re-added column_exist and matrix_to_dtable as exported utilities, changed col_name length 1 dependency to infinite

Author: agusinac

R/omics-class.R

@@ -1002,8 +1002,8 @@ omics <- R6::R6Class(
       #--------------------------------------------------------------------#
 
       if (!is.null(col_name)) {
-        if (!is.character(col_name) || length(col_name) != 1) {
-          cli::cli_abort("{.val col_name} must be a character and of length 1.")
+        if (!is.character(col_name)) {
+          cli::cli_abort("{.val col_name} must be a character.")
         } else if (!column_exists(col_name, private$.metaData)) {
           cli::cli_abort("The specified {.val {col_name}} does not exist in the {.field metaData}.")
         }

R/utils.R

@@ -4,7 +4,7 @@
 #'
 #' @param x A \link[base]{matrix}, \link[Matrix]{sparseMatrix} or \link[Matrix]{Matrix}.
 #' @return A \link[data.table]{data.table} class.
-#' @noRd
+#' @export
 matrix_to_dtable <- function(x) {
   if (inherits(x, "denseMatrix") || inherits(x, "matrix") || inherits(x, "sparseMatrix")) {
       return(data.table::data.table(as.matrix(x)))
@@ -17,7 +17,7 @@ matrix_to_dtable <- function(x) {
 #' @param column A character vector.
 #' @param table A \link[data.table]{data.table} or \link[base]{data.frame}.
 #' @return A boolean value.
-#' @noRd
+#' @export
 column_exists <- function(column, table) {
 
   ## Error handling

tests/testthat/_snaps/omics-composition.md

@@ -6,14 +6,6 @@
       Error in `taxa$composition()`:
       ! The specified "1" does not exist in the metaData.
 
----
-
-    Code
-      taxa$composition(feature_rank = "Genus", col_name = c("treatment", "sex"))
-    Condition
-      Error in `taxa$composition()`:
-      ! "col_name" must be a character and of length 1.
-
 ---
 
     Code

tests/testthat/test-omics-composition.R

@@ -8,7 +8,6 @@ taxa <- metagenomics$new(
 test_that("`omics$composition()` -- Argument checks", {
   ## feature_rank and feature_filter are already tested in `omics-feature_merge`
   expect_snapshot(taxa$composition(feature_rank = "Genus", col_name = "1"), error = TRUE)
-  expect_snapshot(taxa$composition(feature_rank = "Genus", col_name = c("treatment", "sex")), error = TRUE)
   expect_snapshot(taxa$composition(feature_rank = "Genus", col_name = "nonexisting"), error = TRUE)
 
   expect_snapshot(taxa$composition(feature_rank = "Genus", feature_top = "10"), error = TRUE)