outs woes again

Author: lambdamoses

R/coerce.R

@@ -117,7 +117,7 @@
 #' )
 #' ## using spacerangerOut folder
 #' tv <- TENxVisium(
-#'     spacerangerOut = sample_dir, processing = "raw", images = "lowres"
+#'     spacerangerOut = file.path(sample_dir, "outs"), processing = "raw", images = "lowres"
 #' )
 #' spe <- import(tv)
 #' # There can't be duplicate barcodes

R/dimGeometries.R

@@ -625,7 +625,7 @@ txSpots <- function(x, sample_id = 1L, withDimnames = TRUE) {
 #' )
 #' ## using spacerangerOut folder
 #' tv <- TENxVisium(
-#'     spacerangerOut = sample_dir, processing = "raw", images = "lowres"
+#'     spacerangerOut = file.path(sample_dir, "outs"), processing = "raw", images = "lowres"
 #' )
 #' spe <- import(tv)
 #' # There can't be suplicate barcodes

man/SpatialFeatureExperiment-coercion.Rd

@@ -33,7 +33,7 @@ test_that("Convert SPE and SCE to SFE, no images", {
 })
 
 test_that("Convert SPE to SFE, loaded images", {
-    spe <- TENxVisium(spacerangerOut = dir, processing = "filtered",
+    spe <- TENxVisium(spacerangerOut = file.path(dir, "outs"), processing = "filtered",
                       images = c("lowres", "hires")) |> import()
     sfe <- toSpatialFeatureExperiment(spe)
     img1 <- getImg(spe)
@@ -54,7 +54,7 @@ test_that("Convert SPE to SFE, loaded images", {
 })
 
 test_that("Convert SPE to SFE, stored images", {
-    spe <- TENxVisium(spacerangerOut = dir, processing = "filtered",
+    spe <- TENxVisium(spacerangerOut = file.path(dir, "outs"), processing = "filtered",
                       images = c("lowres", "hires")) |> import()
     sfe <- toSpatialFeatureExperiment(spe)
     img1 <- getImg(spe)
@@ -75,7 +75,7 @@ test_that("Convert SPE to SFE, stored images", {
 })
 
 test_that("Convert SPE to SFE, with SpatRaster image", {
-    spe <- TENxVisium(spacerangerOut = dir, processing = "filtered",
+    spe <- TENxVisium(spacerangerOut = file.path(dir, "outs"), processing = "filtered",
                       images = c("lowres", "hires")) |> import()
     suppressWarnings(Img(spe, image_id = "lowres") <- rast(imgSource(getImg(spe))) |> SpatRasterImage())
     sfe <- toSpatialFeatureExperiment(spe)

man/addVisiumSpotPoly.Rd

@@ -438,7 +438,7 @@ A read function for Visium HD is in progress. Contribution for Akoya, Molecular
 ## Coercion from `SpatialExperiment`
 SPE objects can be coerced into SFE objects. If column geometries or spot diameter are not specified, then a column geometry called "centroids" will be created.
 ```{r}
-spe <- TENxVisium(spacerangerOut = samples[1], processing = "filtered",
+spe <- TENxVisium(spacerangerOut = file.path(samples[1], "outs"), processing = "filtered",
                   images = c("lowres", "hires")) |> import()
 ```