update PCA module

insightsengineering · Oct 17, 2024 · ccd3d9f · ccd3d9f
1 parent 0e67ed5
commit ccd3d9f
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Showing 3 changed files with 16 additions and 36 deletions.
diff --git a/tests/testthat/_snaps/boxplot.md b/tests/testthat/_snaps/boxplot.md
@@ -7,14 +7,14 @@
        $ fill       : chr  "#F8766D" "#F8766D" "#F8766D" "#F8766D" ...
        $ x          : 'mapped_discrete' num  1 1 1 1 1 1 1 1 1 1 ...
        $ density    : num  0.000161 0.000161 0.000161 0.00016 0.00016 ...
-       $ scaled     : num  0.492 0.492 0.492 0.492 0.492 ...
-       $ ndensity   : num  0.492 0.492 0.492 0.492 0.492 ...
+       $ scaled     : num  0.493 0.492 0.492 0.492 0.492 ...
+       $ ndensity   : num  0.493 0.492 0.492 0.492 0.492 ...
        $ count      : num  0.000642 0.000642 0.000642 0.000642 0.000641 ...
        $ n          : int  4 4 4 4 4 4 4 4 4 4 ...
        $ y          : num  650 659 667 676 684 ...
        $ PANEL      : Factor w/ 1 level "1": 1 1 1 1 1 1 1 1 1 1 ...
        $ group      : int  1 1 1 1 1 1 1 1 1 1 ...
-       $ violinwidth: num  0.492 0.492 0.492 0.492 0.492 ...
+       $ violinwidth: num  0.493 0.492 0.492 0.492 0.492 ...
        $ flipped_aes: logi  FALSE FALSE FALSE FALSE FALSE FALSE ...
        $ width      : num  0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 ...
        $ xmin       : 'mapped_discrete' num  0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 ...

diff --git a/tests/testthat/_snaps/pca.md b/tests/testthat/_snaps/pca.md
@@ -54,16 +54,6 @@
       8 -0.30521740 -0.58893592     1    -1    19  black  1.5   NA    NA    0.5
       9 -0.44180789  0.50479025     1    -1    19  black  1.5   NA    NA    0.5
 
----
-
-    Code
-      cat(res)
-    Output
-         colour           x          y PANEL group shape size fill alpha stroke
-      1 #F8766D -0.08263642  0.6615253     1     1    19  1.5   NA    NA    0.5
-      2 #F8766D -0.53157947 -0.4023279     1     1    19  1.5   NA    NA    0.5
-      3 #F8766D  0.61421589 -0.2591974     1     1    19  1.5   NA    NA    0.5
-
 ---
 
     Code

diff --git a/tests/testthat/test-pca.R b/tests/testthat/test-pca.R
@@ -62,19 +62,18 @@ test_that("pca module works as expected in the test app", {
   )
 
   # Add a gene filter and deselect everything and check that it does not crash.
-  app$set_inputs(!!ns2("add-MAE-hd1-row_to_add") := "chromosome_name")
+  app$set_inputs(`teal-teal_modules-pca-filter_panel-filters-MAE-MAE-hd1-row_to_add` = "chromosome", allow_no_input_binding_ = TRUE)
+  app$set_inputs(`teal-teal_modules-pca-filter_panel-filters-MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection` = character())
+  app$set_inputs(`teal-teal_modules-pca-filter_panel-filters-MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection_open` = FALSE, allow_no_input_binding_ = TRUE)
   app$wait_for_idle()
-  app$set_inputs(!!ns2("active-MAE-hd1-MAE_chromosome_name_hd1_subset-inputs-selection_open") := TRUE, allow_no_input_binding_ = TRUE)
-  app$set_inputs(!!ns2("active-MAE-hd1-MAE_chromosome_name_hd1_subset-inputs-keep_na-value") := FALSE)
-  app$set_inputs(!!ns2("active-MAE-hd1-MAE_chromosome_name_hd1_subset-inputs-selection") := character())
-  app$set_inputs(!!ns2("active-MAE-hd1-MAE_chromosome_name_hd1_subset-inputs-selection_open") := FALSE, allow_no_input_binding_ = TRUE)
 
-  app$wait_for_idle()
   res <- app$get_value(output = ns("test_pca"))
   expect_match(res$message, "No genes or samples included in this experiment, please adjust filters")
 
   # Remove filters
-  app$click(ns2("active-MAE-hd1-MAE_chromosome_name_hd1_subset-remove"))
+  # app$click(ns2("active-MAE-hd1-MAE_chromosome_name_hd1_subset-remove"))
+  app$click("teal-teal_modules-pca-filter_panel-filters-MAE-hd1-MAE_chromosome_hd1_subset-remove")
+  app$wait_for_idle()
 
   # Update the tab selection.
   app$set_inputs(!!ns("tab_selected") := "PC and Sample Correlation")
@@ -171,33 +170,24 @@ test_that("pca module works as expected in the test app", {
   app$set_inputs(!!ns("label") := TRUE)
   app$set_inputs(!!ns("show_matrix") := TRUE)
 
-  app$set_inputs(!!ns2("add-MAE-subjects-var_to_add") := "SEX")
   app$wait_for_idle(timeout = 40000)
-  app$set_inputs(!!ns2("active-MAE-subjects-MAE_SEX-inputs-selection") := "M")
+  app$set_inputs(`teal-teal_modules-pca-filter_panel-filters-MAE-MAE-subjects-var_to_add` = "SEX", allow_no_input_binding_ = TRUE)
+  app$set_inputs(`teal-teal_modules-pca-filter_panel-filters-MAE-subjects-MAE_SEX-inputs-selection` = "F")
+  app$set_inputs(`teal-teal_modules-pca-filter_panel-filters-MAE-subjects-MAE_SEX-inputs-selection_open` = FALSE, allow_no_input_binding_ = TRUE)
 
-  # Ensure xvar and yvar get resetted to pc1 and pc2.
+  # Ensure xvar and yvar DONT get reset.
   app$wait_for_idle(timeout = 20000)
   res <- app$get_value(input = ns("x_var"))
-  expect_identical(res, "1")
+  expect_identical(res, "3")
   res <- app$get_value(input = ns("y_var"))
-  expect_identical(res, "2")
-
-  res <- app$get_value(output = ns("test_pca"))
-  expect_snapshot(
-    cat(res)
-  )
-
-  # Update to cor tab.
-  app$set_inputs(!!ns2("active-MAE-subjects-MAE_SEX-inputs-selection_open") := TRUE, allow_no_input_binding_ = TRUE)
-  app$set_inputs(!!ns2("active-MAE-subjects-MAE_SEX-inputs-selection") := "F")
-  app$set_inputs(!!ns2("active-MAE-subjects-MAE_SEX-inputs-selection_open") := FALSE, allow_no_input_binding_ = TRUE)
+  expect_identical(res, "4")
 
   app$wait_for_idle()
   res <- app$get_value(output = ns("test_pca"))
   expect_identical(res$message, "Sample size is too small. PCA needs more than 2 samples.")
 
   # Remove filter.
-  app$click(ns2("active-MAE-subjects-MAE_SEX-remove"))
+  app$click("teal-teal_modules-pca-filter_panel-filters-MAE-subjects-MAE_SEX-remove")
 
   # Initiate the use of Top Variance Genes filtering functionality.
   app$set_inputs(!!ns("filter_top") := TRUE)