@@ -266,8 +266,28 @@ test_that("collapseCellTypes works", {

 #make seurat object:

 options(Seurat.object.assay.version = "v3")

 seur <- SeuratObject::CreateSeuratObject(counts = raw, assay="Spatial")

-test_that("runspatialdecon works on seurat objects", {

+test_that("runspatialdecon works on seurat objects - v3", {

   res <- runspatialdecon(seur)

+  res2 <- spatialdecon(norm = raw, raw = raw, bg = 0.1)

+  

+  expect_true(is.matrix(res$beta)) # test beta is a matrix

+  expect_true(is.matrix(res$yhat)) 

+  expect_true(is.matrix(res$resids))

+  expect_true(length(dim(res$sigmas)) == 3) # test sigmas is a 3d assar

+  expect_true(is.matrix(res$p))

+  expect_true(is.matrix(res$t))

+  expect_true(is.matrix(res$se))

+  expect_true(is.matrix(res$prop_of_all))

+  expect_true(is.matrix(res$prop_of_nontumor))

+  expect_true(is.matrix(res$X))

+  

+  expect_identical(res, res2)

+})

+

+options(Seurat.object.assay.version = "v5")

+seur <- suppressWarnings(SeuratObject::CreateSeuratObject(counts = raw, assay="Spatial"))

+test_that("runspatialdecon works on seurat objects - v5", {

+  res <- suppressWarnings(runspatialdecon(seur))

   res2 <- spatialdecon(norm = raw, raw = raw, bg = 0.1)

@@ -206,6 +206,7 @@ example of creating a matrix using a Seurat object.

 ```{r createSeuratmatrix}

 library(SeuratObject)

+library(Seurat)

 data("mini_singleCell_dataset")

@@ -220,9 +221,9 @@ rm(mini_singleCell_dataset)

 annots <- data.frame(cbind(cellType=as.character(Idents(seuratObject)), 

                            cellID=names(Idents(seuratObject))))

-custom_mtx_seurat <- create_profile_matrix(mtx = GetAssayData(object = seuratObject, 

-                                                              assay = "RNA", 

-                                                              slot = "counts"), 

+custom_mtx_seurat <- create_profile_matrix(mtx = Seurat::GetAssayData(object = seuratObject, 

+                                                                      assay = "RNA", 

+                                                                      slot = "counts"), 

                                            cellAnnots = annots, 

                                            cellTypeCol = "cellType", 

                                            cellNameCol = "cellID",