Merge pull request #1011 from jiajic/suite_dev

Suite devfix: allow instructions passing for Xenium conv.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 4.1.0
+Version: 4.1.1
 Authors@R: c(
 	person("Ruben", "Dries", email = "rubendries@gmail.com",
 		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),

NEWS.md

@@ -1,3 +1,10 @@
+
+# Giotto 4.1.1
+
+## Bug fixes
+* Allow `giottoInstructions` passing for Xenium convenience functions
+
+
 # Giotto 4.1.0 (2024/07/31)
 
 ## Breaking changes

R/convenience_visiumHD.R

@@ -138,7 +138,7 @@ setMethod("print", signature("VisiumHDReader"), function(x, ...) show(x))
 #'                                            array_subset_col = c(500, 1000))
 #'
 #' # Create a `giotto` object and add the loaded data
-#' TODO
+#' # TODO
 #' }
 #' @export
 importVisiumHD <- function(

R/convenience_xenium.R

@@ -373,6 +373,7 @@ setMethod(
             load_aligned_images = NULL,
             load_expression = FALSE,
             load_cellmeta = FALSE,
+            instructions = NULL,
             verbose = NULL
         ) {
             load_expression <- as.logical(load_expression)
@@ -413,7 +414,7 @@ setMethod(
             funs <- obj@calls
 
             # init gobject
-            g <- giotto()
+            g <- giotto(instructions = instructions)
 
 
             # transcripts
@@ -1215,8 +1216,10 @@ importXenium <- function(
 #' slower in our imaging pipeline.
 #' @param load_expression logical. Default = FALSE. Whether to load in 10X
 #' provided expression matrix.
-#' @param load_cellmeta logical. Default = FALSE. Whether to laod in 10X
+#' @param load_cellmeta logical. Default = FALSE. Whether to load in 10X
 #' provided cell metadata information
+#' @param instructions list of instructions or output result from
+#' [createGiottoInstructions()]
 #' @param verbose logical or NULL. NULL uses the `giotto.verbose` option
 #' setting and defaults to TRUE.
 #' @returns `giotto` object
@@ -1282,6 +1285,7 @@ createGiottoXeniumObject <- function(
         load_aligned_images = NULL,
         load_expression = FALSE,
         load_cellmeta = FALSE,
+        instructions = NULL,
         verbose = NULL
 ) {
     x <- importXenium(xenium_dir)
@@ -1296,6 +1300,7 @@ createGiottoXeniumObject <- function(
               load_aligned_images = load_aligned_images,
               load_expression = load_expression,
               load_cellmeta = load_cellmeta,
+              instructions = instructions,
               verbose = verbose)
 
     # only passed if not null

R/feature_set_enrichment.R

@@ -46,7 +46,7 @@
 #' for more details, see:
 #' https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#RNK:_Ranked_list_file_format_.28.2A.rnk.29
 #'
-#' For more information on parameter convetions,
+#' For more information on parameter conventions,
 #' please reference GSEA's documentation here:
 #' https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideTEXT.htm#_Syntax
 #' @export