replace small latent space error by warning

gagneurlab · Jul 16, 2024 · ee5ee2e · ee5ee2e
1 parent a2032ba
commit ee5ee2e
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Showing 2 changed files with 8 additions and 7 deletions.
diff --git a/R/controlForConfounders.R b/R/controlForConfounders.R
@@ -180,11 +180,12 @@ estimateBestQ <- function(ods=NULL, zScores=NULL){
   if (any(sv > cutoff)){
     latentDim <- max(which(sv > cutoff))
   } else {
-    stop(paste("Latent space dimension is smaller than 2. Check your count matrix and",
+    warning(paste("Optimal latent space dimension is smaller than 2. Check your count matrix and",
          "verify that all samples have the expected number of counts.",
-         "hist(colSums(counts(ods)))", collapse = "\n"))
-    latentDim <- 0} 
-  cat("Target rank:", latentDim, "\n")
+         "(hist(colSums(counts(ods)))).",
+         "For now, the latent space dimension is set to 2.", collapse = "\n"))
+    latentDim <- 2} 
+  cat("Optimal encoding dimension:", latentDim, "\n")
   return(latentDim)
 }
 

diff --git a/tests/testthat/test_estimateBestQ.R b/tests/testthat/test_estimateBestQ.R
@@ -71,11 +71,11 @@ test_that("Encoding dimensions are properly calculated for simulated z-scores",
   set.seed(42)
   latentDim <- 0
   zTilde <- matrix(rnorm(numGenes * numSamples), nrow = numGenes, ncol = numSamples)
-  expect_error(expect_equal(estimateBestQ(zScores = zTilde), 
-                            latentDim),
+  expect_warning(expect_equal(estimateBestQ(zScores = zTilde), 2),
                paste("Latent space dimension is smaller than 2\\. Check your count matrix and",
                  "verify that all samples have the expected number of counts\\.",
-                 "hist\\(colSums\\(counts\\(ods\\)\\)\\)", collapse = "\n"))
+                 "\\(hist\\(colSums\\(counts\\(ods\\)\\)\\)\\)\\.",
+                 "For now\\, the latent space dimension is set to 2\\.", collapse = "\n"))
 })
 
 test_that("Encoding dimensions are properly calculated for real ODS", {