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Simplify default specification and remove unused code #238

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Simplify default specification and remove unused code #238

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06e3975
Simplify if with NROW()
Bisaloo Jun 6, 2026
9ff3cdf
Remove unused code portion
Bisaloo Jun 6, 2026
2482505
Leverage more opportunities to use %||%
Bisaloo Jun 6, 2026
494d1d3
Expand on comment about vapply vs lapply
Bisaloo Jun 23, 2026
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3 changes: 1 addition & 2 deletions R/combine.R
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Expand Up @@ -57,8 +57,7 @@ setMethod("combine", c("list", "missing"), \(x, y, ...) {
# get current element names
old <- lapply(x, \(z) unlist(colnames(z)))
# get list names; if missing, use empty strings
if (is.null(nms <- names(x)))
nms <- character(length(x))
nms <- names(x) %||% character(length(x))
# prepend list names to element names where available
new <- lapply(seq_along(x), \(i) {
if (nms[i] == "") return(old[[i]])
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10 changes: 0 additions & 10 deletions R/crop.R
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Expand Up @@ -109,16 +109,6 @@ NULL
# get transformation for space 'j'
j <- .val_id(j, CTname(x))
ct <- CTlist(x)[[j]]
# helper to adapt transformation data to spatial (XY) dims
axs <- axes(x)
nms <- vapply(axs, \(.) .$name, character(1))
ix <- match("x", nms)
iy <- match("y", nms)
if (is.na(ix) || is.na(iy)) {
# default to last two (YX)
n <- length(nms)
ix <- n; iy <- n-1
}
ax <- .get_xy_axes(x)
.adapt <- \(t, type) {
if (is.null(t)) return(NULL)
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3 changes: 2 additions & 1 deletion R/sdArray.R
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Expand Up @@ -120,7 +120,8 @@ setMethod("data_type", "DelayedArray", \(x) {
if (is.null(v)) return()
if (v == "0.5") x <- x$ome
# NOTE: can't use 'vapply' as we
# have encountered integer 'label's
# have encountered integer 'label's
# Tracked in https://github.com/scverse/spatialdata/issues/1136
x <- x$omero$channels
x$label %||% unlist(lapply(x, `[[`, "label"))
}
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9 changes: 3 additions & 6 deletions R/sdAttrs.R
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Expand Up @@ -216,8 +216,7 @@ setMethod("regions", "SingleCellExperiment", \(x) {
#' @importFrom SingleCellExperiment int_metadata<-
setReplaceMethod("region", c("SingleCellExperiment", "character"), \(x, value) {
stopifnot(all(nchar(value) > 0, na.rm=TRUE))
if (is.null(rk <- region_key(x)))
rk <- region_key(x) <- "region"
rk <- region_key(x) <- region_key(x) %||% "region"
int_metadata(x)$spatialdata_attrs[[rk]] <- sort(unique(value))
return(x)
})
Expand All @@ -237,7 +236,7 @@ setReplaceMethod("region", c("SingleCellExperiment", "NULL"), \(x, value) {
setReplaceMethod("regions", c("SingleCellExperiment", "character"), \(x, value) {
stopifnot(length(value) %in% c(1, ncol(x)))
stopifnot(all(nchar(value) > 0, na.rm=TRUE))
if (is.null(rk <- region_key(x))) region_key(x) <- "region"
rk <- region_key(x) <- region_key(x) %||% "region"
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int_metadata(x)$spatialdata_attrs[[rk]] <- sort(unique(value))
int_colData(x)[[rk]] <- value
return(x)
Expand Down Expand Up @@ -314,9 +313,7 @@ setMethod("instances", "SingleCellExperiment", \(x) {
#' @rdname SpatialDataAttrs
#' @importFrom SingleCellExperiment int_colData<-
setReplaceMethod("instances", c("SingleCellExperiment", "ANY"), \(x, value) {
ik <- instance_key(x)
if (is.null(ik))
ik <- "instance_id"
ik <- instance_key(x) %||% "instance_id"
int_colData(x)[[ik]] <- value
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return(x)
})
5 changes: 2 additions & 3 deletions R/sdFrame.R
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Expand Up @@ -77,7 +77,7 @@ NULL
#' @importFrom sf st_sf st_sfc st_as_sf st_point st_polygon
.df_to_sf <- \(data, type=c("POINT", "POLYGON")) {
type <- match.arg(type)
if (is.null(data) || isTRUE(nrow(data) == 0)) {
if (isTRUE(NROW(data) == 0)) {
# return empty data.frame with geometry column
fn <- switch(type, POINT=st_point, st_polygon)
return(st_sf(geometry=st_sfc(fn())[0], crs=NA))
Expand Down Expand Up @@ -134,8 +134,7 @@ SpatialDataPoint <- \(data=NULL, meta=SpatialDataAttrs(type="frame"), metadata=l
if (!is(data, "duckspatial_df"))
data <- .duck(data, "sdPoint")
za <- as.list(meta)
if (is.null(za$spatialdata_attrs))
za$spatialdata_attrs <- list()
za$spatialdata_attrs <- za$spatialdata_attrs %||% list()
if (!is.null(ik)) {
stopifnot(ik %in% colnames(data))
instance_key(za) <- ik
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4 changes: 2 additions & 2 deletions R/tables.R
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Expand Up @@ -182,8 +182,8 @@ setMethod("setTable", c("SpatialData", "character"), \(x, i, y,
if (!. %in% c("labels", "shapes"))
stop("can't add 'table' for", .)

if (is.null(region_key(y))) region_key(y) <- rk
if (is.null(instance_key(y))) instance_key(y) <- ik
region_key(y) <- region_key(y) %||% rk
instance_key(y) <- instance_key(y) %||% ik

if (is.null(region(y))) {
regions(y) <- i
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