Merge pull request #47 from stemangiola/print_hotifx

Print hotifx

DESCRIPTION

@@ -1,11 +1,11 @@
 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 = "[email protected]",
                   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),
@@ -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

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
+}
+
 
 

R/print_method.R

@@ -26,7 +26,6 @@
 #' @export
 #'
 NULL
-NULL
 
 #' @importFrom rlang names2
 #' @importFrom pillar align
@@ -63,6 +62,7 @@ tbl_format_header.tidySingleCellExperiment <- function(x, setup, ...){
         assay_names %>% paste(collapse=", ")
       ), after = 1)
   }
+
   style_subtle(pillar___format_comment(header, width = setup$width))
 
 }
@@ -91,7 +91,7 @@ tbl_format_header.tidySingleCellExperiment <- function(x, setup, ...){
 #'
 #' The following options are used by the tibble and pillar packages
 #' to format and print `tbl_df` objects.
-#' Used by the formatting workhorse `trunc_mat()` and, therefore,
+#' Used by the formatting workhorse `trunc_mat()` and therefore,
 #' indirectly, by `print.tbl()`.
 #'
 #' * `tibble.print_max`: Row number threshold: Maximum number of rows printed.
@@ -135,19 +135,15 @@ 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") %>%
     add_attr( assays(x) %>% names , "assay_names") %>%
+
     print()
 
   invisible(x)
 }
 
 
-
-
-
-
-
-