Terra update problems and get rid of warning from cropping

pachterlab · Jan 21, 2025 · edab6fd · edab6fd
1 parent 2169a8b
commit edab6fd
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Showing 4 changed files with 13 additions and 6 deletions.
diff --git a/R/coerce.R b/R/coerce.R
@@ -44,7 +44,8 @@
                 terra::RGB(im_new) <- seq_len(3)
             } else if (inherits(img, "RemoteSpatialImage") || inherits(img, "StoredSpatialImage")) {
                 suppressWarnings(im_new <- rast(imgSource(img)))
-                if (packageVersion('terra') == as.package_version("1.7.83"))
+                if (packageVersion('terra') == as.package_version("1.7.83") ||
+                    packageVersion('terra') == as.package_version("1.8.10"))
                     im_new <- terra::flip(im_new)
             } else {
                 warning("Don't know how to convert image ", i, " to SpatRaster, ",

diff --git a/R/geometry_operation.R b/R/geometry_operation.R
@@ -463,6 +463,7 @@ crop <- function(x, y = NULL, colGeometryName = 1L, sample_id = "all",
             " was/were removed by the cropping."
         )
     }
+    samples_use <- intersect(samples_use, sampleIDs(out))
     if (!"col" %in% keep_whole) {
         # colGeometries should have already been subsetted here
         # Also actually crop all geometries for the samples of interest.

diff --git a/R/read.R b/R/read.R
@@ -79,7 +79,8 @@ read10xVisiumSFE <- function(samples = "",
     data <- match.arg(data)
     unit <- match.arg(unit)
     flip <- match.arg(flip)
-    if (packageVersion('terra') == as.package_version("1.7.83"))
+    if (packageVersion('terra') == as.package_version("1.7.83") ||
+        packageVersion('terra') == as.package_version("1.8.10"))
         flip <- "none"
     if (is_present(load)) {
         deprecate_warn("1.8.0", "read10xVisiumSFE(load)")
@@ -326,7 +327,8 @@ readVisiumHD <- function(data_dir, bin_size = c(2L, 8L, 16L),
     data <- match.arg(data)
     unit <- match.arg(unit)
     flip <- match.arg(flip)
-    if (packageVersion('terra') == as.package_version("1.7.83"))
+    if (packageVersion('terra') == as.package_version("1.7.83") ||
+        packageVersion('terra') == as.package_version("1.8.10"))
         flip <- "none"
     images <- match.arg(images, several.ok = TRUE)
     bin_size <- match.arg(as.character(bin_size), choices = c("2", "8", "16"),
@@ -747,7 +749,8 @@ readVizgen <- function(data_dir,
     check_installed("sfarrow")
     data_dir <- normalizePath(data_dir, mustWork = TRUE)
     flip <- match.arg(flip)
-    if (packageVersion('terra') == as.package_version("1.7.83"))
+    if (packageVersion('terra') == as.package_version("1.7.83") ||
+        packageVersion('terra') == as.package_version("1.8.10"))
         flip <- "none"
     image <- match.arg(image, several.ok = TRUE)
     if ((any(z < 0) || any(z > 6)) && z != "all") {

diff --git a/tests/testthat/test-image.R b/tests/testthat/test-image.R
@@ -197,7 +197,8 @@ test_that("mirrorImg, SpatRasterImage method", {
     img_m2 <- mirrorImg(img, maxcell = 100)
     expect_equal(dim(img_m2), c(13,8,3))
     # check content
-    if (packageVersion('terra') == as.package_version("1.7.83"))
+    if (packageVersion('terra') == as.package_version("1.7.83") ||
+        packageVersion('terra') == as.package_version("1.8.10"))
         expect_equal(imgRaster(img_m2)[4,3,2][[1]], 190)
 
     # Use filename
@@ -243,7 +244,8 @@ test_that("scaleImg, SpatRasterImage method, EBI behind the scene", {
 
 test_that("affineImg, SpatRasterImage method, EBI behind the scene", {
     suppressWarnings(spi <- SpatRasterImage(rast(img_path)))
-    if (packageVersion('terra') == as.package_version("1.7.83"))
+    if (packageVersion('terra') == as.package_version("1.7.83") ||
+        packageVersion('terra') == as.package_version("1.8.10"))
         spi <- mirrorImg(spi, "vertical")
     # Should rotate clockwise somewhat, squished to be flatter, shear to the right
     M <- matrix(c(0.6, -0.2, 0.2, 0.3), nrow = 2)