Merge pull request #236 from josschavezf/dev

fix errors when running rcmdcheck

NAMESPACE

@@ -2,6 +2,7 @@
 
 S3method(.DollarNames,affine2d)
 S3method(.DollarNames,dimObj)
+S3method(.DollarNames,giotto)
 S3method(.DollarNames,metaData)
 S3method(.DollarNames,spatEnrObj)
 S3method(.DollarNames,spatLocsObj)

R/methods-extract.R

@@ -131,6 +131,13 @@ NULL
 #' This may remove some unexpected information. For specifically splitting the
 #' `giotto` object by spatial unit and/or feature type while keeping all
 #' expected information, use [sliceGiotto()]
+#' @param x giotto object
+#' @param spat_unit spatial unit (e.g. "cell")
+#' @param feat_type feature type to use (e.g. "rna", "protein")
+#' @param i character. Indicates the slot name
+#' @param j character. Indicates the subobject name
+#' @param drop logical. Default = TRUE
+#' @param \dots additional arguments
 #' @examples
 #' g <- GiottoData::loadGiottoMini("vizgen")
 #' force(g)
@@ -1277,8 +1284,6 @@ setMethod(
 
 
 #' @rdname subset_giotto
-#' @param feat_ids feature IDs to select
-#' @param cell_ids cell/spatial IDs to select
 #' @param subset Logical expression evaluated in expression values
 #' @param negate logical. if `TRUE` all IDs that are **not** in the `subset` 
 #' are selected
@@ -1480,6 +1485,9 @@ sliceGiotto <- function(
 #' @param x the object to coerce
 #' @param slots character vector. Which data slots to include in list. See
 #'   details
+#' @param spat_unit spatial unit (e.g. "cell")
+#' @param feat_type feature type to use (e.g. "rna", "protein")
+#' @param name name of the elements to select from the slot
 #' @param \dots additional arguments
 #' @details
 #' * Giotto method - the slots argument currently accepts any or multiple of:
@@ -1530,4 +1538,4 @@ setMethod("as.list", signature("giotto"), function(
 }
 .dbrkt_on_filter <- function(x, y) {
     x[objName(x) %in% y]
-}
+}

R/save_load.R

@@ -92,7 +92,7 @@ saveGiotto <- function(gobject,
                 )
                 terra::writeVector(
                     x = gobject@feat_info[[feat]]@spatVector,
-                    filename = filename
+                    filename = filename, overwrite = TRUE
                 )
             }
 
@@ -134,7 +134,7 @@ saveGiotto <- function(gobject,
                 )
                 terra::writeVector(
                     gobject@spatial_info[[spatinfo]]@spatVector,
-                    filename = filename
+                    filename = filename, overwrite = TRUE
                 )
             }
 
@@ -162,7 +162,7 @@ saveGiotto <- function(gobject,
                 )
                 terra::writeVector(
                     gobject@spatial_info[[spatinfo]]@spatVectorCentroids,
-                    filename = filename
+                    filename = filename, overwrite = TRUE
                 )
             }
 
@@ -197,7 +197,7 @@ saveGiotto <- function(gobject,
                     )
                     terra::writeVector(
                         gobject@spatial_info[[spatinfo]]@overlaps[[feature]],
-                        filename = filename
+                        filename = filename, overwrite = TRUE
                     )
                 }
             }

tests/testthat/test-GiottoInstructions.R

@@ -41,35 +41,31 @@ test_that("Instructions are created", {
     expect_type(instrs, "list")
 })
 
-# readGiottoInstructions
-test_that("readGiottoInstructions reads a few giotto object params correctly", {
-    expect_type(readGiottoInstructions(gobject, param = "show_plot"), "logical")
-    expect_type(readGiottoInstructions(gobject, param = "plot_format"), "character")
-    expect_type(readGiottoInstructions(gobject, param = "dpi"), "double")
+# read GiottoInstructions
+test_that("instructions reads a few giotto object params correctly", {
+    expect_type(instructions(gobject, param = "show_plot"), "logical")
+    expect_type(instructions(gobject, param = "plot_format"), "character")
+    expect_type(instructions(gobject, param = "dpi"), "double")
 })
 
-# showGiottoInstructions
-test_that("showGiottoInstructions returns expected list", {
-    expect_type(showGiottoInstructions(gobject), "list")
+# show GiottoInstructions
+test_that("instructions returns expected list", {
+    expect_type(instructions(gobject), "list")
 })
 
-# changeGiottoInstructions
-gobject <- changeGiottoInstructions(
-    gobject,
-    params = c("show_plot", "save_plot"),
-    new_values = c(FALSE, TRUE),
-    return_gobject = TRUE
-)
+# change GiottoInstructions
+instructions(gobject,
+             param = c("show_plot", "save_plot")) <- list(FALSE, TRUE)
 
-test_that("changeGiottoInstructions changes instruction params in object", {
-    expect_false(readGiottoInstructions(gobject, param = "show_plot"))
-    expect_true(readGiottoInstructions(gobject, param = "save_plot"))
+test_that("change GiottoInstructions changes instruction params in object", {
+    expect_false(instructions(gobject, param = "show_plot"))
+    expect_true(instructions(gobject, param = "save_plot"))
 })
 
-# replaceGiottoInstructions
-gobject <- replaceGiottoInstructions(gobject, instrs)
+# replace GiottoInstructions
+instructions(gobject) <- instrs
 
-test_that("replaceGiottoInstructions returns object instructions to original", {
-    expect_true(readGiottoInstructions(gobject, param = "show_plot"))
-    expect_false(readGiottoInstructions(gobject, param = "save_plot"))
+test_that("instructions returns object instructions to original", {
+    expect_true(instructions(gobject, param = "show_plot"))
+    expect_false(instructions(gobject, param = "save_plot"))
 })

tests/testthat/test-interoperability.R

@@ -6,9 +6,6 @@ giotto_obj <- GiottoData::loadGiottoMini("visium")
 seurat_obj <- giottoToSeuratV5(giotto_obj)
 spe_obj <- giottoToSpatialExperiment(giotto_obj)
 
-Seurat_obj2 <- SeuratData::LoadData("stxBrain", type = "anterior1" )
-giotto_obj2 <- seuratToGiottoV5(Seurat_obj2)
-
 giotto_obj_roundtrip <- seuratToGiottoV5(seurat_obj, "rna")
 
 test_that("giottotoseurat function handles basic conversion", {
@@ -66,4 +63,4 @@ test_that("Giotto to SpatialExperiment Conversion Works",{
 
 #TODO
 #spe
-#annData
+#annData

tests/testthat/test-save_load.R

@@ -17,3 +17,20 @@ test_that("gobject an be ovewritten and loaded - qs", {
 
     expect_true(methods::validObject(g3))
 })
+
+test_that("gobject can be saved and loaded - RDS", {
+    rlang::local_options(lifecycle_verbosity = "quiet")
+    saveGiotto(g, dir = test, overwrite = TRUE, verbose = FALSE)
+    g2 <<- loadGiotto(file.path(test, "saveGiottoDir"))
+
+    expect_true(methods::validObject(g2))
+})
+
+test_that("gobject an be ovewritten and loaded - RDS", {
+    rlang::local_options(lifecycle_verbosity = "quiet")
+    saveGiotto(g2, dir = test, overwrite = TRUE, verbose = FALSE)
+    g3 <- loadGiotto(file.path(test, "saveGiottoDir"))
+
+    expect_true(methods::validObject(g3))
+})
+