Merge pull request satijalab#559 from satijalab/feat/AddAzimuthResults

Add Azimuth Results to Seurat Object

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.0.1.9013
-Date: 2021-05-14
+Version: 4.0.1.9014
+Date: 2021-05-17
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
 Authors@R: c(

NAMESPACE

@@ -117,6 +117,7 @@ export("Project<-")
 export("SCTResults<-")
 export("Tool<-")
 export("VariableFeatures<-")
+export(AddAzimuthResults)
 export(AddMetaData)
 export(AddModuleScore)
 export(AggregateExpression)

NEWS.md

@@ -1,6 +1,6 @@
 # Seurat develop
 ## Added
-- New `AddAzimuthScores()` function
+- New `AddAzimuthScores()` and `AddAzimuthResults()` functions
 - Add `shuffle` parameter to `FeatureScatter()` ([#4280](https://github.com/satijalab/seurat/pull/4280))
 - Add `lsiproject` and `rpca` options for `FindTransferAnchors()`
 - Add `rlsi` option for `FindIntegrationAnchors()`

R/utilities.R

@@ -6,6 +6,72 @@ NULL
 # Functions
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
+#' Add Azimuth Results
+#'
+#' Add mapping and prediction scores, UMAP embeddings, and imputed assay (if
+#' available)
+#' from Azimuth to an existing or new \code{\link[SeuratObject]{Seurat}} object
+#'
+#' @param object A \code{\link[SeuratObject]{Seurat}} object
+#' @param filename Path to Azimuth mapping scores file
+#'
+#' @return \code{object} with Azimuth results added
+#'
+#' @examples
+#' \dontrun{
+#' object <- AddAzimuthResults(object, filename = "azimuth_results.Rds")
+#' }
+#'
+#' @export
+AddAzimuthResults <- function(object = NULL, filename) {
+  if (is.null(x = filename)) {
+    stop("No Azimuth results provided.")
+  }
+  azimuth_results <- readRDS(file = filename)
+  if (!is.list(x = azimuth_results) || any(!(c('umap', 'pred.df') %in% names(x = azimuth_results)))) {
+    stop("Expected following format for azimuth_results:
+           `list(umap = <DimReduc>, pred.df = <data.frame>[, impADT = <Assay>])`")
+  }
+
+  if (is.null(x = object)) {
+    message("No existing Seurat object provided. Creating new one.")
+    object <- CreateSeuratObject(
+      counts = matrix(
+        nrow = 1,
+        ncol = nrow(x = azimuth_results$umap),
+        dimnames = list(
+          row.names = 'Dummy.feature',
+          col.names = rownames(x = azimuth_results$umap))
+      ),
+      assay = 'Dummy'
+    )
+  } else {
+    overlap.cells <- intersect(
+      x = Cells(x = object),
+      y = rownames(x = azimuth_results$umap)
+    )
+    if (!(all(overlap.cells %in% Cells(x = object)))) {
+      stop("Cells in object do not match cells in download")
+    } else if (length(x = overlap.cells) < length(x = Cells(x = object))) {
+      warning(paste0("Subsetting out ", length(x = Cells(x = object)) - length(x = overlap.cells),
+                     " cells that are absent in downloaded results (perhaps filtered by Azimuth)"))
+      object <- subset(x = object, cells = overlap.cells)
+    }
+  }
+
+  azimuth_results$pred.df$cell <- NULL
+  object <- AddMetaData(object = object, metadata = azimuth_results$pred.df)
+  object[['umap.proj']] <- azimuth_results$umap
+  if ('impADT' %in% names(x = azimuth_results)) {
+    object[['impADT']] <- azimuth_results$impADT
+    if ('Dummy' %in% Assays(object = object)) {
+      DefaultAssay(object = object) <- 'impADT'
+      object[['Dummy']] <- NULL
+    }
+  }
+  return(object)
+}
+
 #' Add Azimuth Scores
 #'
 #' Add mapping and prediction scores from Azimuth to a