Merge pull request #52 from satijalab/feat/azimuth-refs

support for azimuth references

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SeuratData
 Type: Package
 Title: Install and Manage Seurat Datasets
-Version: 0.2.1
+Version: 0.2.2
 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')),
@@ -17,7 +17,7 @@ BugReports: https://github.com/satijalab/seurat-data/issues
 License: GPL-3 | file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.2
 Depends:
     R (>= 3.5.0)
 Imports:

NAMESPACE

@@ -6,6 +6,14 @@ export(InstalledData)
 export(LoadData)
 export(RemoveData)
 export(UpdateData)
+importFrom(Matrix,sparseMatrix)
+importFrom(Seurat,LoadAnnoyIndex)
+importFrom(SeuratObject,"Idents<-")
+importFrom(SeuratObject,AddMetaData)
+importFrom(SeuratObject,Cells)
+importFrom(SeuratObject,CreateSeuratObject)
+importFrom(SeuratObject,Misc)
+importFrom(SeuratObject,Tool)
 importFrom(cli,rule)
 importFrom(cli,symbol)
 importFrom(crayon,blue)
@@ -19,6 +27,7 @@ importFrom(rappdirs,user_data_dir)
 importFrom(stats,na.omit)
 importFrom(utils,available.packages)
 importFrom(utils,data)
+importFrom(utils,download.file)
 importFrom(utils,install.packages)
 importFrom(utils,packageVersion)
 importFrom(utils,remove.packages)

R/seurat_data.R

@@ -128,6 +128,7 @@ InstalledData <- function() {
 # \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{azimuth}{Load the dataset as an azimuth reference}
 #   \item{processed}{The proccessed data, modular loading avaible by setting other parameters}
 # }
 #'
@@ -161,9 +162,11 @@ LoadData <- function(
   )
   type <- match.arg(
     arg = tolower(x = type),
-    choices = c('raw', 'default', datasets)
+    choices = c('raw', 'default', 'azimuth', datasets)
   )
-  if (type %in% c('raw', 'default')) {
+  if (type == 'azimuth') {
+    return(LoadReference(file.path(system.file(package=ds), type)))
+  } else 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')
@@ -255,3 +258,72 @@ UpdateData <- function(ask = TRUE, lib.loc = NULL) {
   UpdateManifest()
   invisible(x = NULL)
 }
+
+#' Load the reference RDS files
+#'
+#' Read in a reference \code{\link[Seurat]{Seurat}} object and annoy index. This
+#' function can read from a file path. In order to read properly,
+#' there must be the following files:
+#' \itemize{
+#'  \item \dQuote{ref.Rds} for the downsampled reference \code{Seurat}
+#'  object (for mapping)
+#'  \item \dQuote{idx.annoy} for the nearest-neighbor index object
+#' }
+#'
+#' @param path Pathto the two RDS files
+#'
+#' @return A list with two entries:
+#' \describe{
+#'  \item{\code{map}}{
+#'   The downsampled reference \code{\link[Seurat]{Seurat}}
+#'   object (for mapping)
+#'  }
+#'  \item{\code{plot}}{The reference \code{Seurat} object (for plotting)}
+#' }
+#'
+#' @importFrom SeuratObject Idents<- Tool Cells Misc AddMetaData CreateSeuratObject
+#' @importFrom Seurat LoadAnnoyIndex
+#' @importFrom utils download.file
+#' @importFrom Matrix sparseMatrix
+#'
+LoadReference <- function(path) {
+  ref.names <- list(
+    map = 'ref.Rds',
+    ann = 'idx.annoy'
+  )
+  mapref <- file.path(path, ref.names$map)
+  annref <- file.path(path, ref.names$ann)
+  exists <- file.exists(c(mapref, annref))
+  if (!all(exists)) {
+    stop(
+      "Missing the following files from the directory provided: ",
+      unlist(x = ref.names)[!exists]
+    )
+  }
+  # Load the map reference
+  map <- readRDS(file = mapref)
+  # Load the annoy index into the Neighbor object in the neighbors slot
+  map[["refdr.annoy.neighbors"]] <- LoadAnnoyIndex(
+    object = map[["refdr.annoy.neighbors"]],
+    file = annref
+  )
+  # Create plotref
+  ad <- Tool(object = map, slot = "AzimuthReference")
+  # plotref.dr <- GetPlotRef(object = ad)
+  print(ad)
+  plotref.dr <- slot(object = ad, name = "plotref")
+  cm <- sparseMatrix(
+    i = 1, j = 1, x = 0, dims = c(1, nrow(x = plotref.dr)),
+    dimnames = list("placeholder", Cells(x = plotref.dr))
+  )
+  plot <- CreateSeuratObject(
+    counts = cm
+  )
+  plot[["refUMAP"]] <- plotref.dr
+  plot <- AddMetaData(object = plot, metadata = Misc(object = plotref.dr, slot = "plot.metadata"))
+  gc(verbose = FALSE)
+  return(list(
+    map = map,
+    plot = plot
+  ))
+}