R CMD check issues

NEWS.md

@@ -1,3 +1,8 @@
+# Version 1.6.1
+* readRDS converts old style SpatRasterImage to the new style
+* readSelectTx and addSelectTx functions to read transcript spots from a few select genes from the parquet output of formatTxSpots or add them to an SFE object
+* Added formatTxTech and addTxTech functions, basically thin wrappers of formatTxSpots and addTxSpots with presets for Vizgen, Xenium, and CosMX
+
 # Version 1.6.0 (04/29/2024)
 * Changed defaults from sample_id = NULL to sample_id = 1L when dealing with 1 sample or "all" when dealing with multiple samples
 * dim method for BioFormatsImage that doesn't load the image into memory

R/formatTxSpots.R

@@ -493,6 +493,9 @@ addTxSpots <- function(sfe, file, sample_id = 1L,
 #' technology.
 #'
 #' @inheritParams formatTxSpots
+#' @inheritParams readVizgen
+#' @param tech Which technology whose output to read, must be one of "Vizgen",
+#' "Xenium", or "CosMX" though more technologies may be added later.
 #' @param z Which z-planes to read. Always "all" for Xenium where the z
 #'   coordinates are not discrete.
 #' @param split_cell_comps Only relevant to CosMX whose transcript spot file

R/read.R

@@ -332,10 +332,7 @@ read10xVisiumSFE <- function(samples = "",
 #'
 #' @inheritParams SpatialFeatureExperiment
 #' @inheritParams formatTxSpots
-#' @param data_dir Top level directory of Vizgen output, which contains
-#'   directories \code{cell_boundaries} and \code{images}, and files
-#'   \code{cell_by_gene.csv}, \code{cell_metadata.csv}, and
-#'   \code{detected_transcripts.csv}.
+#' @param data_dir Top level output directory.
 #' @param z Integer, z index to read, or "all", indicating z-planes of the
 #'   images and transcript spots to read. While cell segmentation seems to have
 #'   multiple z-planes, the segmentation in all z-planes are the same so in
@@ -558,9 +555,6 @@ readVizgen <- function(data_dir,
 
     # Column without colname is read as V1
     mat <- fread(mat_fn, colClasses = list(character = 1))
-    # TODO: write the sparse matrix to disk as hdf5 or mtx and check for the file
-    # next time, so the costly step using a lot of memory to read in the dense
-    # matrix can be avoided
     # get spatial metadata file---------
     meta_fn <- .check_vizgen_fns(data_dir, "cell_metadata")
     metadata <- fread(meta_fn, colClasses = list(character = 1))
@@ -684,7 +678,7 @@ readVizgen <- function(data_dir,
 #' @examples
 #' fp <- tempdir()
 #' dir_use <- SFEData::CosMXOutput(file_path = file.path(fp, "cosmx_test"))
-#' sfe <- readCosMX("cosmx", z = "all", add_molecules = TRUE)
+#' sfe <- readCosMX(dir_use, z = "all", add_molecules = TRUE)
 #' # Clean up
 #' unlink(dir_use, recursive = TRUE)
 readCosMX <- function(data_dir,