Use tidyprint

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidySummarizedExperiment
 Title: Brings SummarizedExperiment to the Tidyverse 
-Version: 1.20.3
+Version: 1.23.2
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre")) )
 Author: Stefano Mangiola [aut, cre] <mangiolastefano@gmail.com>
@@ -21,7 +21,8 @@ Depends:
     SummarizedExperiment,
     ttservice (>= 0.5.0)
 Imports:
-	dplyr,
+    tidyprint,
+    dplyr,
     tibble (>= 3.0.4),
     magrittr,
     tidyr,

NAMESPACE

@@ -39,6 +39,9 @@ S3method(unnest,tidySummarizedExperiment_nested)
 export("%>%")
 export(subset_feature_data)
 export(subset_sample_data)
+export(tidy_print_enabled)
+export(tidy_print_off)
+export(tidy_print_on)
 export(unnest_summarized_experiment)
 exportMethods(subset_feature_data)
 exportMethods(subset_sample_data)
@@ -124,6 +127,10 @@ importFrom(tibble,as_tibble)
 importFrom(tibble,enframe)
 importFrom(tibble,rowid_to_column)
 importFrom(tibble,tibble)
+importFrom(tidyprint,tidy_message)
+importFrom(tidyprint,tidy_print_enabled)
+importFrom(tidyprint,tidy_print_off)
+importFrom(tidyprint,tidy_print_on)
 importFrom(tidyr,extract)
 importFrom(tidyr,gather)
 importFrom(tidyr,nest)

R/dplyr_methods.R

@@ -11,6 +11,7 @@
 #' @importFrom SummarizedExperiment assays<-
 #' @importFrom S4Vectors SimpleList
 #' @importFrom ttservice bind_rows
+#' @importFrom tidyprint tidy_message
 #' @importFrom lifecycle deprecate_warn
 #' @references
 #' Hutchison, W.J., Keyes, T.J., The tidyomics Consortium. et al. The tidyomics ecosystem: enhancing omic data analyses. Nat Methods 21, 1166–1170 (2024). https://doi.org/10.1038/s41592-024-02299-2
@@ -25,7 +26,7 @@ bind_rows.SummarizedExperiment <- function(..., .id=NULL, add.cell.ids=NULL) {
     tts <- flatten_if(dots_values(...), is_spliced)
 
     if (is_split_by_sample(tts) && is_split_by_transcript(tts)) {
-        stop("tidySummarizedExperiment says: bind_rows cannot be applied to splits both by sample- and feature-wise information")
+        tidy_stop("bind_rows cannot be applied to splits both by sample- and feature-wise information")
     }
     new_obj <- if (is_split_by_sample(tts)) {
         cbind(tts[[1]], tts[[2]])
@@ -38,8 +39,7 @@ bind_rows.SummarizedExperiment <- function(..., .id=NULL, add.cell.ids=NULL) {
 
     # If duplicated sample names
     if (new_obj |> colnames() |> duplicated() |> which() |> length() |> gt(0)) {
-        warning("tidySummarizedExperiment says:",
-            " you have duplicated sample names, they will be made unique.")
+        tidy_warning("you have duplicated sample names, they will be made unique.")
     }
     unique_colnames <- make.unique(colnames(new_obj), sep="_")
 
@@ -91,8 +91,7 @@ append_samples.SummarizedExperiment <- function(x, ..., .id = NULL) {
 
     # If duplicated sample names
     if (any(duplicated(colnames(new_obj)))) {
-        warning("tidySummarizedExperiment says:",
-                " you have duplicated sample names, they will be made unique.")
+        tidy_warning("you have duplicated sample names, they will be made unique.")
         unique_colnames <- make.unique(colnames(new_obj), sep = "_")
         colnames(new_obj) <- unique_colnames
 
@@ -176,7 +175,7 @@ bind_cols_internal <- function(..., .id=NULL, column_belonging=NULL) {
       ))) {
         update_SE_from_tibble(bound, tts[[1]], column_belonging = column_belonging)
       } else {
-        warning("tidySummarizedExperiment says: The new columns do not include pure sample-wise or feature-wise. A data frame is returned for independent data analysis.")
+        tidy_warning("The new columns do not include pure sample-wise or feature-wise. A data frame is returned for independent data analysis.")
         bound
       }
     }
@@ -254,7 +253,7 @@ distinct.SummarizedExperiment <- function(.data, ..., .keep_all=FALSE) {
 #' @export
 group_by.SummarizedExperiment <- function(.data, ...,
     .add=FALSE, .drop=group_by_drop_default(.data)) {
-    message(data_frame_returned_message)
+    tidy_message(data_frame_returned_message)
 
     # Deprecation of special column names
     .cols <- enquos(..., .ignore_empty="all") %>% 
@@ -285,7 +284,7 @@ group_by.SummarizedExperiment <- function(.data, ...,
 #' Wickham, H., François, R., Henry, L., Müller, K., Vaughan, D. (2023). dplyr: A Grammar of Data Manipulation. R package version 2.1.4, https://CRAN.R-project.org/package=dplyr
 #' @export
 summarise.SummarizedExperiment <- function(.data, ...) {
-    message(data_frame_returned_message)
+    tidy_message(data_frame_returned_message)
 
     # Deprecation of special column names
     .cols <- enquos(..., .ignore_empty="all") %>% 
@@ -333,7 +332,7 @@ summarize.SummarizedExperiment <- summarise.SummarizedExperiment
 #' Wickham, H., François, R., Henry, L., Müller, K., Vaughan, D. (2023). dplyr: A Grammar of Data Manipulation. R package version 2.1.4, https://CRAN.R-project.org/package=dplyr
 #' @export
 rowwise.SummarizedExperiment <- function(data, ...) {
-    message(data_frame_returned_message)
+    tidy_message(data_frame_returned_message)
 
     data |>
         as_tibble() |>
@@ -406,7 +405,7 @@ sample_n.SummarizedExperiment <- function(tbl, size, replace=FALSE,
     weight=NULL, .env=NULL, ...) {
     lifecycle::signal_superseded("1.0.0", "sample_n()", "slice_sample()")
 
-    message(data_frame_returned_message)
+    tidy_message(data_frame_returned_message)
 
     tbl |>
         as_tibble() |>
@@ -425,7 +424,7 @@ sample_frac.SummarizedExperiment <- function(tbl, size=1, replace=FALSE,
     weight=NULL, .env=NULL, ...) {
     lifecycle::signal_superseded("1.0.0", "sample_frac()", "slice_sample()")
 
-    message(data_frame_returned_message)
+    tidy_message(data_frame_returned_message)
 
     tbl |>
         as_tibble() |>
@@ -448,7 +447,7 @@ sample_frac.SummarizedExperiment <- function(tbl, size=1, replace=FALSE,
 #' @export
 count.SummarizedExperiment <- function(x, ..., wt=NULL,
     sort=FALSE, name=NULL, .drop=group_by_drop_default(x)) {
-    message(data_frame_returned_message)
+    tidy_message(data_frame_returned_message)
 
     # Deprecation of special column names
     .cols <- enquos(..., .ignore_empty="all") %>% 
@@ -528,14 +527,13 @@ pull.SummarizedExperiment <- function(.data, var=-1, name=NULL, ...) {
 
         # Warning if column names of assays do not overlap
         if (check_if_assays_are_NOT_consistently_ordered(.data)) {
-            warning(
-                "tidySummarizedExperiment says:",
-                " the assays in your SummarizedExperiment have column names, ",
+            tidy_warning(paste0(
+                "the assays in your SummarizedExperiment have column names, ",
                 "but their order is not the same. Pulling assays can return ",
-                "data in a order you don't expect. To avoid unwanted behaviour",
-                " it is highly recommended to have assays with the same order",
-                " of colnames and rownames" 
-            )
+                "data in a order you don't expect. To avoid unwanted behaviour ",
+                "it is highly recommended to have assays with the same order ",
+                "of colnames and rownames."
+            ))
 
             # reorder assay colnames before printing
             # Rearrange if assays has colnames and rownames

R/filter.R

@@ -56,6 +56,7 @@ analyze_query_scope_filter <- function(se, ...) {
 #' # Learn more in ?dplyr_tidy_eval
 #' 
 #' @importFrom purrr map
+#' @importFrom tidyprint tidy_message
 #' @importFrom dplyr filter
 #' @references
 #' Hutchison, W.J., Keyes, T.J., The tidyomics Consortium. et al. The tidyomics ecosystem: enhancing omic data analyses. Nat Methods 21, 1166–1170 (2024). https://doi.org/10.1038/s41592-024-02299-2
@@ -90,10 +91,11 @@ filter.SummarizedExperiment <- function(.data, ..., .preserve=FALSE) {
             dplyr::filter(..., .preserve=.preserve)
 
         if (!is_rectangular(new_meta, .data)) {
-            message("tidySummarizedExperiment says:",
-                " The resulting data frame is not rectangular",
-                " (all genes for all samples), a tibble is returned",
-                " for independent data analysis.")
+            tidy_message(paste0(
+                "The resulting data frame is not rectangular ",
+                "(all genes for all samples), a tibble is returned ",
+                "for independent data analysis."
+            ))
             return(new_meta)
         } else {
             .data[  

R/join.R

@@ -73,14 +73,14 @@ join_efficient_for_SE <- function(x, y, by = NULL, copy = FALSE,
     force_tibble_route) {
 
     # If I have a big dataset
-    if (ncol(x) > 100) message("tidySummarizedExperiment says: if you are joining a dataframe both sample-wise and feature-wise, for efficiency (until further development), it is better to separate your joins and join datasets sample-wise OR feature-wise.")
+    if (ncol(x) > 100) tidyprint::tidy_message("If you are joining a dataframe both sample-wise and feature-wise, for efficiency (until further development), it is better to separate your joins and join datasets sample-wise OR feature-wise.", type = "warning")
 
     joined <- x %>%
       as_tibble(skip_GRanges = TRUE) %>%
       join_function(y, by = by, copy = copy, suffix = suffix, ...)
     out <- if (!is_not_duplicated(joined, x) || !is_rectangular(joined, x)) {
-      message(duplicated_cell_names)
-      message(data_frame_returned_message)
+      tidyprint::tidy_message(duplicated_cell_names, type = "warning")
+      tidyprint::tidy_message(data_frame_returned_message)
       joined
     } else {
       update_SE_from_tibble(joined, x)
@@ -173,7 +173,7 @@ join_efficient_for_SE <- function(x, y, by = NULL, copy = FALSE,
     x
   }
 
-  else stop("tidySummarizedExperiment says: ERROR FOR DEVELOPERS: this option should not exist. In join utility.")
+  else tidy_stop("ERROR FOR DEVELOPERS: this option should not exist. In join utility.")
 }
 
 #' @name left_join
@@ -190,6 +190,7 @@ join_efficient_for_SE <- function(x, y, by = NULL, copy = FALSE,
 #'     slice(1))
 #'
 #' @importFrom dplyr left_join
+#' @importFrom tidyprint tidy_message
 #' @references
 #' Hutchison, W.J., Keyes, T.J., The tidyomics Consortium. et al. The tidyomics ecosystem: enhancing omic data analyses. Nat Methods 21, 1166–1170 (2024). https://doi.org/10.1038/s41592-024-02299-2
 #' 

R/mutate.R

@@ -216,14 +216,13 @@ mutate_via_tibble <- function(.data, ...) {
         columns <-
             special_columns |>
                 paste(collapse=", ")
-        stop(
-            "tidySummarizedExperiment says:",
-            " you are trying to rename a column that is view only",
+        tidy_stop(paste0(
+            "you are trying to rename a column that is view only ",
             columns,
-            "(it is not present in the colData).",
-            " If you want to mutate a view-only column,",
-            " make a copy and mutate that one."
-        )
+            " (it is not present in the colData). ",
+            "If you want to mutate a view-only column, ",
+            "make a copy and mutate that one."
+        ))
     }
 
     # If Ranges column not in query perform fast as_tibble

R/rename.R

@@ -44,14 +44,13 @@ rename.SummarizedExperiment <- function(.data, ...) {
 
     if (any(old_names %in% special_columns)) {
         columns <- intersect(old_names, special_columns) |> paste(collapse=", ")
-        stop(
-            "tidySummarizedExperiment says:",
-            " you are trying to rename a column that is view only: ",
+        tidy_stop(paste0(
+            "you are trying to rename a column that is view only: ",
             columns,
-            " (it is not present in the colData or rowData).",
-            " If you want to mutate a view-only column,",
-            " make a copy and mutate that one."
-        )
+            " (it is not present in the colData or rowData). ",
+            "If you want to mutate a view-only column, ",
+            "make a copy and mutate that one."
+        ))
     }
 
     # Dispatch to appropriate domain-specific function
@@ -63,9 +62,10 @@ rename.SummarizedExperiment <- function(.data, ...) {
         return(modify_features(.data, "rename", ...))
     } else {
         # No matching columns found
-        stop("tidySummarizedExperiment says:",
-            " the columns you are trying to rename (",
+        tidy_stop(paste0(
+            "the columns you are trying to rename (",
             paste(old_names, collapse=", "),
-            ") are not found in colData or rowData.")
+            ") are not found in colData or rowData."
+        ))
     }
 }

R/select.R

@@ -62,6 +62,7 @@ analyze_query_scope_select <- function(se, ...) {
 #' 
 #' @importFrom SummarizedExperiment colData
 #' @importFrom dplyr select
+#' @importFrom tidyprint tidy_message
 #' @importFrom tidyselect all_of
 #' @importFrom tidyselect any_of
 #' @export
@@ -82,14 +83,13 @@ select.SummarizedExperiment <- function(.data, ...) {
     # Warning if column names of assays do not overlap
     if (check_if_assays_are_NOT_consistently_ordered(.data)) {
 
-        warning(
-            "tidySummarizedExperiment says:",
-            " the assays in your SummarizedExperiment have column names,",
-            " but their order is not the same. Assays were internally",
-            " reordered to be consistent with each other.",
-            " To avoid unwanted behaviour it is highly reccomended",
-            " to have assays with the same order of colnames and rownames."
-        )
+        tidy_warning(paste0(
+            "the assays in your SummarizedExperiment have column names, ",
+            "but their order is not the same. Assays were internally ",
+            "reordered to be consistent with each other. ",
+            "To avoid unwanted behaviour it is highly recommended ",
+            "to have assays with the same order of colnames and rownames."
+        ))
 
         # reorder assay colnames before printing
         # Rearrange if assays has colnames and rownames
@@ -106,11 +106,10 @@ select.SummarizedExperiment <- function(.data, ...) {
         col_data_tibble <- 
             colData(.data) |> 
             as_tibble(rownames = s_(.data)$name)
-        message(
-            "tidySummarizedExperiment says:",
-            " Key columns are missing.",
-            " A data frame is returned for independent data analysis."
-        )
+        tidy_message(paste0(
+            "Key columns are missing. ",
+            "A data frame is returned for independent data analysis."
+        ))
         return(
             col_data_tibble |> 
                 dplyr::select(tidyselect::eval_select(rlang::expr(c(...)), col_data_tibble)) |> 
@@ -121,9 +120,10 @@ select.SummarizedExperiment <- function(.data, ...) {
         row_data_tibble <-
             rowData(.data) |> 
             as_tibble(rownames=f_(.data)$name)
-        message("tidySummarizedExperiment says:",
-            " Key columns are missing.",
-            " A data frame is returned for independent data analysis.")
+        tidy_message(paste0(
+            "Key columns are missing. ",
+            "A data frame is returned for independent data analysis."
+        ))
         return(
             row_data_tibble |> 
                 dplyr::select(tidyselect::eval_select(rlang::expr(c(...)), row_data_tibble)) |> 
@@ -184,15 +184,17 @@ select.SummarizedExperiment <- function(.data, ...) {
     # convert to tibble and delegate selection to dplyr
     if (!all(c(get_needed_columns(.data)) %in% scope_report$selected_columns)) {
         if (ncol(.data)>100) {
-            message("tidySummarizedExperiment says:",
-                " You are doing a complex selection both sample-wise",
-                " and feature-wise. In the latter case, for efficiency",
-                " (until further development), it is better to separate",
-                " your selects sample-wise OR feature-wise.")
+            tidy_message(
+                paste0(
+                    "You are doing a complex selection both sample-wise ",
+                    "and feature-wise. In the latter case, for efficiency ",
+                    "(until further development), it is better to separate ",
+                    "your selects sample-wise OR feature-wise."
+                ),
+                type = "warning"
+            )
         }
-        message("tidySummarizedExperiment says:",
-            " Key columns are missing.",
-            " A data frame is returned for independent data analysis.")
+        tidy_message(data_frame_returned_message)
 
         .data |>
             as_tibble(skip_GRanges=TRUE) |>