add tests for ExpressionSet

R/clanc-fit.R

@@ -237,7 +237,8 @@ clanc.ExpressionSet <- function(x,
   pd_names <- colnames(Biobase::pData(x))
 
   if (!spec_in_cd(classes, pd_names) &&
-        (spec_in_cd(priors, pd_names) || spec_in_cd(active, pd_names))) {
+        ((!priors %in% c("equal", "class") && (spec_in_cd(priors, pd_names))) ||
+         spec_in_cd(active, pd_names))) {
     cli::cli_abort(
       "`classes` must be specified as a column name in pData if `active` or `priors` are." #nolint
     )
@@ -253,11 +254,11 @@ clanc.ExpressionSet <- function(x,
 
   if (spec_in_cd(classes, pd_names) &&
         nrow(unique(metadata)) > length(unique(metadata$class))) {
-    cli::cli_abort(
+    cli::cli_abort(c(
       "More than one prior and/or active for each class",
       "i" = "Each class must have exactly 1 prior and active",
       "i" = "To test across many `active`, use `tune::tune_grid`"
-    )
+    ))
   } else {
     metadata <- unique(metadata)
     classes <- x[[classes]]

tests/testthat/test-clanc-fit.R

@@ -2,22 +2,60 @@ test_that("catch unsupported types", {
   expect_error(clanc(numeric()))
 })
 
-test_that("catch bad args", {
+test_that("SummarizedExperiment catch bad args", {
   library(SummarizedExperiment)
   assay <- matrix(1:4, nrow = 2)
-  cd <- DataFrame(a = c("one", "two"), active = c(3, 4), prior = c(0.5, 0.5))
+  cd <- DataFrame(
+    a = c("one", "two"),
+    active = c(3, 4),
+    prior = c(0.5, 0.5)
+  )
   rd <- DataFrame(gene = c("g1", "g2"))
   se <- SummarizedExperiment(assay, rowData = rd, colData = cd)
   expect_error(clanc(se, classes = "b"))
   expect_error(clanc(se, active = "active", classes = c("one", "two")))
   expect_error(clanc(se, priors = "prior", classes = c("one", "two")))
+
   # Too many attributes per class:
   assay <- matrix(1:6, nrow = 2)
-  cd <- DataFrame(a = c("one", "two", "one"), active = c(3, 4, 2), prior = c(0.5, 0.5, 0.5))
+  cd <- DataFrame(
+    a = c("one", "two", "one"),
+    active = c(3, 4, 2),
+    prior = c(0.5, 0.5, 0.5)
+  )
   rd <- DataFrame(gene = c("g1", "g2"))
   se <- SummarizedExperiment(assay, rowData = rd, colData = cd)
   expect_error(
     clanc(se, classes = "a", active = "active", priors = "prior"),
     "More than one prior"
   )
 })
+
+test_that("SummarizedExperiment catch bad args", {
+  library(Biobase)
+  assay <- matrix(1:4, nrow = 2)
+  pdata <- AnnotatedDataFrame(
+    data.frame(a = c("one", "two"), active = c(3, 4), prior = c(0.5, 0.5))
+  )
+  fdata <- AnnotatedDataFrame(data.frame(gene = c("g1", "g2")))
+  es <- ExpressionSet(assay, pdata, fdata)
+  expect_error(clanc(es, classes = "b"))
+  expect_error(clanc(es, active = "active", classes = c("one", "two")))
+  expect_error(clanc(es, priors = "prior", classes = c("one", "two")))
+
+  # Too many attributes per class:
+  assay <- matrix(1:6, nrow = 2)
+  pdata <- AnnotatedDataFrame(
+    data.frame(
+      a = c("one", "two", "one"),
+      active = c(3, 4, 2),
+      prior = c(0.5, 0.5, 0.5)
+    )
+  )
+  fdata <- AnnotatedDataFrame(data.frame(gene = c("g1", "g2")))
+  es <- ExpressionSet(assay, pdata, fdata)
+  expect_error(
+    clanc(es, classes = "a", active = "active", priors = "prior"),
+    "More than one prior"
+  )
+})