Added test for gs_score function and bump version.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: smartid
 Title: Scoring and Marker Selection Method Based on Modified TF-IDF
-Version: 0.99.1
+Version: 0.99.2
 Authors@R: 
     person("Jinjin", "Chen", email = "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-7923-5723"))

NEWS.md

@@ -5,3 +5,7 @@
 # smartid 0.99.1
 
 * Ready for submission to Bioconductor.
+
+# smartid 0.99.2
+
+* Added test for `gs_score` function.

R/AllGenerics.R

@@ -89,6 +89,7 @@ setGeneric(
 #'
 #' @inheritParams gs_score_init
 #' @param data an expression object, can be matrix or SummarizedExperiment
+#' @param features vector or named list, feature names to compute score
 #' @param slot a character, specify which slot to use when data is se object,
 #'             optional, default 'score'
 #' @param suffix a character, specify the name suffix to save score when

tests/testthat/test-gs_score.R

@@ -0,0 +1,26 @@
+test_that("gs_score works", {
+  ## sim data
+  set.seed(123)
+  data <- matrix(rnorm(100), 10, dimnames = list(seq_len(10)))
+
+  se <- SummarizedExperiment::SummarizedExperiment(
+    assays = list(counts = data)
+  )
+
+  ## test matrix
+  res <- gs_score(data, features = seq_len(3))
+  expect_type(res, "double")
+
+  ## test matrix, feature list
+  res <- gs_score(data, features = list(a = seq_len(3), b = seq_len(5)))
+  expect_type(res, "list")
+
+  ## test se
+  res <- gs_score(se, features = seq_len(3), slot = "counts")
+  expect_type(res$score, "double")
+
+  ## test se, feature list
+  res <- gs_score(se, features = list(a = seq_len(3), b = seq_len(5)),
+                  slot = "counts")
+  expect_type(colnames(res@colData), "character")
+})

tests/testthat/test-marker_selection.R

@@ -12,11 +12,17 @@ test_that("marker selection works", {
   res <- markers_mixmdl(top_n, k = 3, dist = "gamma")
   expect_type(res, "list")
 
-  ## test mclust
+  ## test mclust max.one
   res <- markers_mclust(top_n)
   expect_type(res, "list")
+  ## test mclust remove.min
+  res <- markers_mclust(top_n, method = "remove.min")
+  expect_type(res, "list")
 
-  ## test hdbscan
+  ## test hdbscan max.one
   res <- markers_hdbscan(top_n, minPts = 2)
   expect_type(res, "list")
+  ## test hdbscan remove.min
+  res <- markers_hdbscan(top_n, minPts = 2, method = "remove.min")
+  expect_type(res, "list")
 })

tests/testthat/test-plot.R

@@ -42,7 +42,7 @@ test_that("plot works", {
   p <- plot_mm(mixmdl = mixmdl, dist = "gamma")
   expect_true(is.ggplot(p))
 
-  ## test plot_mm for gamma
+  ## test plot_mm_clust for gamma
   set.seed(123)
   p <- plot_mm_clust(score = rnorm(50), clust = rep(c("A","B"), 25))
   expect_true(is.ggplot(p))