test: fix usage of reneeDS class

CCBR · Jul 31, 2024 · 1789b4f · 1789b4f
1 parent db29180
commit 1789b4f
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Showing 2 changed files with 23 additions and 21 deletions.
diff --git a/R/0_renee-class.R b/R/0_renee-class.R
@@ -39,14 +39,18 @@ reneeDataSet <- S7::new_class("renee",
 #'
 #' @examples
 #' create_reneeDataSet_from_files(
-#'   system.file("extdata", "sample_metadata.tsv", package = "reneeTools"),
-#'   system.file("extdata", "RSEM.genes.expected_count.all_samples.txt", package = "reneeTools")
+#'   sample_meta_filepath = system.file("extdata", "sample_metadata.tsv", package = "reneeTools"),
+#'   gene_counts_filepath = system.file("extdata", "RSEM.genes.expected_count.all_samples.txt", package = "reneeTools")
 #' )
 create_reneeDataSet_from_files <- function(sample_meta_filepath, gene_counts_filepath,
                                            count_type = "raw") {
   count_dat <- readr::read_tsv(gene_counts_filepath)
   sample_meta_dat <- readr::read_tsv(sample_meta_filepath)
-  return(create_reneeDataSet_from_dataframes(sample_meta_dat, list(count_type = count_dat)))
+  return(create_reneeDataSet_from_dataframes(
+    sample_meta_dat = sample_meta_dat,
+    count_dat = count_dat,
+    count_type = "raw"
+  ))
 }
 
 #' Construct a reneeDataSet object from data frames
@@ -67,15 +71,16 @@ create_reneeDataSet_from_files <- function(sample_meta_filepath, gene_counts_fil
 #' create_reneeDataSet_from_dataframes(sample_meta, gene_counts)
 create_reneeDataSet_from_dataframes <- function(sample_meta_dat,
                                                 count_dat,
-                                                sample_id_colname = sample_id,
+                                                sample_id_colname = "sample_id",
                                                 count_type = "raw") {
-  gene_id <- GeneName <- NULL
-
-  # sample_meta_dat <- sample_meta_dat %>% meta_tbl_to_dat(sample_id_colname = {{ sample_id_colname }})
-
-
+  gene_columns <- c("gene_id", "GeneName", "Gene")
   # sample IDs must be in the same order
-  if (!all(colnames(count_dat %>% dplyr::select(-c(gene_id, GeneName, Gene))) == (sample_meta_dat %>% dplyr::pull({{ sample_id_colname }})))) {
+  gene_sample_colnames <- count_dat %>%
+    dplyr::select(-tidyselect::any_of(gene_columns)) %>%
+    colnames()
+  meta_sample_colnames <- sample_meta_dat %>%
+    dplyr::pull(!!rlang::sym(sample_id_colname))
+  if (!all(gene_sample_colnames == meta_sample_colnames)) {
     stop("Not all columns in the count data equal the rows in the sample metadata. Sample IDs must be in the same order.")
   }
   counts <- list()

diff --git a/tests/testthat/test-0_renee-class.R b/tests/testthat/test-0_renee-class.R
@@ -1,10 +1,10 @@
 test_that("reneeDataSet from files works", {
   rds <- create_reneeDataSet_from_files(
-    system.file("extdata", "RSEM.genes.expected_count.all_samples.txt", package = "reneeTools"),
-    system.file("extdata", "sample_metadata.tsv", package = "reneeTools")
+    system.file("extdata", "sample_metadata.tsv", package = "reneeTools"),
+    system.file("extdata", "RSEM.genes.expected_count.all_samples.txt", package = "reneeTools")
   )
   expect_equal(
-    rds@counts %>% head(),
+    rds@counts$raw %>% head(),
     structure(
       list(
         gene_id = c(
@@ -28,13 +28,10 @@ test_that("reneeDataSet from files works", {
       class = c("tbl_df", "tbl", "data.frame")
     )
   )
-  expect_equal(
-    rds@sample_meta,
-    structure(list(condition = c(
-      "knockout", "knockout", "wildtype",
-      "wildtype"
-    )), row.names = c("KO_S3", "KO_S4", "WT_S1", "WT_S2"), class = "data.frame")
-  )
+  expect_equal(rds@sample_meta, tibble::tibble(
+    sample_id = c("KO_S3", "KO_S4", "WT_S1", "WT_S2"),
+    condition = c("knockout", "knockout", "wildtype", "wildtype")
+  ))
 })
 
 test_that("reneeDataSet from data frames detect problems", {
@@ -46,7 +43,7 @@ test_that("reneeDataSet from data frames detect problems", {
     )
   )
   expect_error(
-    create_reneeDataSet_from_dataframes(gene_counts[, 1:4], sample_meta),
+    create_reneeDataSet_from_dataframes(sample_meta, gene_counts[, 1:4]),
     "Not all columns"
   )
 })