Merge pull request satijalab#42 from satijalab/integration-bugfix

Fix error when using projected loadings
ws2260 · Apr 10, 2019 · d9bffe5 · d9bffe5
2 parents 1a36031 + ad5a94f
commit d9bffe5
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Showing 2 changed files with 16 additions and 6 deletions.
diff --git a/R/dimensional_reduction.R b/R/dimensional_reduction.R
@@ -160,8 +160,8 @@ L2Dim <- function(object, reduction, new.dr = NULL, new.key = NULL){
   colnames(x = l2.norm) <- paste0(new.key, 1:ncol(x = l2.norm))
   l2.dr <- CreateDimReducObject(
     embeddings = l2.norm,
-    loadings = Loadings(object = object[[reduction]]),
-    projected = Loadings(object = object[[reduction]]),
+    loadings = Loadings(object = object[[reduction]], projected = FALSE),
+    projected = Loadings(object = object[[reduction]], projected = TRUE),
     assay = DefaultAssay(object = object),
     stdev = slot(object = object[[reduction]], name = 'stdev'),
     key = new.key,

diff --git a/R/integration.R b/R/integration.R
@@ -227,6 +227,11 @@ FindTransferAnchors <- function(
   if (!reduction %in% c("pcaproject", "cca", "pcaqueryproject")) {
     stop("Please select either pcaproject, cca, or pcaqueryproject for the reduction parameter.")
   }
+  if (reduction %in% c('pcaproject', 'pcaqueryproject')) {
+    projected = TRUE
+  } else {
+    projected = FALSE
+  }
   query <- RenameCells(
     object = query,
     new.names = paste0(Cells(x = query), "_", "query")
@@ -326,6 +331,7 @@ FindTransferAnchors <- function(
     k.score = k.score,
     max.features = max.features,
     eps = eps,
+    projected = projected,
     verbose = verbose
   )
   command <- LogSeuratCommand(object = combined.ob, return.command = TRUE)
@@ -1249,6 +1255,7 @@ FindAnchors <- function(
   k.score = 30,
   max.features = 200,
   eps = 0,
+  projected = FALSE,
   verbose = TRUE
 ) {
   # compute local neighborhoods, use max of k.anchor and k.score if also scoring to avoid
@@ -1279,7 +1286,8 @@ FindAnchors <- function(
       reduction = reduction,
       dims = dims,
       features.per.dim = 100,
-      max.features = max.features
+      max.features = max.features,
+      projected = projected
     )
     object.pair <- FilterAnchors(
       object = object.pair,
@@ -1797,24 +1805,26 @@ ScoreAnchors <- function(
 # @param dims Which dimensions to use
 # @param features.per.dim How many features to consider per dimension
 # @param max.features Number of features to return at most
+# @param projected Use projected loadings
 #
 TopDimFeatures <- function(
   object,
   reduction,
   dims = 1:10,
   features.per.dim = 100,
-  max.features = 200
+  max.features = 200,
+  projected = FALSE
 ) {
   dim.reduction <- object[[reduction]]
   max.features <- max(length(x = dims) * 2, max.features)
   num.features <- sapply(X = 1:features.per.dim, FUN = function(y) {
     length(x = unique(x = as.vector(x = sapply(X = dims, FUN = function(x) {
-      unlist(x = TopFeatures(object = dim.reduction, dim = x, nfeatures = y, balanced = TRUE))
+      unlist(x = TopFeatures(object = dim.reduction, dim = x, nfeatures = y, balanced = TRUE, projected = projected))
     }))))
   })
   max.per.pc <- which.max(x = num.features[num.features < max.features])
   features <- unique(x = as.vector(x = sapply(X = dims, FUN = function(x) {
-    unlist(x = TopFeatures(object = dim.reduction, dim = x, nfeatures = max.per.pc, balanced = TRUE))
+    unlist(x = TopFeatures(object = dim.reduction, dim = x, nfeatures = max.per.pc, balanced = TRUE, projected = projected))
   })))
   features <- unique(x = features)
   return(features)