diff --git a/NAMESPACE b/NAMESPACE index 8d56a05..6e15caf 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -319,6 +319,7 @@ importFrom(methods,slot) importFrom(methods,slotNames) importFrom(methods,validObject) importFrom(rjson,fromJSON) +importFrom(rlang,"%||%") importFrom(rlang,check_installed) importFrom(sf,"st_agr<-") importFrom(sf,"st_geometry<-") diff --git a/R/aggregate.R b/R/aggregate.R index bf9f8b5..a119178 100644 --- a/R/aggregate.R +++ b/R/aggregate.R @@ -374,6 +374,7 @@ aggregateTxTech <- function(data_dir, df = NULL, by = NULL, #' #' @inheritParams sf::st_make_grid #' @inheritParams sf::aggregate +#' @inheritParams aggregateTx #' @param x An SFE object to be aggregated. #' @param by A \code{sf} data frame whose geometry column is used for #' aggregation or \code{sfc} or for multiple samples a list of \code{sfc} diff --git a/man/aggregate-SpatialFeatureExperiment-method.Rd b/man/aggregate-SpatialFeatureExperiment-method.Rd index 774fc00..09032b8 100644 --- a/man/aggregate-SpatialFeatureExperiment-method.Rd +++ b/man/aggregate-SpatialFeatureExperiment-method.Rd @@ -59,6 +59,11 @@ output. Defaults to "bins".} \item{join}{logical spatial predicate function to use if \code{by} is a simple features object or geometry; see \link[sf]{st_join}} +\item{sparse}{Logical, whether the gene count matrix from aggregating +transcript spots should be sparse. When the bins are large, the matrix will +not be very sparse so using sparse matrix will not save memory, but when +the bins are small, sparsity is worth it.} + \item{BPPARAM}{A \code{\link{BiocParallelParam}} object specifying parallel computing when aggregating data with functions other than sum and mean when aggregating cells. When aggregating transcript spots, this specifies diff --git a/man/aggregateTx.Rd b/man/aggregateTx.Rd index 3cb279b..c72c504 100644 --- a/man/aggregateTx.Rd +++ b/man/aggregateTx.Rd @@ -21,7 +21,8 @@ aggregateTx( new_geometry_name = "bins", unit = "micron", sparse = FALSE, - BPPARAM = SerialParam() + BPPARAM = SerialParam(), + .orig_nrows = NULL ) aggregateTxTech( @@ -92,6 +93,8 @@ the bins are small, sparsity is worth it.} \item{BPPARAM}{bpparam object to specify parallel computing over genes. If a lot of memory is used, then stick to `SerialParam()`.} +\item{.orig_nrows}{Only used internally in the SFE method of \code{aggregate}} + \item{data_dir}{Top level output directory.} \item{tech}{Which technology whose output to read, must be one of "Vizgen",