fixes for updated v0.3 sctransform

DESCRIPTION

@@ -58,7 +58,7 @@ Imports:
     rsvd,
     Rtsne,
     scales,
-    sctransform (>= 0.2.0),
+    sctransform (>= 0.3.0),
     shiny,
     spatstat,
     stats,

R/preprocessing.R

@@ -3313,7 +3313,7 @@ GetResidualVstOut <- function(
     umi = umi,
     residual_type = "pearson",
     res_clip_range = c(clip.min, clip.max),
-    show_progress = verbose
+    verbosity = verbose
   )
   new_residual <- as.matrix(x = new_residual)
   # centered data

tests/testthat/test_objects.R

@@ -4,6 +4,7 @@
 # ------------------------------------------------------------------------------
 context("Metadata")
 
+pbmc_small <- suppressWarnings(suppressMessages(UpdateSeuratObject(pbmc_small)))
 cluster_letters <- LETTERS[Idents(object = pbmc_small)]
 names(cluster_letters) <- colnames(x = pbmc_small)
 cluster_letters_shuffled <- sample(x = cluster_letters)
@@ -205,9 +206,9 @@ context("Neighbor")
 # converting to Graph and back
 
 n.rann.ob <- NNHelper(
-  data = Embeddings(object = pbmc_small[["pca"]]), 
-  query = Embeddings(object = pbmc_small[["pca"]]), 
-  k = 10, 
+  data = Embeddings(object = pbmc_small[["pca"]]),
+  query = Embeddings(object = pbmc_small[["pca"]]),
+  k = 10,
   method = "rann")
 
 test_that("Neighbor object methods work", {
@@ -230,12 +231,12 @@ test_that("Neighbor object methods work", {
   expect_true(inherits(x = nro2, what = "Neighbor"))
   expect_equal(Distances(object = n.rann.ob)[2, 3], Distances(object = nro2)[2, 3])
   expect_equal(Indices(object = n.rann.ob)[1, 6], Indices(object = nro2)[1, 6])
-})  
+})
 
 n.annoy.ob <- NNHelper(
-  data = Embeddings(object = pbmc_small[["pca"]]), 
-  query = Embeddings(object = pbmc_small[["pca"]]), 
-  k = 10, 
+  data = Embeddings(object = pbmc_small[["pca"]]),
+  query = Embeddings(object = pbmc_small[["pca"]]),
+  k = 10,
   method = "annoy",
   cache.index = TRUE)
 idx.file <-  tempfile()

tests/testthat/test_preprocessing.R

@@ -292,11 +292,11 @@ object <- suppressWarnings(SCTransform(object = object, verbose = FALSE))
 
 test_that("SCTransform wrapper works as expected", {
   expect_true("SCT" %in% names(object))
-  expect_equal(as.numeric(colSums(GetAssayData(object = object[["SCT"]], slot = "scale.data"))[1]), 13.33038640)
+  expect_equal(as.numeric(colSums(GetAssayData(object = object[["SCT"]], slot = "scale.data"))[1]), 11.40288448)
   expect_equal(as.numeric(rowSums(GetAssayData(object = object[["SCT"]], slot = "scale.data"))[5]), 0)
   expect_equal(as.numeric(colSums(GetAssayData(object = object[["SCT"]], slot = "data"))[1]), 55.29678, tolerance = 1e6)
   expect_equal(as.numeric(rowSums(GetAssayData(object = object[["SCT"]], slot = "data"))[5]), 11.74404, tolerance = 1e6)
-  expect_equal(as.numeric(colSums(GetAssayData(object = object[["SCT"]], slot = "counts"))[1]), 123)
+  expect_equal(as.numeric(colSums(GetAssayData(object = object[["SCT"]], slot = "counts"))[1]), 129)
   expect_equal(as.numeric(rowSums(GetAssayData(object = object[["SCT"]], slot = "counts"))[5]), 28)
   expect_equal(length(VariableFeatures(object[["SCT"]])), 220)
   expect_equal(object[["SCT"]][[]]["MS4A1", "sct.detection_rate"], 0.15)
@@ -309,12 +309,12 @@ test_that("SCTransform wrapper works as expected", {
 object <- suppressWarnings(SCTransform(object = object, ncells = 40, verbose = FALSE))
 test_that("SCTransform ncells param works", {
   expect_true("SCT" %in% names(object))
-  expect_equal(as.numeric(colSums(GetAssayData(object = object[["SCT"]], slot = "scale.data"))[1]), 11.834969847)
+  expect_equal(as.numeric(colSums(GetAssayData(object = object[["SCT"]], slot = "scale.data"))[1]), 9.411835306)
   expect_equal(as.numeric(rowSums(GetAssayData(object = object[["SCT"]], slot = "scale.data"))[5]), 0)
   expect_equal(as.numeric(colSums(GetAssayData(object = object[["SCT"]], slot = "data"))[1]), 55.29678, tolerance = 1e6)
   expect_equal(as.numeric(rowSums(GetAssayData(object = object[["SCT"]], slot = "data"))[5]), 11.74404, tolerance = 1e6)
-  expect_equal(as.numeric(colSums(GetAssayData(object = object[["SCT"]], slot = "counts"))[1]), 121)
-  expect_equal(as.numeric(rowSums(GetAssayData(object = object[["SCT"]], slot = "counts"))[5]), 25)
+  expect_equal(as.numeric(colSums(GetAssayData(object = object[["SCT"]], slot = "counts"))[1]), 119)
+  expect_equal(as.numeric(rowSums(GetAssayData(object = object[["SCT"]], slot = "counts"))[5]), 26)
   expect_equal(length(VariableFeatures(object[["SCT"]])), 220)
   expect_equal(object[["SCT"]][[]]["MS4A1", "sct.detection_rate"], 0.15)
   expect_equal(object[["SCT"]][[]]["MS4A1", "sct.gmean"], 0.2027364, tolerance = 1e6)