Initial commit

.Rbuildignore

@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

@@ -0,0 +1,4 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

@@ -0,0 +1,15 @@
+Package: SeuratData
+Type: Package
+Title: What the Package Does (Title Case)
+Version: 0.1.0
+Author: Who wrote it
+Maintainer: The package maintainer <[email protected]>
+Description: More about what it does (maybe more than one line)
+    Use four spaces when indenting paragraphs within the Description.
+License: What license is it under?
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 6.1.1
+Collate: 
+    'zzz.R'
+    'seurat_data.R'

NAMESPACE

@@ -0,0 +1,8 @@
+# Generated by roxygen2: do not edit by hand
+
+export(AvailableData)
+export(InstallData)
+export(InstalledData)
+importFrom(utils,available.packages)
+importFrom(utils,install.packages)
+importFrom(utils,remove.packages)

R/seurat_data.R

@@ -0,0 +1,87 @@
+#' @include zzz.R
+#'
+NULL
+
+#' Get list of available datasets
+#'
+#' @return A vector of dataset names
+#'
+#' @export
+#'
+AvailableData <- function() {
+  UpdateManifest()
+  return(manifest)
+}
+
+#' Install a dataset
+#'
+#' @param pkgs List of datasets to install
+#' @param ... Extra parameters passed to \code{\link[utils]{install.packages}}
+#'
+#' @importFrom utils install.packages
+#'
+#' @export
+#'
+InstallData <- function(pkgs, ...) {
+  UpdateManifest()
+  pkgs <- pkgs[pkgs %in% manifest]
+  if (length(x = pkgs) < 1) {
+    stop("No datasets provided", call. = FALSE)
+  }
+  install.packages(
+    pkgs = pkgs,
+    repos = 'http://satijalab04.nygenome.org',
+    type = 'source',
+    ...
+  )
+  for (pkg in pkgs) {
+    attachNamespace(ns = pkg)
+    attached <<- c(attached, pkg)
+  }
+}
+
+#' Get a list of installed datasets
+#'
+#' @return A vector of installed datasets
+#'
+#' @export
+#'
+InstalledData <- function() {
+  installed <- vector(mode = 'character')
+  for (pkg in manifest) {
+    if (requireNamespace(pkg, quietly = TRUE)) {
+      installed <- c(installed, pkg)
+    }
+  }
+  return(installed)
+}
+
+#' Remove a dataset
+#'
+#' @inheritDotParams utils::remove.packages
+#' @param pkgs List of dataset to remove
+#'
+#' @importFrom utils remove.packages
+#'
+RemoveData <- function(pkgs, lib) {
+  UpdateManifest()
+  pkgs <- pkgs[pkgs %in% manifest]
+  if (length(x = pkgs) < 1) {
+    stop("No datasets provided", call. = FALSE)
+  }
+  remove.packages(pkgs = pkgs, lib = lib)
+}
+
+#' Update the available package manifest
+#'
+#' @importFrom utils available.packages
+#'
+UpdateManifest <- function() {
+  repo.use <- 'http://satijalab04.nygenome.org'
+  avail.pkgs <- available.packages(
+    contriburl = paste(repo.use, 'src/contrib', sep = '/'),
+    type = 'source'
+  )
+  manifest <<- rownames(x = avail.pkgs)
+  invisible(x = NULL)
+}

R/zzz.R

@@ -0,0 +1,21 @@
+manifest <- vector(mode = 'character')
+
+attached <- vector(mode = 'character')
+
+.onLoad <- function(libname, pkgname) {
+  UpdateManifest()
+  for (pkg in manifest) {
+    if (requireNamespace(pkg, quietly = TRUE)) {
+      message("Attaching ", pkg)
+      try(expr = attachNamespace(ns = pkg), silent = TRUE)
+      attached <<- c(attached, pkg)
+    }
+  }
+}
+
+.onUnload <- function(libpath) {
+  for (pkg in attached) {
+    message("Detaching ", pkg)
+    unloadNamespace(ns = pkg)
+  }
+}

seurat-data.Rproj

@@ -0,0 +1,19 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source