiment)
 S3method(unnest,tidySingleCellExperiment_nested)
@@ -72,6 +73,7 @@ export(select)
 export(separate)
 export(slice)
 export(summarise)
+export(tbl_format_header)
 export(tidy)
 export(unite)
 export(unnest)
@@ -114,9 +116,10 @@ importFrom(lifecycle,deprecate_warn)
 importFrom(magrittr,"%$%")
 importFrom(magrittr,"%>%")
 importFrom(methods,as)
-importFrom(pillar,extra_cols)
-importFrom(pillar,squeeze)
+importFrom(pillar,align)
+importFrom(pillar,get_extent)
 importFrom(pillar,style_subtle)
+importFrom(pillar,tbl_format_header)
 importFrom(plotly,plot_ly)
 importFrom(purrr,imap)
 importFrom(purrr,map)
@@ -141,7 +144,6 @@ importFrom(stringr,str_replace)
 importFrom(tibble,as_tibble)
 importFrom(tibble,enframe)
 importFrom(tibble,glimpse)
-importFrom(tibble,trunc_mat)
 importFrom(tidyr,extract)
 importFrom(tidyr,nest)
 importFrom(tidyr,pivot_longer)
diff --git a/R/pillar_utilities.R b/R/pillar_utilities.R
new file mode 100644
index 0000000..b84d179
--- /dev/null
+++ b/R/pillar_utilities.R
@@ -0,0 +1,26 @@
+NBSP <- "\U00A0"
+
+pillar___format_comment = function (x, width)
+{
+  if (length(x) == 0L) {
+    return(character())
+  }
+  map_chr(x, pillar___wrap, prefix = "# ", width = min(width, cli::console_width()))
+}
+
+#' @importFrom fansi strwrap_ctl
+pillar___strwrap2 = function (x, width, indent)
+{
+  fansi::strwrap_ctl(x, width = max(width, 0), indent = indent,
+                     exdent = indent + 2)
+}
+
+
+pillar___wrap = function (..., indent = 0, prefix = "", width)
+{
+  x <- paste0(..., collapse = "")
+  wrapped <- pillar___strwrap2(x, width - get_extent(prefix), indent)
+  wrapped <- paste0(prefix, wrapped)
+  wrapped <- gsub(NBSP, " ", wrapped)
+  paste0(wrapped, collapse = "\n")
+}
diff --git a/R/print_method.R b/R/print_method.R
index 4241726..2c4805c 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -1,5 +1,56 @@
 # This file is a replacement of the unexported functions in the tibble package, in order to specify "tibble abstraction in the header"
 
+#' tbl_format_header
+#'
+#' @rdname tbl_format_header-methods
+#' @name tbl_format_header
+#' @importFrom pillar tbl_format_header
+#'
+#' @noRd
+#'
+#' @export
+NULL
+
+#' @importFrom rlang names2
+#' @importFrom pillar align
+#' @importFrom pillar get_extent
+#' @importFrom pillar style_subtle
+#' @export
+#' @inheritParams tbl_format_header
+tbl_format_header.tidySingleCellExperiment <- function(x, setup, ...){
+
+  number_of_features = x |> attr("number_of_features")
+  assay_names = x |> attr("assay_names")
+
+  named_header <- setup$tbl_sum
+
+  # Change name
+  names(named_header) = "A SingleCellExperiment-tibble abstraction"
+
+  if (all(names2(named_header) == "")) {
+    header <- named_header
+  }
+  else {
+    header <-
+      paste0(
+        align(paste0(names2(named_header), ":"), space = NBSP),
+        " ",
+        named_header
+      ) %>%
+
+      # Add further info single-cell
+      append(sprintf(
+        "\033[90m Features=%s | cells=%s | Assays=%s\033[39m",
+        number_of_features,
+        nrow(x),
+        assay_names %>% paste(collapse=", ")
+      ), after = 1)
+  }
+  style_subtle(pillar___format_comment(header, width = setup$width))
+
+}
+
+
 #' Printing tibbles
 #'
 #' @description
@@ -65,295 +116,20 @@ NULL
 #' @export
 print.SingleCellExperiment <- function(x, ..., n = NULL, width = NULL, n_extra = NULL) {
 
-  x %>%
-    as_tibble(n_dimensions_to_return = 5) %>%
-
-    # Get formatting
-    tidySingleCellExperiment_format_tbl(..., n = n, width = width, n_extra = n_extra) %>%
-
-    # Hijack the tibble header
-    map_chr(~ .x %>% str_replace("A tibble:", "A SingleCellExperiment-tibble abstraction:")) %>%
-
-    # Insert more info
-    append(sprintf(
-      "\033[90m# Features=%s | Assays=%s\033[39m",
-      nrow(x),
-      assays(x) %>% names %>% paste(collapse=", ")
-    ), after = 1) %>%
-
-    # Output
-    cat_line()
+  x |>
+    as_tibble(n_dimensions_to_return = 5) |>
+    vctrs::new_data_frame(class = c("tidySingleCellExperiment", "tbl")) %>%
+    tidybulk:::add_attr( nrow(x),  "number_of_features") %>%
+    tidybulk:::add_attr( assays(x) %>% names , "assay_names") %>%
+    print()
 
   invisible(x)
 }
 
-#' @importFrom tibble trunc_mat
-tidySingleCellExperiment_format_tbl <- function(x, ..., n = NULL, width = NULL, n_extra = NULL) {
-  mat <- trunc_mat(x, n = n, width = width, n_extra = n_extra)
-  tidySingleCellExperiment_format_truncated_mat(mat)
-}
-
-tidySingleCellExperiment_pluralise_n <- function(message, n) {
-  stopifnot(n >= 0)
-
-
-  # Don't strip parens if they have a space in between
-  # (but not if the space comes before the closing paren)
-
-  if (n == 1) {
-    # strip [
-    message <- gsub("\\[([^\\] ]* *)\\]", "\\1", message, perl = TRUE)
-    # remove ( and its content
-    message <- gsub("\\([^\\) ]* *\\)", "", message, perl = TRUE)
-  } else {
-    # strip (
-    message <- gsub("\\(([^\\) ]* *)\\)", "\\1", message, perl = TRUE)
-    # remove [ and its content
-    message <- gsub("\\[[^\\] ]* *\\]", "", message, perl = TRUE)
-  }
-
-  message
-}
-
-tidySingleCellExperiment_nchar_width <- function(x) {
-  nchar(x, type = "width")
-}
-
-#' @importFrom pillar style_subtle
-#' @importFrom rlang names2
-#' @importFrom pillar squeeze
-tidySingleCellExperiment_format_truncated_mat <- function(x, width = NULL, ...) {
-  if (is.null(width)) {
-    width <- x$width
-  }
-
-  width <- tidySingleCellExperiment_tibble_width(width)
-
-  named_header <- tidySingleCellExperiment_format_header(x)
-  if (all(names2(named_header) == "")) {
-    header <- named_header
-  } else {
-    header <- paste0(
-      tidySingleCellExperiment_justify(
-        paste0(names2(named_header), ":"),
-        right = FALSE, space = NBSP
-      ),
-      # We add a space after the NBSP inserted by tidySingleCellExperiment_justify()
-      # so that wrapping occurs at the right location for very narrow outputs
-      " ",
-      named_header
-    )
-  }
-
-  comment <- tidySingleCellExperiment_format_comment(header, width = width)
-  squeezed <- squeeze(x$mcf, width = width)
-  mcf <- tidySingleCellExperiment_format_body(squeezed)
-
-  # Splitting lines is important, otherwise subtle style may be lost
-  # if column names contain spaces.
-  footer <- tidySingleCellExperiment_pre_dots(tidySingleCellExperiment_format_footer(x, squeezed))
-  footer_comment <- tidySingleCellExperiment_split_lines(tidySingleCellExperiment_format_comment(footer, width = width))
-
-  c(style_subtle(comment), mcf, style_subtle(footer_comment))
-}
-
-tidySingleCellExperiment_format_header <- function(x) {
-  x$summary
-}
-
-tidySingleCellExperiment_format_body <- function(x) {
-  format(x)
-}
-
-#' @importFrom pillar extra_cols
-tidySingleCellExperiment_format_footer <- function(x, squeezed_colonnade) {
-  extra_rows <- tidySingleCellExperiment_format_footer_rows(x)
-  extra_cols <- tidySingleCellExperiment_format_footer_cols(x, extra_cols(squeezed_colonnade, n = x$n_extra))
-
-  extra <- c(extra_rows, extra_cols)
-  if (length(extra) >= 1) {
-    extra[[1]] <- paste0("with ", extra[[1]])
-    extra[-1] <- map_chr(extra[-1], function(ex) paste0("and ", ex))
-    collapse(extra)
-  } else {
-    character()
-  }
-}
-
-tidySingleCellExperiment_format_footer_rows <- function(x) {
-  if (length(x$mcf) != 0) {
-    if (is.na(x$rows_missing)) {
-      "more rows"
-    } else if (x$rows_missing > 0) {
-      paste0(tidySingleCellExperiment_big_mark(x$rows_missing), tidySingleCellExperiment_pluralise_n(" more row(s)", x$rows_missing))
-    }
-  } else if (is.na(x$rows_total) && x$rows_min > 0) {
-    paste0("at least ", tidySingleCellExperiment_big_mark(x$rows_min), tidySingleCellExperiment_pluralise_n(" row(s) total", x$rows_min))
-  }
-}
-
-tidySingleCellExperiment_format_footer_cols <- function(x, extra_cols) {
-  if (length(extra_cols) == 0) return(NULL)
-
-  vars <- tidySingleCellExperiment_format_extra_vars(extra_cols)
-  paste0(
-    tidySingleCellExperiment_big_mark(length(extra_cols)), " ",
-    if (!identical(x$rows_total, 0L) && x$rows_min > 0) "more ",
-    pluralise("variable(s)", extra_cols), vars
-  )
-}
-
-tidySingleCellExperiment_format_extra_vars <- function(extra_cols) {
-  # Also covers empty extra_cols vector!
-  if (is.na(extra_cols[1])) return("")
-
-  if (anyNA(extra_cols)) {
-    extra_cols <- c(extra_cols[!is.na(extra_cols)], cli::symbol$ellipsis)
-  }
-
-  paste0(": ", collapse(extra_cols))
-}
-
-tidySingleCellExperiment_format_comment <- function(x, width) {
-  if (length(x) == 0L) return(character())
-  map_chr(x, tidySingleCellExperiment_wrap, prefix = "# ", width = min(width, getOption("width")))
-}
-
-tidySingleCellExperiment_pre_dots <- function(x) {
-  if (length(x) > 0) {
-    paste0(cli::symbol$ellipsis, " ", x)
-  } else {
-    character()
-  }
-}
-
-tidySingleCellExperiment_justify <- function(x, right = TRUE, space = " ") {
-  if (length(x) == 0L) return(character())
-  width <- tidySingleCellExperiment_nchar_width(x)
-  max_width <- max(width)
-  spaces_template <- paste(rep(space, max_width), collapse = "")
-  spaces <- map_chr(max_width - width, substr, x = spaces_template, start = 1L)
-  if (right) {
-    paste0(spaces, x)
-  } else {
-    paste0(x, spaces)
-  }
-}
-
-tidySingleCellExperiment_split_lines <- function(x) {
-  # Avoid .ptype argument to vec_c()
-  if (is_empty(x)) return(character())
-
-  unlist(strsplit(x, "\n", fixed = TRUE))
-}
-
-tidySingleCellExperiment_big_mark <- function(x, ...) {
-  # The thousand separator,
-  # "," unless it's used for the decimal point, in which case "."
-  mark <- if (identical(getOption("OutDec"), ",")) "." else ","
-  ret <- formatC(x, big.mark = mark, format = "d", ...)
-  ret[is.na(x)] <- "??"
-  ret
-}
-
-collapse <- function(x) paste(x, collapse = ", ")
-
-# tidySingleCellExperiment_wrap --------------------------------------------------------------------
-
-NBSP <- "\U00A0"
-
-tidySingleCellExperiment_wrap <- function(..., indent = 0, prefix = "", width) {
-  x <- paste0(..., collapse = "")
-  wrapped <- tidySingleCellExperiment_strwrap2(x, width - tidySingleCellExperiment_nchar_width(prefix), indent)
-  wrapped <- paste0(prefix, wrapped)
-  wrapped <- gsub(NBSP, " ", wrapped)
-
-  paste0(wrapped, collapse = "\n")
-}
-
-#' @importFrom fansi strwrap_ctl
-tidySingleCellExperiment_strwrap2 <- function(x, width, indent) {
-  strwrap_ctl(x, width = max(width, 0), indent = indent, exdent = indent + 2)
-}
-
-
-op.tibble <- list(
-  tibble.print_max = 20L,
-  tibble.print_min = 10L,
-  tibble.width = NULL,
-  tibble.max_extra_cols = 100L,
-  tibble.view_max = 1000L
-)
-
-tidySingleCellExperiment_tibble_opt <- function(x, dplyr = TRUE) {
-  x_tibble <- paste0("tibble.", x)
-  res <- getOption(x_tibble)
-  if (!is.null(res)) {
-    return(res)
-  }
-
-  if (dplyr) {
-    x_dplyr <- paste0("dplyr.", x)
-    res <- getOption(x_dplyr)
-    if (!is.null(res)) {
-      return(res)
-    }
-  }
-
-  op.tibble[[x_tibble]]
-}
-
-tidySingleCellExperiment_tibble_width <- function(width) {
-  if (!is.null(width)) {
-    return(width)
-  }
-
-  width <- tidySingleCellExperiment_tibble_opt("width")
-  if (!is.null(width)) {
-    return(width)
-  }
-
-  getOption("width")
-}
-
-tidySingleCellExperiment_tibble_glimpse_width <- function(width) {
-  if (!is.null(width)) {
-    return(width)
-  }
-
-  width <- tidySingleCellExperiment_tibble_opt("width")
-  if (!is.null(width) && is.finite(width)) {
-    return(width)
-  }
-
-  getOption("width")
-}
-
-# Pluralise if there are many columns
 
-pluralise <- function(message, objects) {
-  pluralise_n(message, length(objects))
-}
 
-pluralise_n <- function(message, n) {
-  stopifnot(n >= 0)
 
 
-  # Don't strip parens if they have a space in between
-  # (but not if the space comes before the closing paren)
 
-  if (n == 1) {
-    # strip [
-    message <- gsub("\\[([^\\] ]* *)\\]", "\\1", message, perl = TRUE)
-    # remove ( and its content
-    message <- gsub("\\([^\\) ]* *\\)", "", message, perl = TRUE)
-  } else {
-    # strip (
-    message <- gsub("\\(([^\\) ]* *)\\)", "\\1", message, perl = TRUE)
-    # remove [ and its content
-    message <- gsub("\\[[^\\] ]* *\\]", "", message, perl = TRUE)
-  }
 
-  message
-}
 
diff --git a/R/utilities.R b/R/utilities.R
index 64e717a..3745997 100755
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -383,3 +383,19 @@ c_ =  function(x){
   if("cell__" %in% names(metadata(x))) cell__ = metadata(x)$cell__
   return(cell__)
 }
+
+#' Add attribute to abject
+#'
+#' @keywords internal
+#' @noRd
+#'
+#'
+#' @param var A tibble
+#' @param attribute An object
+#' @param name A character name of the attribute
+#'
+#' @return A tibble with an additional attribute
+add_attr = function(var, attribute, name) {
+  attr(var, name) <- attribute
+  var
+}
diff --git a/man/extract-methods.Rd b/man/extract-methods.Rd
index e496a0a..834f879 100644
--- a/man/extract-methods.Rd
+++ b/man/extract-methods.Rd
@@ -23,7 +23,7 @@ expression groups}
 \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
+\link[rlang:topic-inject]{quasiquotation} (you can unquote column
 names or column positions).}
 
 \item{into}{Names of new variables to create as character vector.
diff --git a/man/unite-methods.Rd b/man/unite-methods.Rd
index fb19305..0309420 100644
--- a/man/unite-methods.Rd
+++ b/man/unite-methods.Rd
@@ -9,9 +9,9 @@
 \item{col}{The name of the new column, as a string or symbol.
 
 This argument is passed by expression and supports
-\link[rlang:nse-force]{quasiquotation} (you can unquote strings
+\link[rlang:topic-inject]{quasiquotation} (you can unquote strings
 and symbols). The name is captured from the expression with
-\code{\link[rlang:nse-defuse]{rlang::ensym()}} (note that this kind of interface where
+\code{\link[rlang:defusing-advanced]{rlang::ensym()}} (note that this kind of interface where
 symbols do not represent actual objects is now discouraged in the
 tidyverse; we support it here for backward compatibility).}
 
diff --git a/man/unnest-methods.Rd b/man/unnest-methods.Rd
index abd7ddb..7787fa8 100644
--- a/man/unnest-methods.Rd
+++ b/man/unnest-methods.Rd
@@ -20,7 +20,6 @@
   .preserve
 )
 
-
 unnest_single_cell_experiment(
   data,
   cols,
@@ -77,7 +76,6 @@ stripped. This makes \code{names_sep} roughly symmetric between nesting and unne
 
 \item{.sep}{tidyr::unnest}
 
-
 \item{.preserve}{See tidyr::unnest}
 
 \item{sep}{tidyr::unnest}

From 8e7a0c49ef13f7b63e17ddcc870452e016fcfc35 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:19:59 +1000
Subject: [PATCH 02/34] version UP

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

diff --git a/DESCRIPTION b/DESCRIPTION
index 8cac75d..e1ee1ee 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: tidySingleCellExperiment
 Title: Brings SingleCellExperiment to the Tidyverse 
-Version: 1.7.0
+Version: 1.7.1
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre")) )
 Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCellExperiment' container 

From 30e2316e16ec724cc2e0765d10bdae1e88dbeee0 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:31:25 +1000
Subject: [PATCH 03/34] fix bug tidybulk reference

---
 DESCRIPTION      | 2 +-
 R/print_method.R | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e1ee1ee..14f4203 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: tidySingleCellExperiment
 Title: Brings SingleCellExperiment to the Tidyverse 
-Version: 1.7.1
+Version: 1.7.2
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre")) )
 Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCellExperiment' container 
diff --git a/R/print_method.R b/R/print_method.R
index 2c4805c..b9caead 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -119,8 +119,8 @@ print.SingleCellExperiment <- function(x, ..., n = NULL, width = NULL, n_extra =
   x |>
     as_tibble(n_dimensions_to_return = 5) |>
     vctrs::new_data_frame(class = c("tidySingleCellExperiment", "tbl")) %>%
-    tidybulk:::add_attr( nrow(x),  "number_of_features") %>%
-    tidybulk:::add_attr( assays(x) %>% names , "assay_names") %>%
+    add_attr( nrow(x),  "number_of_features") %>%
+    add_attr( assays(x) %>% names , "assay_names") %>%
     print()
 
   invisible(x)

From e58f39619c6c31877019d1b0ce7defa0087a49e0 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:57:03 +1000
Subject: [PATCH 04/34] typo

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

diff --git a/R/print_method.R b/R/print_method.R
index b9caead..5217396 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -40,7 +40,7 @@ tbl_format_header.tidySingleCellExperiment <- function(x, setup, ...){
 
       # Add further info single-cell
       append(sprintf(
-        "\033[90m Features=%s | cells=%s | Assays=%s\033[39m",
+        "\033[90m Features=%s | Cells=%s | Assays=%s\033[39m",
         number_of_features,
         nrow(x),
         assay_names %>% paste(collapse=", ")

From aab95cb3ec4a4c137415aba520e745432612514c Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 19:35:22 +1000
Subject: [PATCH 05/34] fix CHECK

---
 DESCRIPTION                      |  3 ++-
 NAMESPACE                        |  1 +
 R/print_method.R                 | 28 +++++++++++++++++++++++-----
 man/tbl_format_header-methods.Rd | 19 +++++++++++++++++++
 4 files changed, 45 insertions(+), 6 deletions(-)
 create mode 100644 man/tbl_format_header-methods.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 14f4203..57b580b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -5,7 +5,7 @@ Version: 1.7.2
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre")) )
 Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCellExperiment' container 
-    in the form of tibble and allows the data manipulation, plotting and nesting using 'tidyverse' 
+    in the form of tibble and allows the data manipulation, plotting and nesting using 'tidyverse'.
 License: GPL-3
 Depends:
     R (>= 4.0.0),
@@ -27,6 +27,7 @@ Imports:
     S4Vectors,
     tidyselect,
     ellipsis,
+    vctrs,
     pillar,
     stringr,
     cli,
diff --git a/NAMESPACE b/NAMESPACE
index f18e25d..992c1af 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -154,3 +154,4 @@ importFrom(tidyr,unnest)
 importFrom(tidyselect,eval_select)
 importFrom(ttservice,join_features)
 importFrom(utils,tail)
+importFrom(vctrs,new_data_frame)
diff --git a/R/print_method.R b/R/print_method.R
index 5217396..25f2969 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -1,14 +1,31 @@
 # This file is a replacement of the unexported functions in the tibble package, in order to specify "tibble abstraction in the header"
 
-#' tbl_format_header
+#' Format the header of a tibble
+#'
+#' @description
+#' `r lifecycle::badge("experimental")`
+#'
+#' For easier customization, the formatting of a tibble is split
+#' into three components: header, body, and footer.
+#' The `tbl_format_header()` method is responsible for formatting the header
+#' of a tibble.
+#'
+#' Override this method if you need to change the appearance
+#' of the entire header.
+#' If you only need to change or extend the components shown in the header,
+#' override or extend [tbl_sum()] for your class which is called by the
+#' default method.
 #'
-#' @rdname tbl_format_header-methods
-#' @name tbl_format_header
 #' @importFrom pillar tbl_format_header
+#' @inheritParams tbl_format_body
+#' @inherit tbl_format_body return
 #'
-#' @noRd
+#' @rdname tbl_format_header-methods
+#' @name tbl_format_header
 #'
 #' @export
+#'
+NULL
 NULL
 
 #' @importFrom rlang names2
@@ -113,12 +130,13 @@ NULL
 #' @rdname print
 #' @importFrom cli cat_line
 #' @importFrom SingleCellExperiment counts
+#' @importFrom vctrs new_data_frame
 #' @export
 print.SingleCellExperiment <- function(x, ..., n = NULL, width = NULL, n_extra = NULL) {
 
   x |>
     as_tibble(n_dimensions_to_return = 5) |>
-    vctrs::new_data_frame(class = c("tidySingleCellExperiment", "tbl")) %>%
+    new_data_frame(class = c("tidySingleCellExperiment", "tbl")) %>%
     add_attr( nrow(x),  "number_of_features") %>%
     add_attr( assays(x) %>% names , "assay_names") %>%
     print()
diff --git a/man/tbl_format_header-methods.Rd b/man/tbl_format_header-methods.Rd
new file mode 100644
index 0000000..a1f630c
--- /dev/null
+++ b/man/tbl_format_header-methods.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/print_method.R
+\name{tbl_format_header}
+\alias{tbl_format_header}
+\title{Format the header of a tibble}
+\description{
+\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
+
+For easier customization, the formatting of a tibble is split
+into three components: header, body, and footer.
+The \code{tbl_format_header()} method is responsible for formatting the header
+of a tibble.
+
+Override this method if you need to change the appearance
+of the entire header.
+If you only need to change or extend the components shown in the header,
+override or extend \code{\link[=tbl_sum]{tbl_sum()}} for your class which is called by the
+default method.
+}

From 3e372b733ef36517aac0fc22fc3deb0075d507b4 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Tue, 26 Jul 2022 09:03:02 +1000
Subject: [PATCH 06/34] dummy change

---
 R/print_method.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/print_method.R b/R/print_method.R
index 25f2969..a8303b8 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -26,7 +26,6 @@
 #' @export
 #'
 NULL
-NULL
 
 #' @importFrom rlang names2
 #' @importFrom pillar align

From 179891a1e18cf2f8be58cd20a68ade04a4d9881c Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Tue, 26 Jul 2022 10:28:24 +1000
Subject: [PATCH 07/34] print restore show

---
 DESCRIPTION  |  2 +-
 R/methods.R  | 89 ++++++++++++++++++++++++++--------------------------
 man/print.Rd |  2 +-
 3 files changed, 47 insertions(+), 46 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 57b580b..d72619d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -57,7 +57,7 @@ Biarch: true
 biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression, GeneExpression, Normalization, Clustering, QualityControl, Sequencing
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0
 Roxygen: list(markdown = TRUE)
 URL: https://github.com/stemangiola/tidySingleCellExperiment
 BugReports: https://github.com/stemangiola/tidySingleCellExperiment/issues
diff --git a/R/methods.R b/R/methods.R
index 15d4977..b8f30de 100755
--- a/R/methods.R
+++ b/R/methods.R
@@ -1,57 +1,24 @@
-setClass("tidySingleCellExperiment", contains = "SingleCellExperiment")
-
-#' tidy for SingleCellExperiment
-#'
-#' @param object A SingleCellExperiment object
-#'
-#' @return A tidySingleCellExperiment object
-#'
-#' @name tidy
-#'
-#' @examples
-#'
-#' tidySingleCellExperiment::pbmc_small
-#' @export
-tidy <- function(object) {
-    UseMethod("tidy", object)
-}
-
-#' @importFrom methods as
-#' @importFrom lifecycle deprecate_warn
-#'
-#' @param object A SingleCellExperiment object
-#'
-#' @export
-tidy.SingleCellExperiment <- function(object) {
-
-    # DEPRECATE
-    deprecate_warn(
-        when = "1.1.1",
-        what = "tidy()",
-        details = "tidySingleCellExperiment says: tidy() is not needed anymore."
-    )
-
-    object
-}
 
 setMethod(
     f = "show",
     signature = "SingleCellExperiment",
     definition = function(object) {
-        if (isTRUE(x = getOption(x = "restore_SingleCellExperiment_show", default = FALSE))) {
-            f <- getMethod(
-                f = "show",
-                signature = "SingleCellExperiment",
-                where = asNamespace(ns = "SingleCellExperiment")
+        if (
+          isTRUE(x = getOption(x = "restore_SingleCellExperiment_show", default = FALSE))
+        ) {
+            f <-getMethod(
+              f = "show",
+              signature = "SummarizedExperiment",
+              where = asNamespace(ns = "SummarizedExperiment")
             )
             f(object = object)
-        } else {
-            object %>%
-                print()
-        }
+
+        } else {  print(object)  }
     }
 )
 
+setClass("tidySingleCellExperiment", contains = "SingleCellExperiment")
+
 #' Extract and join information for features.
 #'
 #'
@@ -130,5 +97,39 @@ setMethod("join_features", "SingleCellExperiment",  function(.data,
 })
 
 
+#' tidy for SingleCellExperiment
+#'
+#' @param object A SingleCellExperiment object
+#'
+#' @return A tidySingleCellExperiment object
+#'
+#' @name tidy
+#'
+#' @examples
+#'
+#' tidySingleCellExperiment::pbmc_small
+#' @export
+tidy <- function(object) {
+  UseMethod("tidy", object)
+}
+
+#' @importFrom methods as
+#' @importFrom lifecycle deprecate_warn
+#'
+#' @param object A SingleCellExperiment object
+#'
+#' @export
+tidy.SingleCellExperiment <- function(object) {
+
+  # DEPRECATE
+  deprecate_warn(
+    when = "1.1.1",
+    what = "tidy()",
+    details = "tidySingleCellExperiment says: tidy() is not needed anymore."
+  )
+
+  object
+}
+
 
 
diff --git a/man/print.Rd b/man/print.Rd
index 53d4817..bad962f 100644
--- a/man/print.Rd
+++ b/man/print.Rd
@@ -51,7 +51,7 @@ Only the first 5 reduced dimensions are displayed, while all of them are queriab
 
 The following options are used by the tibble and pillar packages
 to format and print \code{tbl_df} objects.
-Used by the formatting workhorse \code{trunc_mat()} and, therefore,
+Used by the formatting workhorse \code{trunc_mat()} and therefore,
 indirectly, by \code{print.tbl()}.
 \itemize{
 \item \code{tibble.print_max}: Row number threshold: Maximum number of rows printed.

From ced353122bfac63ec18cb236375c616dcc82d5a9 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:16:51 +1000
Subject: [PATCH 08/34] use new pillar methods

---
 NAMESPACE              |   8 +-
 R/pillar_utilities.R   |  26 ++++
 R/print_method.R       | 338 +++++++----------------------------------
 R/utilities.R          |  16 ++
 man/extract-methods.Rd |   2 +-
 man/unite-methods.Rd   |   4 +-
 man/unnest-methods.Rd  |   2 -
 7 files changed, 107 insertions(+), 289 deletions(-)
 create mode 100644 R/pillar_utilities.R

diff --git a/NAMESPACE b/NAMESPACE
index a334cf0..f18e25d 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -37,6 +37,7 @@ S3method(select,SingleCellExperiment)
 S3method(separate,SingleCellExperiment)
 S3method(slice,SingleCellExperiment)
 S3method(summarise,SingleCellExperiment)
+S3method(tbl_format_header,tidySingleCellExperiment)
 S3method(tidy,SingleCellExperiment)
 S3method(unite,SingleCellExperiment)
 S3method(unnest,tidySingleCellExperiment_nested)
@@ -72,6 +73,7 @@ export(select)
 export(separate)
 export(slice)
 export(summarise)
+export(tbl_format_header)
 export(tidy)
 export(unite)
 export(unnest)
@@ -114,9 +116,10 @@ importFrom(lifecycle,deprecate_warn)
 importFrom(magrittr,"%$%")
 importFrom(magrittr,"%>%")
 importFrom(methods,as)
-importFrom(pillar,extra_cols)
-importFrom(pillar,squeeze)
+importFrom(pillar,align)
+importFrom(pillar,get_extent)
 importFrom(pillar,style_subtle)
+importFrom(pillar,tbl_format_header)
 importFrom(plotly,plot_ly)
 importFrom(purrr,imap)
 importFrom(purrr,map)
@@ -141,7 +144,6 @@ importFrom(stringr,str_replace)
 importFrom(tibble,as_tibble)
 importFrom(tibble,enframe)
 importFrom(tibble,glimpse)
-importFrom(tibble,trunc_mat)
 importFrom(tidyr,extract)
 importFrom(tidyr,nest)
 importFrom(tidyr,pivot_longer)
diff --git a/R/pillar_utilities.R b/R/pillar_utilities.R
new file mode 100644
index 0000000..b84d179
--- /dev/null
+++ b/R/pillar_utilities.R
@@ -0,0 +1,26 @@
+NBSP <- "\U00A0"
+
+pillar___format_comment = function (x, width)
+{
+  if (length(x) == 0L) {
+    return(character())
+  }
+  map_chr(x, pillar___wrap, prefix = "# ", width = min(width, cli::console_width()))
+}
+
+#' @importFrom fansi strwrap_ctl
+pillar___strwrap2 = function (x, width, indent)
+{
+  fansi::strwrap_ctl(x, width = max(width, 0), indent = indent,
+                     exdent = indent + 2)
+}
+
+
+pillar___wrap = function (..., indent = 0, prefix = "", width)
+{
+  x <- paste0(..., collapse = "")
+  wrapped <- pillar___strwrap2(x, width - get_extent(prefix), indent)
+  wrapped <- paste0(prefix, wrapped)
+  wrapped <- gsub(NBSP, " ", wrapped)
+  paste0(wrapped, collapse = "\n")
+}
diff --git a/R/print_method.R b/R/print_method.R
index 4241726..2c4805c 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -1,5 +1,56 @@
 # This file is a replacement of the unexported functions in the tibble package, in order to specify "tibble abstraction in the header"
 
+#' tbl_format_header
+#'
+#' @rdname tbl_format_header-methods
+#' @name tbl_format_header
+#' @importFrom pillar tbl_format_header
+#'
+#' @noRd
+#'
+#' @export
+NULL
+
+#' @importFrom rlang names2
+#' @importFrom pillar align
+#' @importFrom pillar get_extent
+#' @importFrom pillar style_subtle
+#' @export
+#' @inheritParams tbl_format_header
+tbl_format_header.tidySingleCellExperiment <- function(x, setup, ...){
+
+  number_of_features = x |> attr("number_of_features")
+  assay_names = x |> attr("assay_names")
+
+  named_header <- setup$tbl_sum
+
+  # Change name
+  names(named_header) = "A SingleCellExperiment-tibble abstraction"
+
+  if (all(names2(named_header) == "")) {
+    header <- named_header
+  }
+  else {
+    header <-
+      paste0(
+        align(paste0(names2(named_header), ":"), space = NBSP),
+        " ",
+        named_header
+      ) %>%
+
+      # Add further info single-cell
+      append(sprintf(
+        "\033[90m Features=%s | cells=%s | Assays=%s\033[39m",
+        number_of_features,
+        nrow(x),
+        assay_names %>% paste(collapse=", ")
+      ), after = 1)
+  }
+  style_subtle(pillar___format_comment(header, width = setup$width))
+
+}
+
+
 #' Printing tibbles
 #'
 #' @description
@@ -65,295 +116,20 @@ NULL
 #' @export
 print.SingleCellExperiment <- function(x, ..., n = NULL, width = NULL, n_extra = NULL) {
 
-  x %>%
-    as_tibble(n_dimensions_to_return = 5) %>%
-
-    # Get formatting
-    tidySingleCellExperiment_format_tbl(..., n = n, width = width, n_extra = n_extra) %>%
-
-    # Hijack the tibble header
-    map_chr(~ .x %>% str_replace("A tibble:", "A SingleCellExperiment-tibble abstraction:")) %>%
-
-    # Insert more info
-    append(sprintf(
-      "\033[90m# Features=%s | Assays=%s\033[39m",
-      nrow(x),
-      assays(x) %>% names %>% paste(collapse=", ")
-    ), after = 1) %>%
-
-    # Output
-    cat_line()
+  x |>
+    as_tibble(n_dimensions_to_return = 5) |>
+    vctrs::new_data_frame(class = c("tidySingleCellExperiment", "tbl")) %>%
+    tidybulk:::add_attr( nrow(x),  "number_of_features") %>%
+    tidybulk:::add_attr( assays(x) %>% names , "assay_names") %>%
+    print()
 
   invisible(x)
 }
 
-#' @importFrom tibble trunc_mat
-tidySingleCellExperiment_format_tbl <- function(x, ..., n = NULL, width = NULL, n_extra = NULL) {
-  mat <- trunc_mat(x, n = n, width = width, n_extra = n_extra)
-  tidySingleCellExperiment_format_truncated_mat(mat)
-}
-
-tidySingleCellExperiment_pluralise_n <- function(message, n) {
-  stopifnot(n >= 0)
-
-
-  # Don't strip parens if they have a space in between
-  # (but not if the space comes before the closing paren)
-
-  if (n == 1) {
-    # strip [
-    message <- gsub("\\[([^\\] ]* *)\\]", "\\1", message, perl = TRUE)
-    # remove ( and its content
-    message <- gsub("\\([^\\) ]* *\\)", "", message, perl = TRUE)
-  } else {
-    # strip (
-    message <- gsub("\\(([^\\) ]* *)\\)", "\\1", message, perl = TRUE)
-    # remove [ and its content
-    message <- gsub("\\[[^\\] ]* *\\]", "", message, perl = TRUE)
-  }
-
-  message
-}
-
-tidySingleCellExperiment_nchar_width <- function(x) {
-  nchar(x, type = "width")
-}
-
-#' @importFrom pillar style_subtle
-#' @importFrom rlang names2
-#' @importFrom pillar squeeze
-tidySingleCellExperiment_format_truncated_mat <- function(x, width = NULL, ...) {
-  if (is.null(width)) {
-    width <- x$width
-  }
-
-  width <- tidySingleCellExperiment_tibble_width(width)
-
-  named_header <- tidySingleCellExperiment_format_header(x)
-  if (all(names2(named_header) == "")) {
-    header <- named_header
-  } else {
-    header <- paste0(
-      tidySingleCellExperiment_justify(
-        paste0(names2(named_header), ":"),
-        right = FALSE, space = NBSP
-      ),
-      # We add a space after the NBSP inserted by tidySingleCellExperiment_justify()
-      # so that wrapping occurs at the right location for very narrow outputs
-      " ",
-      named_header
-    )
-  }
-
-  comment <- tidySingleCellExperiment_format_comment(header, width = width)
-  squeezed <- squeeze(x$mcf, width = width)
-  mcf <- tidySingleCellExperiment_format_body(squeezed)
-
-  # Splitting lines is important, otherwise subtle style may be lost
-  # if column names contain spaces.
-  footer <- tidySingleCellExperiment_pre_dots(tidySingleCellExperiment_format_footer(x, squeezed))
-  footer_comment <- tidySingleCellExperiment_split_lines(tidySingleCellExperiment_format_comment(footer, width = width))
-
-  c(style_subtle(comment), mcf, style_subtle(footer_comment))
-}
-
-tidySingleCellExperiment_format_header <- function(x) {
-  x$summary
-}
-
-tidySingleCellExperiment_format_body <- function(x) {
-  format(x)
-}
-
-#' @importFrom pillar extra_cols
-tidySingleCellExperiment_format_footer <- function(x, squeezed_colonnade) {
-  extra_rows <- tidySingleCellExperiment_format_footer_rows(x)
-  extra_cols <- tidySingleCellExperiment_format_footer_cols(x, extra_cols(squeezed_colonnade, n = x$n_extra))
-
-  extra <- c(extra_rows, extra_cols)
-  if (length(extra) >= 1) {
-    extra[[1]] <- paste0("with ", extra[[1]])
-    extra[-1] <- map_chr(extra[-1], function(ex) paste0("and ", ex))
-    collapse(extra)
-  } else {
-    character()
-  }
-}
-
-tidySingleCellExperiment_format_footer_rows <- function(x) {
-  if (length(x$mcf) != 0) {
-    if (is.na(x$rows_missing)) {
-      "more rows"
-    } else if (x$rows_missing > 0) {
-      paste0(tidySingleCellExperiment_big_mark(x$rows_missing), tidySingleCellExperiment_pluralise_n(" more row(s)", x$rows_missing))
-    }
-  } else if (is.na(x$rows_total) && x$rows_min > 0) {
-    paste0("at least ", tidySingleCellExperiment_big_mark(x$rows_min), tidySingleCellExperiment_pluralise_n(" row(s) total", x$rows_min))
-  }
-}
-
-tidySingleCellExperiment_format_footer_cols <- function(x, extra_cols) {
-  if (length(extra_cols) == 0) return(NULL)
-
-  vars <- tidySingleCellExperiment_format_extra_vars(extra_cols)
-  paste0(
-    tidySingleCellExperiment_big_mark(length(extra_cols)), " ",
-    if (!identical(x$rows_total, 0L) && x$rows_min > 0) "more ",
-    pluralise("variable(s)", extra_cols), vars
-  )
-}
-
-tidySingleCellExperiment_format_extra_vars <- function(extra_cols) {
-  # Also covers empty extra_cols vector!
-  if (is.na(extra_cols[1])) return("")
-
-  if (anyNA(extra_cols)) {
-    extra_cols <- c(extra_cols[!is.na(extra_cols)], cli::symbol$ellipsis)
-  }
-
-  paste0(": ", collapse(extra_cols))
-}
-
-tidySingleCellExperiment_format_comment <- function(x, width) {
-  if (length(x) == 0L) return(character())
-  map_chr(x, tidySingleCellExperiment_wrap, prefix = "# ", width = min(width, getOption("width")))
-}
-
-tidySingleCellExperiment_pre_dots <- function(x) {
-  if (length(x) > 0) {
-    paste0(cli::symbol$ellipsis, " ", x)
-  } else {
-    character()
-  }
-}
-
-tidySingleCellExperiment_justify <- function(x, right = TRUE, space = " ") {
-  if (length(x) == 0L) return(character())
-  width <- tidySingleCellExperiment_nchar_width(x)
-  max_width <- max(width)
-  spaces_template <- paste(rep(space, max_width), collapse = "")
-  spaces <- map_chr(max_width - width, substr, x = spaces_template, start = 1L)
-  if (right) {
-    paste0(spaces, x)
-  } else {
-    paste0(x, spaces)
-  }
-}
-
-tidySingleCellExperiment_split_lines <- function(x) {
-  # Avoid .ptype argument to vec_c()
-  if (is_empty(x)) return(character())
-
-  unlist(strsplit(x, "\n", fixed = TRUE))
-}
-
-tidySingleCellExperiment_big_mark <- function(x, ...) {
-  # The thousand separator,
-  # "," unless it's used for the decimal point, in which case "."
-  mark <- if (identical(getOption("OutDec"), ",")) "." else ","
-  ret <- formatC(x, big.mark = mark, format = "d", ...)
-  ret[is.na(x)] <- "??"
-  ret
-}
-
-collapse <- function(x) paste(x, collapse = ", ")
-
-# tidySingleCellExperiment_wrap --------------------------------------------------------------------
-
-NBSP <- "\U00A0"
-
-tidySingleCellExperiment_wrap <- function(..., indent = 0, prefix = "", width) {
-  x <- paste0(..., collapse = "")
-  wrapped <- tidySingleCellExperiment_strwrap2(x, width - tidySingleCellExperiment_nchar_width(prefix), indent)
-  wrapped <- paste0(prefix, wrapped)
-  wrapped <- gsub(NBSP, " ", wrapped)
-
-  paste0(wrapped, collapse = "\n")
-}
-
-#' @importFrom fansi strwrap_ctl
-tidySingleCellExperiment_strwrap2 <- function(x, width, indent) {
-  strwrap_ctl(x, width = max(width, 0), indent = indent, exdent = indent + 2)
-}
-
-
-op.tibble <- list(
-  tibble.print_max = 20L,
-  tibble.print_min = 10L,
-  tibble.width = NULL,
-  tibble.max_extra_cols = 100L,
-  tibble.view_max = 1000L
-)
-
-tidySingleCellExperiment_tibble_opt <- function(x, dplyr = TRUE) {
-  x_tibble <- paste0("tibble.", x)
-  res <- getOption(x_tibble)
-  if (!is.null(res)) {
-    return(res)
-  }
-
-  if (dplyr) {
-    x_dplyr <- paste0("dplyr.", x)
-    res <- getOption(x_dplyr)
-    if (!is.null(res)) {
-      return(res)
-    }
-  }
-
-  op.tibble[[x_tibble]]
-}
-
-tidySingleCellExperiment_tibble_width <- function(width) {
-  if (!is.null(width)) {
-    return(width)
-  }
-
-  width <- tidySingleCellExperiment_tibble_opt("width")
-  if (!is.null(width)) {
-    return(width)
-  }
-
-  getOption("width")
-}
-
-tidySingleCellExperiment_tibble_glimpse_width <- function(width) {
-  if (!is.null(width)) {
-    return(width)
-  }
-
-  width <- tidySingleCellExperiment_tibble_opt("width")
-  if (!is.null(width) && is.finite(width)) {
-    return(width)
-  }
-
-  getOption("width")
-}
-
-# Pluralise if there are many columns
 
-pluralise <- function(message, objects) {
-  pluralise_n(message, length(objects))
-}
 
-pluralise_n <- function(message, n) {
-  stopifnot(n >= 0)
 
 
-  # Don't strip parens if they have a space in between
-  # (but not if the space comes before the closing paren)
 
-  if (n == 1) {
-    # strip [
-    message <- gsub("\\[([^\\] ]* *)\\]", "\\1", message, perl = TRUE)
-    # remove ( and its content
-    message <- gsub("\\([^\\) ]* *\\)", "", message, perl = TRUE)
-  } else {
-    # strip (
-    message <- gsub("\\(([^\\) ]* *)\\)", "\\1", message, perl = TRUE)
-    # remove [ and its content
-    message <- gsub("\\[[^\\] ]* *\\]", "", message, perl = TRUE)
-  }
 
-  message
-}
 
diff --git a/R/utilities.R b/R/utilities.R
index 64e717a..3745997 100755
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -383,3 +383,19 @@ c_ =  function(x){
   if("cell__" %in% names(metadata(x))) cell__ = metadata(x)$cell__
   return(cell__)
 }
+
+#' Add attribute to abject
+#'
+#' @keywords internal
+#' @noRd
+#'
+#'
+#' @param var A tibble
+#' @param attribute An object
+#' @param name A character name of the attribute
+#'
+#' @return A tibble with an additional attribute
+add_attr = function(var, attribute, name) {
+  attr(var, name) <- attribute
+  var
+}
diff --git a/man/extract-methods.Rd b/man/extract-methods.Rd
index e496a0a..834f879 100644
--- a/man/extract-methods.Rd
+++ b/man/extract-methods.Rd
@@ -23,7 +23,7 @@ expression groups}
 \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
+\link[rlang:topic-inject]{quasiquotation} (you can unquote column
 names or column positions).}
 
 \item{into}{Names of new variables to create as character vector.
diff --git a/man/unite-methods.Rd b/man/unite-methods.Rd
index fb19305..0309420 100644
--- a/man/unite-methods.Rd
+++ b/man/unite-methods.Rd
@@ -9,9 +9,9 @@
 \item{col}{The name of the new column, as a string or symbol.
 
 This argument is passed by expression and supports
-\link[rlang:nse-force]{quasiquotation} (you can unquote strings
+\link[rlang:topic-inject]{quasiquotation} (you can unquote strings
 and symbols). The name is captured from the expression with
-\code{\link[rlang:nse-defuse]{rlang::ensym()}} (note that this kind of interface where
+\code{\link[rlang:defusing-advanced]{rlang::ensym()}} (note that this kind of interface where
 symbols do not represent actual objects is now discouraged in the
 tidyverse; we support it here for backward compatibility).}
 
diff --git a/man/unnest-methods.Rd b/man/unnest-methods.Rd
index abd7ddb..7787fa8 100644
--- a/man/unnest-methods.Rd
+++ b/man/unnest-methods.Rd
@@ -20,7 +20,6 @@
   .preserve
 )
 
-
 unnest_single_cell_experiment(
   data,
   cols,
@@ -77,7 +76,6 @@ stripped. This makes \code{names_sep} roughly symmetric between nesting and unne
 
 \item{.sep}{tidyr::unnest}
 
-
 \item{.preserve}{See tidyr::unnest}
 
 \item{sep}{tidyr::unnest}

From cb058a3db191953ac128afda520d556d943f629f Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:19:59 +1000
Subject: [PATCH 09/34] version UP

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

diff --git a/DESCRIPTION b/DESCRIPTION
index 8cac75d..e1ee1ee 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: tidySingleCellExperiment
 Title: Brings SingleCellExperiment to the Tidyverse 
-Version: 1.7.0
+Version: 1.7.1
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre")) )
 Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCellExperiment' container 

From 875ede19f01ab29fac18e7c0b10fe7f5b7b29bac Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:31:25 +1000
Subject: [PATCH 10/34] fix bug tidybulk reference

---
 DESCRIPTION      | 2 +-
 R/print_method.R | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e1ee1ee..14f4203 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: tidySingleCellExperiment
 Title: Brings SingleCellExperiment to the Tidyverse 
-Version: 1.7.1
+Version: 1.7.2
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre")) )
 Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCellExperiment' container 
diff --git a/R/print_method.R b/R/print_method.R
index 2c4805c..b9caead 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -119,8 +119,8 @@ print.SingleCellExperiment <- function(x, ..., n = NULL, width = NULL, n_extra =
   x |>
     as_tibble(n_dimensions_to_return = 5) |>
     vctrs::new_data_frame(class = c("tidySingleCellExperiment", "tbl")) %>%
-    tidybulk:::add_attr( nrow(x),  "number_of_features") %>%
-    tidybulk:::add_attr( assays(x) %>% names , "assay_names") %>%
+    add_attr( nrow(x),  "number_of_features") %>%
+    add_attr( assays(x) %>% names , "assay_names") %>%
     print()
 
   invisible(x)

From 19ff7eff8a61619ddb131d750032cd710aa0943e Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:57:03 +1000
Subject: [PATCH 11/34] typo

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

diff --git a/R/print_method.R b/R/print_method.R
index b9caead..5217396 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -40,7 +40,7 @@ tbl_format_header.tidySingleCellExperiment <- function(x, setup, ...){
 
       # Add further info single-cell
       append(sprintf(
-        "\033[90m Features=%s | cells=%s | Assays=%s\033[39m",
+        "\033[90m Features=%s | Cells=%s | Assays=%s\033[39m",
         number_of_features,
         nrow(x),
         assay_names %>% paste(collapse=", ")

From 665217e2c202a711b3deddc4b0d0d34e8ecd0c82 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 19:35:22 +1000
Subject: [PATCH 12/34] fix CHECK

---
 DESCRIPTION                      |  3 ++-
 NAMESPACE                        |  1 +
 R/print_method.R                 | 28 +++++++++++++++++++++++-----
 man/tbl_format_header-methods.Rd | 19 +++++++++++++++++++
 4 files changed, 45 insertions(+), 6 deletions(-)
 create mode 100644 man/tbl_format_header-methods.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 14f4203..57b580b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -5,7 +5,7 @@ Version: 1.7.2
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre")) )
 Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCellExperiment' container 
-    in the form of tibble and allows the data manipulation, plotting and nesting using 'tidyverse' 
+    in the form of tibble and allows the data manipulation, plotting and nesting using 'tidyverse'.
 License: GPL-3
 Depends:
     R (>= 4.0.0),
@@ -27,6 +27,7 @@ Imports:
     S4Vectors,
     tidyselect,
     ellipsis,
+    vctrs,
     pillar,
     stringr,
     cli,
diff --git a/NAMESPACE b/NAMESPACE
index f18e25d..992c1af 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -154,3 +154,4 @@ importFrom(tidyr,unnest)
 importFrom(tidyselect,eval_select)
 importFrom(ttservice,join_features)
 importFrom(utils,tail)
+importFrom(vctrs,new_data_frame)
diff --git a/R/print_method.R b/R/print_method.R
index 5217396..25f2969 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -1,14 +1,31 @@
 # This file is a replacement of the unexported functions in the tibble package, in order to specify "tibble abstraction in the header"
 
-#' tbl_format_header
+#' Format the header of a tibble
+#'
+#' @description
+#' `r lifecycle::badge("experimental")`
+#'
+#' For easier customization, the formatting of a tibble is split
+#' into three components: header, body, and footer.
+#' The `tbl_format_header()` method is responsible for formatting the header
+#' of a tibble.
+#'
+#' Override this method if you need to change the appearance
+#' of the entire header.
+#' If you only need to change or extend the components shown in the header,
+#' override or extend [tbl_sum()] for your class which is called by the
+#' default method.
 #'
-#' @rdname tbl_format_header-methods
-#' @name tbl_format_header
 #' @importFrom pillar tbl_format_header
+#' @inheritParams tbl_format_body
+#' @inherit tbl_format_body return
 #'
-#' @noRd
+#' @rdname tbl_format_header-methods
+#' @name tbl_format_header
 #'
 #' @export
+#'
+NULL
 NULL
 
 #' @importFrom rlang names2
@@ -113,12 +130,13 @@ NULL
 #' @rdname print
 #' @importFrom cli cat_line
 #' @importFrom SingleCellExperiment counts
+#' @importFrom vctrs new_data_frame
 #' @export
 print.SingleCellExperiment <- function(x, ..., n = NULL, width = NULL, n_extra = NULL) {
 
   x |>
     as_tibble(n_dimensions_to_return = 5) |>
-    vctrs::new_data_frame(class = c("tidySingleCellExperiment", "tbl")) %>%
+    new_data_frame(class = c("tidySingleCellExperiment", "tbl")) %>%
     add_attr( nrow(x),  "number_of_features") %>%
     add_attr( assays(x) %>% names , "assay_names") %>%
     print()
diff --git a/man/tbl_format_header-methods.Rd b/man/tbl_format_header-methods.Rd
new file mode 100644
index 0000000..a1f630c
--- /dev/null
+++ b/man/tbl_format_header-methods.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/print_method.R
+\name{tbl_format_header}
+\alias{tbl_format_header}
+\title{Format the header of a tibble}
+\description{
+\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
+
+For easier customization, the formatting of a tibble is split
+into three components: header, body, and footer.
+The \code{tbl_format_header()} method is responsible for formatting the header
+of a tibble.
+
+Override this method if you need to change the appearance
+of the entire header.
+If you only need to change or extend the components shown in the header,
+override or extend \code{\link[=tbl_sum]{tbl_sum()}} for your class which is called by the
+default method.
+}

From dbfd4eb40173201fc102fdf224a607072b412c58 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:16:51 +1000
Subject: [PATCH 13/34] use new pillar methods

---
 R/print_method.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/print_method.R b/R/print_method.R
index 25f2969..7404c0f 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -26,7 +26,6 @@
 #' @export
 #'
 NULL
-NULL
 
 #' @importFrom rlang names2
 #' @importFrom pillar align
@@ -136,9 +135,11 @@ print.SingleCellExperiment <- function(x, ..., n = NULL, width = NULL, n_extra =
 
   x |>
     as_tibble(n_dimensions_to_return = 5) |>
+
     new_data_frame(class = c("tidySingleCellExperiment", "tbl")) %>%
     add_attr( nrow(x),  "number_of_features") %>%
     add_attr( assays(x) %>% names , "assay_names") %>%
+
     print()
 
   invisible(x)

From 4edb3e7a580834ff54d1043e290de13476497552 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:19:59 +1000
Subject: [PATCH 14/34] version UP

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

diff --git a/DESCRIPTION b/DESCRIPTION
index 57b580b..050c389 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -5,7 +5,7 @@ Version: 1.7.2
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre")) )
 Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCellExperiment' container 
-    in the form of tibble and allows the data manipulation, plotting and nesting using 'tidyverse'.
+    in the form of a tibble and allows the data manipulation, plotting and nesting using 'tidyverse'.
 License: GPL-3
 Depends:
     R (>= 4.0.0),

From 2bde91babe3b58abf2dcd8d71d2a6392d8dc0b9d Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:31:25 +1000
Subject: [PATCH 15/34] fix bug tidybulk reference

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

diff --git a/R/print_method.R b/R/print_method.R
index 7404c0f..4d8022a 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -134,7 +134,7 @@ NULL
 print.SingleCellExperiment <- function(x, ..., n = NULL, width = NULL, n_extra = NULL) {
 
   x |>
-    as_tibble(n_dimensions_to_return = 5) |>
+    as_tibble(n_dimensions_to_return = 5 ) |>
 
     new_data_frame(class = c("tidySingleCellExperiment", "tbl")) %>%
     add_attr( nrow(x),  "number_of_features") %>%

From 8b2e38d4f57e2b693efd43b01792a72b3fcb5bf9 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 19:35:22 +1000
Subject: [PATCH 16/34] fix CHECK

---
 R/print_method.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/R/print_method.R b/R/print_method.R
index 4d8022a..3e2c586 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -25,6 +25,10 @@
 #'
 #' @export
 #'
+<<<<<<< HEAD
+=======
+NULL
+>>>>>>> fix CHECK
 NULL
 
 #' @importFrom rlang names2

From 4936f898f93b568e60ba4a824ec754e25b21e765 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Tue, 26 Jul 2022 09:03:02 +1000
Subject: [PATCH 17/34] dummy change

---
 R/print_method.R | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/R/print_method.R b/R/print_method.R
index 3e2c586..4d8022a 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -25,10 +25,6 @@
 #'
 #' @export
 #'
-<<<<<<< HEAD
-=======
-NULL
->>>>>>> fix CHECK
 NULL
 
 #' @importFrom rlang names2

From b4862418310db31bea9eb406cdc820acb030f663 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Tue, 26 Jul 2022 10:28:24 +1000
Subject: [PATCH 18/34] print restore show

---
 DESCRIPTION  |  2 +-
 R/methods.R  | 89 ++++++++++++++++++++++++++--------------------------
 man/print.Rd |  2 +-
 3 files changed, 47 insertions(+), 46 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 050c389..99fd472 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -57,7 +57,7 @@ Biarch: true
 biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression, GeneExpression, Normalization, Clustering, QualityControl, Sequencing
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0
 Roxygen: list(markdown = TRUE)
 URL: https://github.com/stemangiola/tidySingleCellExperiment
 BugReports: https://github.com/stemangiola/tidySingleCellExperiment/issues
diff --git a/R/methods.R b/R/methods.R
index 15d4977..b8f30de 100755
--- a/R/methods.R
+++ b/R/methods.R
@@ -1,57 +1,24 @@
-setClass("tidySingleCellExperiment", contains = "SingleCellExperiment")
-
-#' tidy for SingleCellExperiment
-#'
-#' @param object A SingleCellExperiment object
-#'
-#' @return A tidySingleCellExperiment object
-#'
-#' @name tidy
-#'
-#' @examples
-#'
-#' tidySingleCellExperiment::pbmc_small
-#' @export
-tidy <- function(object) {
-    UseMethod("tidy", object)
-}
-
-#' @importFrom methods as
-#' @importFrom lifecycle deprecate_warn
-#'
-#' @param object A SingleCellExperiment object
-#'
-#' @export
-tidy.SingleCellExperiment <- function(object) {
-
-    # DEPRECATE
-    deprecate_warn(
-        when = "1.1.1",
-        what = "tidy()",
-        details = "tidySingleCellExperiment says: tidy() is not needed anymore."
-    )
-
-    object
-}
 
 setMethod(
     f = "show",
     signature = "SingleCellExperiment",
     definition = function(object) {
-        if (isTRUE(x = getOption(x = "restore_SingleCellExperiment_show", default = FALSE))) {
-            f <- getMethod(
-                f = "show",
-                signature = "SingleCellExperiment",
-                where = asNamespace(ns = "SingleCellExperiment")
+        if (
+          isTRUE(x = getOption(x = "restore_SingleCellExperiment_show", default = FALSE))
+        ) {
+            f <-getMethod(
+              f = "show",
+              signature = "SummarizedExperiment",
+              where = asNamespace(ns = "SummarizedExperiment")
             )
             f(object = object)
-        } else {
-            object %>%
-                print()
-        }
+
+        } else {  print(object)  }
     }
 )
 
+setClass("tidySingleCellExperiment", contains = "SingleCellExperiment")
+
 #' Extract and join information for features.
 #'
 #'
@@ -130,5 +97,39 @@ setMethod("join_features", "SingleCellExperiment",  function(.data,
 })
 
 
+#' tidy for SingleCellExperiment
+#'
+#' @param object A SingleCellExperiment object
+#'
+#' @return A tidySingleCellExperiment object
+#'
+#' @name tidy
+#'
+#' @examples
+#'
+#' tidySingleCellExperiment::pbmc_small
+#' @export
+tidy <- function(object) {
+  UseMethod("tidy", object)
+}
+
+#' @importFrom methods as
+#' @importFrom lifecycle deprecate_warn
+#'
+#' @param object A SingleCellExperiment object
+#'
+#' @export
+tidy.SingleCellExperiment <- function(object) {
+
+  # DEPRECATE
+  deprecate_warn(
+    when = "1.1.1",
+    what = "tidy()",
+    details = "tidySingleCellExperiment says: tidy() is not needed anymore."
+  )
+
+  object
+}
+
 
 
diff --git a/man/print.Rd b/man/print.Rd
index 53d4817..bad962f 100644
--- a/man/print.Rd
+++ b/man/print.Rd
@@ -51,7 +51,7 @@ Only the first 5 reduced dimensions are displayed, while all of them are queriab
 
 The following options are used by the tibble and pillar packages
 to format and print \code{tbl_df} objects.
-Used by the formatting workhorse \code{trunc_mat()} and, therefore,
+Used by the formatting workhorse \code{trunc_mat()} and therefore,
 indirectly, by \code{print.tbl()}.
 \itemize{
 \item \code{tibble.print_max}: Row number threshold: Maximum number of rows printed.

From ebc07b8524f53526354d4693fe51c621faa55217 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:16:51 +1000
Subject: [PATCH 19/34] use new pillar methods

---
 R/print_method.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/print_method.R b/R/print_method.R
index 25f2969..e6527f6 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -136,9 +136,11 @@ print.SingleCellExperiment <- function(x, ..., n = NULL, width = NULL, n_extra =
 
   x |>
     as_tibble(n_dimensions_to_return = 5) |>
+
     new_data_frame(class = c("tidySingleCellExperiment", "tbl")) %>%
     add_attr( nrow(x),  "number_of_features") %>%
     add_attr( assays(x) %>% names , "assay_names") %>%
+
     print()
 
   invisible(x)

From 7c84cc2deddb96ab9219d0e97528a491c35618bc Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:19:59 +1000
Subject: [PATCH 20/34] version UP

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

diff --git a/DESCRIPTION b/DESCRIPTION
index 6e34c07..d68f383 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -5,7 +5,7 @@ Version: 1.7.3
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre")) )
 Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCellExperiment' container 
-    in the form of tibble and allows the data manipulation, plotting and nesting using 'tidyverse'.
+    in the form of a tibble and allows the data manipulation, plotting and nesting using 'tidyverse'.
 License: GPL-3
 Depends:
     R (>= 4.1.0),

From feb66b137a1f44ec29423ff7d2523ab8c9ce2d56 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:31:25 +1000
Subject: [PATCH 21/34] fix bug tidybulk reference

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

diff --git a/R/print_method.R b/R/print_method.R
index e6527f6..1214e05 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -137,6 +137,7 @@ print.SingleCellExperiment <- function(x, ..., n = NULL, width = NULL, n_extra =
   x |>
     as_tibble(n_dimensions_to_return = 5) |>
 
+
     new_data_frame(class = c("tidySingleCellExperiment", "tbl")) %>%
     add_attr( nrow(x),  "number_of_features") %>%
     add_attr( assays(x) %>% names , "assay_names") %>%

From 4dd7cba1daf1536753cb699bc0d5ed4d2df0d22c Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 19:35:22 +1000
Subject: [PATCH 22/34] fix CHECK

---
 R/print_method.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/print_method.R b/R/print_method.R
index 1214e05..e6527f6 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -137,7 +137,6 @@ print.SingleCellExperiment <- function(x, ..., n = NULL, width = NULL, n_extra =
   x |>
     as_tibble(n_dimensions_to_return = 5) |>
 
-
     new_data_frame(class = c("tidySingleCellExperiment", "tbl")) %>%
     add_attr( nrow(x),  "number_of_features") %>%
     add_attr( assays(x) %>% names , "assay_names") %>%

From 7c1dc6e4192021cacf4045d20a4a5ffa8e63f271 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Tue, 26 Jul 2022 09:03:02 +1000
Subject: [PATCH 23/34] dummy change

---
 R/print_method.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/print_method.R b/R/print_method.R
index e6527f6..7404c0f 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -26,7 +26,6 @@
 #' @export
 #'
 NULL
-NULL
 
 #' @importFrom rlang names2
 #' @importFrom pillar align

From 481aebee90f8d2365c18a3b7560914b358109500 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Tue, 26 Jul 2022 10:28:24 +1000
Subject: [PATCH 24/34] print restore show

---
 DESCRIPTION  |  2 +-
 R/methods.R  | 89 ++++++++++++++++++++++++++--------------------------
 man/print.Rd |  2 +-
 3 files changed, 47 insertions(+), 46 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d68f383..be8f047 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -57,7 +57,7 @@ Biarch: true
 biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression, GeneExpression, Normalization, Clustering, QualityControl, Sequencing
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0
 Roxygen: list(markdown = TRUE)
 URL: https://github.com/stemangiola/tidySingleCellExperiment
 BugReports: https://github.com/stemangiola/tidySingleCellExperiment/issues
diff --git a/R/methods.R b/R/methods.R
index 15d4977..b8f30de 100755
--- a/R/methods.R
+++ b/R/methods.R
@@ -1,57 +1,24 @@
-setClass("tidySingleCellExperiment", contains = "SingleCellExperiment")
-
-#' tidy for SingleCellExperiment
-#'
-#' @param object A SingleCellExperiment object
-#'
-#' @return A tidySingleCellExperiment object
-#'
-#' @name tidy
-#'
-#' @examples
-#'
-#' tidySingleCellExperiment::pbmc_small
-#' @export
-tidy <- function(object) {
-    UseMethod("tidy", object)
-}
-
-#' @importFrom methods as
-#' @importFrom lifecycle deprecate_warn
-#'
-#' @param object A SingleCellExperiment object
-#'
-#' @export
-tidy.SingleCellExperiment <- function(object) {
-
-    # DEPRECATE
-    deprecate_warn(
-        when = "1.1.1",
-        what = "tidy()",
-        details = "tidySingleCellExperiment says: tidy() is not needed anymore."
-    )
-
-    object
-}
 
 setMethod(
     f = "show",
     signature = "SingleCellExperiment",
     definition = function(object) {
-        if (isTRUE(x = getOption(x = "restore_SingleCellExperiment_show", default = FALSE))) {
-            f <- getMethod(
-                f = "show",
-                signature = "SingleCellExperiment",
-                where = asNamespace(ns = "SingleCellExperiment")
+        if (
+          isTRUE(x = getOption(x = "restore_SingleCellExperiment_show", default = FALSE))
+        ) {
+            f <-getMethod(
+              f = "show",
+              signature = "SummarizedExperiment",
+              where = asNamespace(ns = "SummarizedExperiment")
             )
             f(object = object)
-        } else {
-            object %>%
-                print()
-        }
+
+        } else {  print(object)  }
     }
 )
 
+setClass("tidySingleCellExperiment", contains = "SingleCellExperiment")
+
 #' Extract and join information for features.
 #'
 #'
@@ -130,5 +97,39 @@ setMethod("join_features", "SingleCellExperiment",  function(.data,
 })
 
 
+#' tidy for SingleCellExperiment
+#'
+#' @param object A SingleCellExperiment object
+#'
+#' @return A tidySingleCellExperiment object
+#'
+#' @name tidy
+#'
+#' @examples
+#'
+#' tidySingleCellExperiment::pbmc_small
+#' @export
+tidy <- function(object) {
+  UseMethod("tidy", object)
+}
+
+#' @importFrom methods as
+#' @importFrom lifecycle deprecate_warn
+#'
+#' @param object A SingleCellExperiment object
+#'
+#' @export
+tidy.SingleCellExperiment <- function(object) {
+
+  # DEPRECATE
+  deprecate_warn(
+    when = "1.1.1",
+    what = "tidy()",
+    details = "tidySingleCellExperiment says: tidy() is not needed anymore."
+  )
+
+  object
+}
+
 
 
diff --git a/man/print.Rd b/man/print.Rd
index 53d4817..bad962f 100644
--- a/man/print.Rd
+++ b/man/print.Rd
@@ -51,7 +51,7 @@ Only the first 5 reduced dimensions are displayed, while all of them are queriab
 
 The following options are used by the tibble and pillar packages
 to format and print \code{tbl_df} objects.
-Used by the formatting workhorse \code{trunc_mat()} and, therefore,
+Used by the formatting workhorse \code{trunc_mat()} and therefore,
 indirectly, by \code{print.tbl()}.
 \itemize{
 \item \code{tibble.print_max}: Row number threshold: Maximum number of rows printed.

From de2c7537aa9d5ec2b09c15efd11f05c615b2461a Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:16:51 +1000
Subject: [PATCH 25/34] use new pillar methods

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

diff --git a/R/print_method.R b/R/print_method.R
index 7404c0f..f10e087 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -62,6 +62,7 @@ tbl_format_header.tidySingleCellExperiment <- function(x, setup, ...){
         assay_names %>% paste(collapse=", ")
       ), after = 1)
   }
+
   style_subtle(pillar___format_comment(header, width = setup$width))
 
 }

From 9e5e47c6be2a3cd0da37821eb82b72b337d00fb0 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:19:59 +1000
Subject: [PATCH 26/34] version UP

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

diff --git a/DESCRIPTION b/DESCRIPTION
index be8f047..d6b80d6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -5,7 +5,7 @@ Version: 1.7.3
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre")) )
 Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCellExperiment' container 
-    in the form of a tibble and allows the data manipulation, plotting and nesting using 'tidyverse'.
+    in the form of tibble and allows the data manipulation, plotting and nesting using 'tidyverse'.
 License: GPL-3
 Depends:
     R (>= 4.1.0),

From d79710d91c9676e45a5ad413350e477a4036dee0 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:31:25 +1000
Subject: [PATCH 27/34] fix bug tidybulk reference

---
 R/print_method.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/print_method.R b/R/print_method.R
index f10e087..8606c6b 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -136,7 +136,6 @@ print.SingleCellExperiment <- function(x, ..., n = NULL, width = NULL, n_extra =
 
   x |>
     as_tibble(n_dimensions_to_return = 5) |>
-
     new_data_frame(class = c("tidySingleCellExperiment", "tbl")) %>%
     add_attr( nrow(x),  "number_of_features") %>%
     add_attr( assays(x) %>% names , "assay_names") %>%

From 72599e1b06dc6c4a9a1fb524c4d5b22baee63627 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 19:35:22 +1000
Subject: [PATCH 28/34] fix CHECK

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

diff --git a/R/print_method.R b/R/print_method.R
index 8606c6b..3492e93 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -27,6 +27,7 @@
 #'
 NULL
 
+
 #' @importFrom rlang names2
 #' @importFrom pillar align
 #' @importFrom pillar get_extent

From b02d844d85706a49f0dbe442a4739aaf689f0dc5 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:16:51 +1000
Subject: [PATCH 29/34] use new pillar methods

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

diff --git a/R/print_method.R b/R/print_method.R
index 3492e93..847aa85 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -137,6 +137,7 @@ print.SingleCellExperiment <- function(x, ..., n = NULL, width = NULL, n_extra =
 
   x |>
     as_tibble(n_dimensions_to_return = 5) |>
+
     new_data_frame(class = c("tidySingleCellExperiment", "tbl")) %>%
     add_attr( nrow(x),  "number_of_features") %>%
     add_attr( assays(x) %>% names , "assay_names") %>%

From 3c85828f5b5c4da89762b0dac9421e37771b7f76 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:19:59 +1000
Subject: [PATCH 30/34] version UP

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

diff --git a/DESCRIPTION b/DESCRIPTION
index d6b80d6..be8f047 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -5,7 +5,7 @@ Version: 1.7.3
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre")) )
 Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCellExperiment' container 
-    in the form of tibble and allows the data manipulation, plotting and nesting using 'tidyverse'.
+    in the form of a tibble and allows the data manipulation, plotting and nesting using 'tidyverse'.
 License: GPL-3
 Depends:
     R (>= 4.1.0),

From f6eefa7baadd00688fa54770bb76b2f253b93884 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 18:31:25 +1000
Subject: [PATCH 31/34] fix bug tidybulk reference

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

diff --git a/R/print_method.R b/R/print_method.R
index 847aa85..176b5cf 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -136,7 +136,7 @@ NULL
 print.SingleCellExperiment <- function(x, ..., n = NULL, width = NULL, n_extra = NULL) {
 
   x |>
-    as_tibble(n_dimensions_to_return = 5) |>
+    as_tibble(n_dimensions_to_return = 5 ) |>
 
     new_data_frame(class = c("tidySingleCellExperiment", "tbl")) %>%
     add_attr( nrow(x),  "number_of_features") %>%

From 209b6d49e5b223dc3ce26b918a5fac1c174a0154 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 20 May 2022 19:35:22 +1000
Subject: [PATCH 32/34] fix CHECK

---
 R/print_method.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/R/print_method.R b/R/print_method.R
index 176b5cf..099d5c0 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -25,6 +25,10 @@
 #'
 #' @export
 #'
+<<<<<<< HEAD
+=======
+NULL
+>>>>>>> fix CHECK
 NULL
 
 

From 683d4480dd1d050ea9084d59d0ed70c010d1291f Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Tue, 26 Jul 2022 09:03:02 +1000
Subject: [PATCH 33/34] dummy change

---
 R/print_method.R | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/R/print_method.R b/R/print_method.R
index 099d5c0..176b5cf 100755
--- a/R/print_method.R
+++ b/R/print_method.R
@@ -25,10 +25,6 @@
 #'
 #' @export
 #'
-<<<<<<< HEAD
-=======
-NULL
->>>>>>> fix CHECK
 NULL
 
 

From c5991fe8c7110320b6d11c8bfbf20bf5e5210ce4 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Tue, 26 Jul 2022 10:45:14 +1000
Subject: [PATCH 34/34] version UP

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

diff --git a/DESCRIPTION b/DESCRIPTION
index be8f047..0a72513 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: tidySingleCellExperiment
 Title: Brings SingleCellExperiment to the Tidyverse 
-Version: 1.7.3
+Version: 1.7.4
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre")) )
 Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCellExperiment' container