Merge pull request #13 from satijalab/develop

SeuratData v0.2.0

Author: mojaveazure

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: SeuratData
 Type: Package
 Title: Install and Manage Seurat Datasets
-Version: 0.1.0
-Date: 2019-07-17
+Version: 0.2.0
+Date: 2019-11-15
 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')),
@@ -18,11 +18,14 @@ License: GPL-3 | file LICENSE
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 6.1.1
+Depends:
+    R (>= 3.5.0)
 Imports:
     cli,
     crayon,
+    rappdirs,
     stats,
     utils
-Collate: 
+Collate:
     'zzz.R'
     'seurat_data.R'

NAMESPACE

@@ -3,6 +3,7 @@
 export(AvailableData)
 export(InstallData)
 export(InstalledData)
+export(LoadData)
 export(RemoveData)
 export(UpdateData)
 importFrom(cli,rule)
@@ -14,8 +15,10 @@ importFrom(crayon,col_nchar)
 importFrom(crayon,green)
 importFrom(crayon,red)
 importFrom(crayon,yellow)
+importFrom(rappdirs,user_data_dir)
 importFrom(stats,na.omit)
 importFrom(utils,available.packages)
+importFrom(utils,data)
 importFrom(utils,install.packages)
 importFrom(utils,packageVersion)
 importFrom(utils,remove.packages)

R/seurat_data.R

@@ -16,7 +16,11 @@ NULL
 #'
 #' @export
 #'
-#' @seealso \code{\link{InstallData}} \code{\link{InstalledData}} \code{\link{RemoveData}} \code{\link{UpdateData}}
+#' @seealso \code{\link{InstallData}} \code{\link{InstalledData}}
+#' \code{\link{RemoveData}} \code{\link{UpdateData}}
+#'
+#' @examples
+#' AvailableData()
 #'
 AvailableData <- function() {
   UpdateManifest()
@@ -35,18 +39,30 @@ AvailableData <- function() {
 #'
 #' @export
 #'
-#' @seealso \code{\link{AvailableData}} \code{\link{InstalledData}} \code{\link{RemoveData}} \code{\link{UpdateData}}
+#' @seealso \code{\link{AvailableData}} \code{\link{InstalledData}}
+#' \code{\link{RemoveData}} \code{\link{UpdateData}}
+#'
+#' @examples
+#' \dontrun{
+#' InstallData('pbmc3k')
+#' }
 #'
 InstallData <- function(ds, force.reinstall = FALSE, ...) {
   UpdateManifest()
+  if (pkg.env$source != 'remote') {
+    stop(
+      "No access to remote SeuratData repository, unable to install new datasets",
+      call. = FALSE
+    )
+  }
   pkgs <- NameToPackage(ds = ds)
   if (!force.reinstall) {
     installed <- intersect(x = pkgs, y = rownames(x = InstalledData()))
     if (length(x = installed) > 0) {
       warning(
         "The following packages are already installed and will not be reinstalled: ",
         paste(
-          gsub(pattern = '\\.SeuratData', replacement = '', x = installed),
+          gsub(pattern = pkg.key, replacement = '', x = installed),
           collapse = ', '
         ),
         call. = FALSE,
@@ -63,7 +79,12 @@ InstallData <- function(ds, force.reinstall = FALSE, ...) {
   for (p in pkgs2[pkgs2 %in% search()]) {
     detach(name = p, unload = TRUE, character.only = TRUE)
   }
-  install.packages(pkgs = pkgs, repos = getOption(x = "SeuratData.repo.use"), type = 'source', ...)
+  install.packages(
+    pkgs = pkgs,
+    repos = getOption(x = "SeuratData.repo.use"),
+    type = 'source',
+    ...
+  )
   for (pkg in pkgs) {
     attachNamespace(ns = pkg)
     pkg.env$attached <- c(pkg.env$attached, pkg)
@@ -86,13 +107,73 @@ InstallData <- function(ds, force.reinstall = FALSE, ...) {
 #'
 #' @export
 #'
-#' @seealso \code{\link{AvailableData}} \code{\link{InstallData}} \code{\link{RemoveData}} \code{\link{UpdateData}}
+#' @seealso \code{\link{AvailableData}} \code{\link{InstallData}}
+#' \code{\link{RemoveData}} \code{\link{UpdateData}}
+#'
+#' @examples
+#' InstalledData()
 #'
 InstalledData <- function() {
   dat <- AvailableData()
   return(dat[which(x = dat$Installed, ), , drop = FALSE])
 }
 
+#' Modularly load a dataset
+#'
+#' @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
+#'
+#' @importFrom utils data
+#'
+#' @export
+#'
+#' @seealso \code{\link[utils]{data}}
+#'
+LoadData <- function(
+  ds,
+  type = c('info', 'raw', 'processed'),
+  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') {
+    e <- new.env()
+    ds <- gsub(pattern = '\\.SeuratData', replacement = '', x = ds)
+    data(list = ds, envir = e)
+    return(e[[ds]])
+  }
+  .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
+  ))
+}
+
 #' Remove a dataset
 #'
 #' @inheritParams utils::remove.packages
@@ -102,7 +183,13 @@ InstalledData <- function() {
 #'
 #' @export
 #'
-#' @seealso \code{\link{AvailableData}} \code{\link{InstallData}} \code{\link{InstalledData}} \code{\link{UpdateData}}
+#' @seealso \code{\link{AvailableData}} \code{\link{InstallData}}
+#' \code{\link{InstalledData}} \code{\link{UpdateData}}
+#'
+#' @examples
+#' \dontrun{
+#' RemoveData('pbmc3k')
+#' }
 #'
 RemoveData <- function(ds, lib) {
   UpdateManifest()
@@ -125,9 +212,22 @@ RemoveData <- function(ds, lib) {
 #'
 #' @export
 #'
-#' @seealso \code{\link{AvailableData}} \code{\link{InstallData}} \code{\link{InstalledData}} \code{\link{RemoveData}}
+#' @seealso \code{\link{AvailableData}} \code{\link{InstallData}}
+#' \code{\link{InstalledData}} \code{\link{RemoveData}}
+#'
+#' @examples
+#' \dontrun{
+#' UpdateData(ask = FALSE)
+#' }
 #'
 UpdateData <- function(ask = TRUE, lib.loc = NULL) {
+  UpdateManifest()
+  if (pkg.env$source != 'remote') {
+    stop(
+      "No access to remote SeuratData repository, unable to update datasets",
+      call. = FALSE
+    )
+  }
   update.packages(lib.loc = lib.loc, repos = getOption(x = "SeuratData.repo.use"), ask = ask, type = 'source')
   UpdateManifest()
   invisible(x = NULL)