diff --git a/DESCRIPTION b/DESCRIPTION index 6b5a1d2..9e2249b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -65,7 +65,6 @@ Suggests: testthat, DT Enhances: - patchwork, anndataR, pizzarr Remotes: diff --git a/R/ImageArray.R b/R/ImageArray.R index e582239..bcdaddc 100644 --- a/R/ImageArray.R +++ b/R/ImageArray.R @@ -16,7 +16,7 @@ #' @examples #' library(SpatialData.data) #' dir.create(td <- tempfile()) -#' pa <- unzip_merfish_demo(td) +#' pa <- SpatialData.data:::.unzip_merfish_demo(td) #' pa <- file.path(pa, "images", "rasterized") #' (ia <- readImage(pa)) #' @@ -128,8 +128,8 @@ setMethod("[", "ImageArray", \(x, i, j, k, ..., drop=FALSE) { if (missing(k)) k <- TRUE else if (isFALSE(k)) k <- 0 else .check_jk(k, "k") ijk <- list(i, j, k) n <- length(data(x, NULL)) + d <- dim(data(x)) x@data <- lapply(seq_len(n), \(.) { - d <- dim(data(x, .)) j <- if (isTRUE(j)) seq_len(d[2]) else j k <- if (isTRUE(k)) seq_len(d[3]) else k jk <- lapply(list(j, k), \(jk) { diff --git a/R/PointFrame.R b/R/PointFrame.R index 49189af..d8476e0 100644 --- a/R/PointFrame.R +++ b/R/PointFrame.R @@ -33,7 +33,7 @@ #' @examples #' library(SpatialData.data) #' dir.create(tf <- tempfile()) -#' base <- unzip_merfish_demo(tf) +#' base <- SpatialData.data:::.unzip_merfish_demo(tf) #' x <- file.path(base, "points", "single_molecule") #' (p <- readPoint(x)) #' diff --git a/R/ShapeFrame.R b/R/ShapeFrame.R index 503f955..7e8bdb5 100644 --- a/R/ShapeFrame.R +++ b/R/ShapeFrame.R @@ -17,7 +17,7 @@ #' @examples #' library(SpatialData.data) #' dir.create(tf <- tempfile()) -#' base <- unzip_merfish_demo(tf) +#' base <- SpatialData.data:::.unzip_merfish_demo(tf) #' y <- file.path(base, "shapes", "cells") #' (s <- readShape(y)) #' plot(sf::st_as_sf(data(s)), cex=0.2) diff --git a/R/read.R b/R/read.R index aa483a2..cd140e8 100644 --- a/R/read.R +++ b/R/read.R @@ -63,7 +63,7 @@ allp = c("session_info==1.0.0", "spatialdata==0.3.0", "spatialdata_io==0.1.7", #' @examples #' library(SpatialData.data) #' dir.create(tf <- tempfile()) -#' base <- unzip_merfish_demo(tf) +#' base <- SpatialData.data:::.unzip_merfish_demo(tf) #' (x <- readSpatialData(base)) NULL diff --git a/man/ImageArray.Rd b/man/ImageArray.Rd index 7f8f78c..30b11bd 100644 --- a/man/ImageArray.Rd +++ b/man/ImageArray.Rd @@ -55,7 +55,7 @@ The `ImageArray` class \examples{ library(SpatialData.data) dir.create(td <- tempfile()) -pa <- unzip_merfish_demo(td) +pa <- SpatialData.data:::.unzip_merfish_demo(td) pa <- file.path(pa, "images", "rasterized") (ia <- readImage(pa)) diff --git a/man/PointFrame.Rd b/man/PointFrame.Rd index aad7e86..b2a140b 100644 --- a/man/PointFrame.Rd +++ b/man/PointFrame.Rd @@ -80,7 +80,7 @@ Currently defined methods (here, \code{x} is a \code{PointFrame}): \examples{ library(SpatialData.data) dir.create(tf <- tempfile()) -base <- unzip_merfish_demo(tf) +base <- SpatialData.data:::.unzip_merfish_demo(tf) x <- file.path(base, "points", "single_molecule") (p <- readPoint(x)) diff --git a/man/ShapeFrame.Rd b/man/ShapeFrame.Rd index 6cc5f6b..bb940c2 100644 --- a/man/ShapeFrame.Rd +++ b/man/ShapeFrame.Rd @@ -58,7 +58,7 @@ The `ShapeFrame` class \examples{ library(SpatialData.data) dir.create(tf <- tempfile()) -base <- unzip_merfish_demo(tf) +base <- SpatialData.data:::.unzip_merfish_demo(tf) y <- file.path(base, "shapes", "cells") (s <- readShape(y)) plot(sf::st_as_sf(data(s)), cex=0.2) diff --git a/man/SpatialData.Rd b/man/SpatialData.Rd index 9521d85..e760cfd 100644 --- a/man/SpatialData.Rd +++ b/man/SpatialData.Rd @@ -50,8 +50,8 @@ \alias{element,SpatialData,ANY,numeric-method} \alias{element,SpatialData,ANY,missing-method} \alias{element,SpatialData,ANY,ANY-method} -\alias{[[<-,SpatialData,numeric,ANY,ANY-method} -\alias{[[<-,SpatialData,character,ANY,ANY-method} +\alias{[[<-,SpatialData,numeric,ANY-method} +\alias{[[<-,SpatialData,character,ANY-method} \title{The `SpatialData` class} \usage{ SpatialData(images, labels, points, shapes, tables) @@ -88,9 +88,9 @@ SpatialData(images, labels, points, shapes, tables) \S4method{element}{SpatialData,ANY,ANY}(x, i, j) -\S4method{[[}{SpatialData,numeric,ANY,ANY}(x, i) <- value +\S4method{[[}{SpatialData,numeric,ANY}(x, i) <- value -\S4method{[[}{SpatialData,character,ANY,ANY}(x, i) <- value +\S4method{[[}{SpatialData,character,ANY}(x, i) <- value } \arguments{ \item{images}{list of \code{\link{ImageArray}}s} diff --git a/man/readSpatialData.Rd b/man/readSpatialData.Rd index 4108509..000ed43 100644 --- a/man/readSpatialData.Rd +++ b/man/readSpatialData.Rd @@ -58,6 +58,6 @@ Reading `SpatialData` \examples{ library(SpatialData.data) dir.create(tf <- tempfile()) -base <- unzip_merfish_demo(tf) +base <- SpatialData.data:::.unzip_merfish_demo(tf) (x <- readSpatialData(base)) }