Merge pull request #612 from satijalab/fix/ProjectUMAP_n_neighbors

Fix ProjectUMAP num of neighbors error and warnings

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: Seurat
-Version: 4.0.5.9005
+Version: 4.0.5.9006
 Date: 2021-12-14
 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.

NAMESPACE

@@ -635,6 +635,7 @@ importFrom(reticulate,py_module_available)
 importFrom(reticulate,py_set_seed)
 importFrom(rlang,"!!")
 importFrom(rlang,as_label)
+importFrom(rlang,invoke)
 importFrom(scales,brewer_pal)
 importFrom(scales,hue_pal)
 importFrom(scales,rescale)

NEWS.md

@@ -9,6 +9,7 @@
 - Set `do.center` to FALSE for `lsiproject` in `FindTransferAnchors`
 - Fix error message in `ReadMtx()` ([#5158](https://github.com/satijalab/seurat/issues/5158))
 - Add `label.color` parameter to `FeaturePlot` ([#5314](https://github.com/satijalab/seurat/pull/5314))
+- Fix issues in `ProjectUMAP` ([#5257](https://github.com/satijalab/seurat/issues/5257), [#5104](https://github.com/satijalab/seurat/issues/5104), [#5373](https://github.com/satijalab/seurat/issues/5373))
 
 # Seurat 4.0.5 (2020-10-04)
 ## Changes

R/dimensional_reduction.R

@@ -335,7 +335,7 @@ ProjectUMAP.default <- function(
   query.dims = NULL,
   reference,
   reference.dims = NULL,
-  k.param = 20,
+  k.param = 30,
   nn.method = "annoy",
   n.trees = 50,
   annoy.metric = "cosine",
@@ -389,7 +389,7 @@ ProjectUMAP.DimReduc <- function(
   query.dims = NULL,
   reference,
   reference.dims = NULL,
-  k.param = 20,
+  k.param = 30,
   nn.method = "annoy",
   n.trees = 50,
   annoy.metric = "cosine",
@@ -439,7 +439,7 @@ ProjectUMAP.Seurat <- function(
   reference,
   reference.reduction,
   reference.dims = NULL,
-  k.param = 20,
+  k.param = 30,
   nn.method = "annoy",
   n.trees = 50,
   annoy.metric = "cosine",
@@ -479,6 +479,7 @@ ProjectUMAP.Seurat <- function(
     neighbor.name = neighbor.name,
     reduction.model = reference[[reduction.model]],
     reduction.key = reduction.key,
+    assay = DefaultAssay(query),
     ...
   )
   query[[reduction.name]] <- proj.umap$proj.umap
@@ -1385,7 +1386,12 @@ RunUMAP.default <- function(
         )
       }
       if (is.list(x = object)) {
-        uwot::umap_transform(
+        if (ncol(object$idx) != model$n_neighbors) {
+          warning("Number of neighbors between query and reference ", 
+          "is not equal to the number of neighbros within reference")
+          model$n_neighbors <- ncol(object$idx)
+        }
+       umap_transform(
           X = NULL,
           nn_method = object,
           model = model,

R/integration.R

@@ -1749,6 +1749,7 @@ IntegrateEmbeddings.TransferAnchorSet <- function(
   }
   slot(object = anchorset, name = "object.list") <- object.list
   new.reduction.name.safe <- gsub(pattern = "_", replacement = "", x = new.reduction.name)
+  new.reduction.name.safe <- gsub(pattern = "[.]", replacement = "", x = new.reduction.name)
   slot(object = anchorset, name = "reference.objects") <- 1
   anchors <- as.data.frame(x = anchors)
   anchors$dataset1 <- 1
@@ -1910,6 +1911,8 @@ LocalStruct <- function(
 #'   reference UMAP using \code{\link{ProjectUMAP}}}
 #' }
 #'
+#' @importFrom rlang invoke
+#' 
 #' @export
 #' @concept integration
 #'
@@ -2002,9 +2005,9 @@ MapQuery <- function(
   slot(object = query, name = "tools")$TransferData <- NULL
   reuse.weights.matrix <- FALSE
   if (!is.null(x = refdata)) {
-    query <- do.call(
-      what = TransferData,
-      args = c(list(
+    query <- invoke(
+      .fn = TransferData,
+      .args  = c(list(
         anchorset = anchorset,
         reference = reference,
         query = query,
@@ -2019,9 +2022,9 @@ MapQuery <- function(
     }
   }
   if (anchor.reduction != "cca"){
-    query <- do.call(
-      what = IntegrateEmbeddings,
-      args = c(list(
+    query <- invoke(
+      .fn = IntegrateEmbeddings,
+      .args  = c(list(
         anchorset = anchorset,
         reference = reference,
         query = query,
@@ -2040,16 +2043,18 @@ MapQuery <- function(
       message("Query and reference dimensions are not equal, proceeding with reference dimensions.")
       query.dims <- reference.dims
     }
-    query <- do.call(
-      what = ProjectUMAP,
-      args = c(list(
+    ref_nn.num <- Misc(object = reference[[reduction.model]], slot = "model")$n_neighbors
+    query <- invoke(
+      .fn = ProjectUMAP,
+      .args  = c(list(
         query = query,
         query.reduction = new.reduction.name,
         query.dims = query.dims,
         reference = reference,
         reference.dims = reference.dims,
         reference.reduction = reference.reduction,
-        reduction.model = reduction.model
+        reduction.model = reduction.model,
+        k.param = ref_nn.num
         ), projectumap.args
       )
     )
@@ -3968,7 +3973,7 @@ MapQueryData <- function(
     X = query.datasets,
     FUN = function(dataset1) {
       if (verbose) {
-        message("Integrating dataset ", dataset1, " with reference dataset")
+        message("\nIntegrating dataset ", dataset1, " with reference dataset")
       }
       filtered.anchors <- anchors[anchors$dataset1 %in% reference.datasets & anchors$dataset2 == dataset1, ]
       integrated <- RunIntegration(