Merge pull request #1111 from jiajic/suite_dev

fix: slide setting passing
drieslab · Mar 1, 2025 · 7b6e6b4 · 7b6e6b4
2 parents a720a10 + 0f6feb8
commit 7b6e6b4
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Showing 2 changed files with 11 additions and 5 deletions.
diff --git a/R/convenience_cosmx.R b/R/convenience_cosmx.R
@@ -360,6 +360,7 @@ setMethod(
                 micron = .Object@micron,
                 px2um = .Object@px2um,
                 offsets = .Object@offsets,
+                slide = .Object@slide,
                 verbose = verbose
             )
         }
@@ -375,7 +376,8 @@ setMethod(
                 path = path,
                 fovs = .Object@fovs %none% NULL,
                 feat_type = feat_type,
-                split_keyword = split_keyword
+                split_keyword = split_keyword,
+                slide = .Object@slide
             )
         }
         .Object@calls$load_expression <- expr_fun
@@ -426,6 +428,7 @@ setMethod(
         verbose = NULL) {
             .cosmx_cellmeta(
                 path = path,
+                slide = .Object@slide,
                 fovs = .Object@fovs %none% NULL,
                 dropcols = dropcols,
                 cores = cores,
@@ -838,7 +841,7 @@ setMethod("$<-", signature("CosmxReader"), function(x, name, value) {
     f <- x <- y <- NULL
 
     path <- normalizePath(path)
-    
+
     GiottoUtils::vmsg(.v = verbose, "loading segmentation masks...")
     vmsg(.v = verbose, .is_debug = TRUE, path)
 
@@ -1368,7 +1371,6 @@ createGiottoCosMxObject <- function(
             "4.2.0", "createGiottoCosMxObject(background_algo)")
     }
 
-
     # setup importer
     x <- importCosMx(cosmx_dir,
         fovs = FOVs,

diff --git a/tests/testthat/test_dataImports.R b/tests/testthat/test_dataImports.R
@@ -10,10 +10,14 @@
 
 test_that("Expression matrix is read correctly", {
     # getSpatialDataset
-    GiottoData::getSpatialDataset(dataset = "scRNA_mouse_brain", directory = paste0(getwd(), "/testdata/"))
+    expect_warning(expect_warning(GiottoData::getSpatialDataset(
+        dataset = "scRNA_mouse_brain", 
+        directory = paste0(getwd(), "/testdata/")
+    ), regexp = "output directory does not exist"), regexp = "footer")
 
     # readExprMatrix
-    expr_mat <- readExprMatrix(paste0(getwd(), "/testdata/brain_sc_expression_matrix.txt.gz"))
+    expr_mat <- readExprMatrix(
+        paste0(getwd(), "/testdata/brain_sc_expression_matrix.txt.gz"))
 
     expect_s4_class(expr_mat, "dgCMatrix")
     expect_equal(expr_mat@Dim, c(27998, 8039))