test-clustering now passing

compbiomed · Jan 28, 2024 · a5a7f91 · a5a7f91
1 parent 9a42b2d
commit a5a7f91
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/R/runCluster.R b/R/runCluster.R
@@ -113,7 +113,7 @@ runScranSNN <- function(inSCE, useReducedDim = "PCA", useAssay = NULL,
             stop("Scran SNN clustering requires one and only one of ",
                  "'useAssay', 'useReducedDim', and 'useAltExp'.")
         }
-        weightType <- match.arg(weightType)
+        weightType <- match.arg(weightType, choices = c("rank", "number", "jaccard"))
         algorithm <- match.arg(algorithm)
 
         graphClustAlgoList = list(leiden = igraph::cluster_leiden,

diff --git a/tests/testthat/test-clustering.R b/tests/testthat/test-clustering.R
@@ -8,7 +8,7 @@ sce <- scaterPCA(sce, useFeatureSubset = NULL)
 altExp(sce, "hvg") <- sce
 
 test_that(desc = "Testing Scran SNN with Assay", {
-  sce <- runScranSNN(sce, useAssay = "logcounts",
+  sce <- runScranSNN(sce, useReducedDim = NULL, k = 8, weightType = "rank", useAssay = "logcounts",
                      clusterName = "logcounts_cluster")
 
   testthat::expect_true("logcounts_cluster" %in% names(colData(sce)))
@@ -22,8 +22,8 @@ test_that(desc = "Testing Scran SNN with PCA", {
 })
 
 test_that(desc = "Testing Scran SNN with altExp", {
-  sce <- runScranSNN(sce, useAltExp = "hvg", altExpAssay = "logcounts",
-                     clusterName = "hvg_cluster")
+  sce <- runScranSNN(sce, useReducedDim = NULL, useAltExp = "hvg", altExpAssay = "logcounts",
+                     clusterName = "hvg_cluster", k = 8, weightType = "rank")
 
   testthat::expect_true("hvg_cluster" %in% names(colData(sce)))
 })