Merge pull request #14 from satijalab/develop

SeuratData v0.2.1

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: SeuratData
 Type: Package
 Title: Install and Manage Seurat Datasets
-Version: 0.2.0
-Date: 2019-11-15
+Version: 0.2.1
+Date: 2019-12-09
 Authors@R: c(
   person(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0001-9448-8833')),
   person(given = 'Paul', family = 'Hoffman', email = 'phoffman@nygenome.org', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-7693-8957')),
@@ -17,7 +17,7 @@ BugReports: https://github.com/satijalab/seurat-data/issues
 License: GPL-3 | file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
 Depends:
     R (>= 3.5.0)
 Imports:

R/seurat_data.R

@@ -120,16 +120,19 @@ InstalledData <- function() {
 
 #' Modularly load a dataset
 #'
-#' @inheritParams LoadH5Seurat
+# @inheritParams LoadH5Seurat
 #' @param ds Optional name of dataset to load
-#' @param type How to load the \code{Seurat} object; choose from
-#' \describe{
-#'   \item{info}{Information about the object and what's stored in it}
-#'   \item{raw}{The raw form of the dataset, no other options are evaluated}
-#'   \item{processed}{The proccessed data, modular loading avaible by setting other parameters}
-#' }
-#'
-#' @inherit LoadH5Seurat return
+#' @param type How to load the \code{Seurat} object; choose from either
+#' 'default' for the default dataset or any dataset listed in the
+#' \code{other.datasets} section of the data manifest
+# \describe{
+#   \item{info}{Information about the object and what's stored in it}
+#   \item{raw}{The raw form of the dataset, no other options are evaluated}
+#   \item{processed}{The proccessed data, modular loading avaible by setting other parameters}
+# }
+#'
+# @inherit LoadH5Seurat return
+#' @return A \code{Seurat} object with the dataset asked for
 #'
 #' @importFrom utils data
 #'
@@ -139,39 +142,59 @@ InstalledData <- function() {
 #'
 LoadData <- function(
   ds,
-  type = c('info', 'raw', 'processed'),
-  assays = NULL,
-  reductions = NULL,
-  graphs = NULL,
-  verbose = TRUE
+  type = 'default'
+  # assays = NULL,
+  # reductions = NULL,
+  # graphs = NULL,
+  # verbose = TRUE
 ) {
-  .NotYetImplemented()
   installed <- InstalledData()
   if (!NameToPackage(ds = ds) %in% rownames(x = installed)) {
     stop("Cannot find dataset ", ds, call. = FALSE)
   }
   ds <- NameToPackage(ds = ds)
-  type <- match.arg(arg = tolower(x = type), choices = c('info', 'raw', 'processed'))
-  if (type == 'raw') {
+  datasets <- c(
+    installed[ds, 'default.dataset', drop = TRUE],
+    trimws(x = unlist(x = strsplit(
+      x = installed[ds, 'other.datasets', drop = TRUE], split = ','
+    )))
+  )
+  type <- match.arg(
+    arg = tolower(x = type),
+    choices = c('raw', 'default', datasets)
+  )
+  if (type %in% c('raw', 'default')) {
+    type <- gsub(pattern = pkg.key, replacement = '', x = ds)
+  } else if (type == 'final') {
+    type <- paste0(gsub(pattern = pkg.key, replacement = '', x = ds), '.final')
+  }
+  if (type %in% data(package = ds)$results[, 'Item', drop = TRUE]) {
     e <- new.env()
-    ds <- gsub(pattern = '\\.SeuratData', replacement = '', x = ds)
-    data(list = ds, envir = e)
-    return(e[[ds]])
+    data(list = type, package = ds, envir = e)
+    # ds <- gsub(pattern = '\\.SeuratData', replacement = '', x = ds)
+    # data(list = ds, envir = e)
+    return(e[[type]])
   }
+  stop(
+    "Could not find dataset '",
+    type,
+    "', please check manifest and try again",
+    call. = FALSE
+  )
   .NotYetImplemented()
-  type <- match.arg(arg = type, choices = c('info', 'processed'))
-  return(LoadH5Seurat(
-    file = system.file(
-      file.path('extdata', 'processed.h5Seurat'),
-      package = ds,
-      mustWork = TRUE
-    ),
-    type = ifelse(test = type == 'processed', yes = 'object', no = type),
-    assays = assays,
-    reductions = reductions,
-    graphs = graphs,
-    verbose = verbose
-  ))
+  # type <- match.arg(arg = type, choices = c('info', 'processed'))
+  # return(LoadH5Seurat(
+  #   file = system.file(
+  #     file.path('extdata', 'processed.h5Seurat'),
+  #     package = ds,
+  #     mustWork = TRUE
+  #   ),
+  #   type = ifelse(test = type == 'processed', yes = 'object', no = type),
+  #   assays = assays,
+  #   reductions = reductions,
+  #   graphs = graphs,
+  #   verbose = verbose
+  # ))
 }
 
 #' Remove a dataset

R/zzz.R

@@ -448,12 +448,12 @@ UpdateManifest <- function() {
     x = avail.pkgs$InstalledVersion,
     strict = FALSE
   )
-  # TODO: remove these when we allow loading of processed datasets
-  cols.remove <- c('default.dataset', 'other.datasets')
-  if (any(cols.remove %in% colnames(x = avail.pkgs))) {
-    ds.index <- which(x = colnames(x = avail.pkgs) %in% cols.remove)
-    avail.pkgs <- avail.pkgs[, -ds.index]
-  }
+  # # TODO: remove these when we allow loading of processed datasets
+  # cols.remove <- c('default.dataset', 'other.datasets')
+  # if (any(cols.remove %in% colnames(x = avail.pkgs))) {
+  #   ds.index <- which(x = colnames(x = avail.pkgs) %in% cols.remove)
+  #   avail.pkgs <- avail.pkgs[, -ds.index]
+  # }
   pkg.env$manifest <- avail.pkgs
   # Cache the manifest
   if (getOption(x = 'SeuratData.manifest.cache', default = FALSE)) {