more test fixes

rnabioco · Oct 1, 2023 · 7b4bbf4 · 7b4bbf4
1 parent 4dc5a8d
commit 7b4bbf4
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Showing 6 changed files with 14 additions and 3 deletions.
diff --git a/tests/testthat/test-calc-diversity.R b/tests/testthat/test-calc-diversity.R
@@ -2,6 +2,7 @@
 df_1 <- vdj_sce@colData
 
 df_2 <- vdj_sce@colData |>
+  as.data.frame() %>%
   as_tibble(rownames = ".cell_id")
 
 # Check all calc_diversity arguments
@@ -93,6 +94,7 @@ mets <- list(
 nms <- paste0("cdr3_", names(mets), "_diversity")
 
 test_div <- vdj_sce@colData |>
+  as.data.frame() |>
   as_tibble(rownames = ".cell_id") |>
   filter(!is.na(cdr3))
 

diff --git a/tests/testthat/test-calc-frequency.R b/tests/testthat/test-calc-frequency.R
@@ -2,6 +2,7 @@
 df_1 <- vdj_sce@colData
 
 df_2 <- vdj_sce@colData |>
+  as.data.frame() |>
   as_tibble(rownames = ".cell_id")
 
 # Check all calc_frequency arguments

diff --git a/tests/testthat/test-calc-gene-usage.R b/tests/testthat/test-calc-gene-usage.R
@@ -2,6 +2,7 @@
 df_1 <- vdj_sce@colData
 
 df_2 <- vdj_sce@colData |>
+  as.data.frame() |>
   as_tibble(rownames = ".cell_id")
 
 # Check all calc_gene_usage arguments

diff --git a/tests/testthat/test-calc-similarity.R b/tests/testthat/test-calc-similarity.R
@@ -2,6 +2,7 @@
 df_1 <- vdj_sce@colData
 
 df_2 <- vdj_sce@colData |>
+  as.data.frame() |>
   as_tibble(rownames = ".cell_id")
 
 test_clsts <- df_1 |>
@@ -34,6 +35,7 @@ test_all_args(
 # Check similarity calculation
 # calculate similarity independently and compare to calc_similarity results
 test_sim <- vdj_sce@colData |>
+  as.data.frame() |>
   as_tibble(rownames = ".cell_id") |>
   filter(!is.na(cdr3)) |>
   group_by(cdr3, seurat_clusters) |>

diff --git a/tests/testthat/test-plots.R b/tests/testthat/test-plots.R
@@ -15,7 +15,8 @@ test_lvls_2 <- unique(test_so$sample) |>
 
 df_1 <- vdj_sce@colData
 
-df_2 <- vdj_sce@colData |>
+df_2 <- df_1 |>
+  as.data.frame() |>
   as_tibble(rownames = ".cell_id")
 
 # Check all plot_features arguments except data_slot

diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
@@ -1,7 +1,8 @@
 # Test data
 df_1 <- vdj_sce@colData
 
-df_2 <- vdj_sce@colData |>
+df_2 <- df_1 |>
+  as.data.frame() |>
   as_tibble(rownames = ".cell_id")
 
 # Check fetch_vdj arguments
@@ -30,7 +31,10 @@ test_that("fetch_vdj sep", {
       sep           = NULL
     )
 
-  expect_identical(res, as_tibble(vdj_sce@colData, rownames = ".cell_id"))
+  expect_identical(
+    res,
+    as_tibble(as.data.frame(vdj_sce@colData), rownames = ".cell_id")
+  )
 
   expect_warning(
     res <- vdj_sce |>