Enhance NAMESPACE and README with new imports and examples; update print method for SummarizedExperiment to improve design handling and output formatting.

Author: stemangiola

NAMESPACE

@@ -19,7 +19,10 @@ importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)
 importFrom(SummarizedExperiment,rowRanges)
 importFrom(cli,col_br_black)
+importFrom(dplyr,full_join)
 importFrom(dplyr,if_else)
+importFrom(dplyr,left_join)
+importFrom(dplyr,select)
 importFrom(fansi,strwrap_ctl)
 importFrom(magrittr,`%>%`)
 importFrom(methods,setMethod)
@@ -41,12 +44,15 @@ importFrom(purrr,map_chr)
 importFrom(purrr,map_int)
 importFrom(purrr,reduce)
 importFrom(purrr,when)
+importFrom(rlang,enquo)
 importFrom(rlang,names2)
 importFrom(stats,setNames)
 importFrom(stringr,str_replace)
 importFrom(stringr,str_replace_all)
 importFrom(tibble,as_tibble)
 importFrom(tibble,enframe)
+importFrom(tidyr,nest)
+importFrom(tidyr,pivot_longer)
 importFrom(tidyr,spread)
 importFrom(vctrs,new_data_frame)
 importFrom(vctrs,vec_rep)

R/print_methods.R

@@ -11,7 +11,7 @@
 #' @importFrom magrittr `%>%`
 #' @importFrom dplyr if_else
 #' @export
-print.SummarizedExperiment <- function(x, design = 1, n_print = 10, ...) {
+print.SummarizedExperiment <- function(x, design = 4, n_print = 10, ...) {
 
   # Match the user-supplied design argument to one of the valid choices:
   if (is.numeric(design)) {
@@ -242,8 +242,8 @@ but they do not completely overlap.")
       out_sub <- out[sub_seq, ]
 
       # Compute the max character width for each column
-      separator_row <- map2_chr(out_sub, names(out_sub), ~ {
-        max_width <- max(nchar(as.character(.x)), na.rm = TRUE) |> max(nchar(.y))  # Get max width in the column
+      separator_row <- sapply(out_sub %>% colnames(), function(col) {
+        max_width <- max(nchar(as.character(col)), na.rm = TRUE)  # Get max width in the column
         paste(rep("-", max_width), collapse = "")  # Generate a separator of the same length
       })
       # Modify the entire tibble to include a separator row across all columns

R/tibble_methods.R

@@ -1,10 +1,11 @@
-
 #' @importFrom purrr reduce
 #' @importFrom purrr map map2
 #' @importFrom tidyr spread
 #' @importFrom tibble enframe
 #' @importFrom SummarizedExperiment colData
 #' @importFrom pkgconfig get_config
+#' @importFrom rlang enquo
+#' @importFrom dplyr left_join
 #' @export
 as_tibble.SummarizedExperiment <- function(x, ...,
                                            .name_repair=c("check_unique", "unique", "universal", "minimal"),
@@ -19,7 +20,7 @@ as_tibble.SummarizedExperiment <- function(x, ...,
                                  .name_repair=c("check_unique", "unique", "universal", "minimal"),
                                  rownames=pkgconfig::get_config("tibble::rownames", NULL)) {
 
-  .subset <- enquo(.subset)
+  .subset <- rlang::enquo(.subset)
 
   sample_info <-
     colData(x) %>%

R/tidyprint_1_utlis.R

@@ -109,7 +109,7 @@ format_covariate_header <- function(separator_row, printed_colnames, covariate_n
 
   covariate_indices <- which(printed_colnames %in% covariate_names)
   covariate_widths <- separator_row[printed_colnames[covariate_indices]] |> purrr::map_int(nchar)
-  total_covariate_width <- sum(covariate_widths) + length(covariate_widths) + 3 # To compensate the white spaces of the tibble
+  total_covariate_width <- sum(covariate_widths) + length(covariate_widths) + 1 # To compensate the white spaces of the tibble
   label_length <- nchar(label)
 
   # Center the label in the total covariate width, using only dashes and the label
@@ -135,7 +135,7 @@ format_covariate_header <- function(separator_row, printed_colnames, covariate_n
   header_row[covariate_indices[-1]] <- ""
 
   # Add row ID spacing at the beginning
-  header_row <- c(paste(rep(" ", number_of_total_rows |> nchar() - 3), collapse = ""), header_row)
+  header_row <- c(paste(rep(" ", number_of_total_rows |> nchar() - 4), collapse = ""), header_row)
 
   # Step 2: Collapse everything with space
   paste(header_row, collapse = " ")

R/tidyse_utils.R

@@ -1,3 +1,7 @@
+#' @importFrom tidyr nest
+#' @importFrom dplyr select
+#' @importFrom tidyr pivot_longer
+#' @importFrom dplyr full_join
 # This file is a replacement of the unexported functions in the tibble
 # package, in order to specify "tibble abstraction in the header"
 
@@ -257,6 +261,14 @@ add_attr <- function(var, attribute, name) {
   var
 }
 
+eliminate_GRanges_metadata_columns_also_present_in_Rowdata <- function(.my_data, se) {
+  .my_data %>%
+    select(-one_of(colnames(rowData(se)))) %>%
+    
+    # In case there is not metadata column
+    suppressWarnings() 
+}
+
 get_special_datasets <- function(se) {
 
   rr =  se %>%
@@ -281,7 +293,7 @@ get_special_datasets <- function(se) {
         tibble::as_tibble(rr) %>%
           eliminate_GRanges_metadata_columns_also_present_in_Rowdata(se) %>%
           nest(GRangesList = -group_name) %>%
-          rename(!!f_(se)$symbol := group_name)
+          dplyr::rename(!!f_(se)$symbol := group_name)
 
       },