coercion to matrix to fit BiocNeighbor changes ( #109 )

plger · Sep 9, 2024 · 39eafb1 · 39eafb1
1 parent 6f82238
commit 39eafb1
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Showing 5 changed files with 5 additions and 5 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: scDblFinder
 Type: Package
 Title: scDblFinder
-Version: 1.19.2
+Version: 1.19.3
 Authors@R: c(
     person("Pierre-Luc", "Germain", email="pierre-luc.germain@hest.ethz.ch", role=c("cre","aut"), comment=c(ORCID="0000-0003-3418-4218")),
     person("Aaron", "Lun", email="infinite.monkeys.with.keyboards@gmail.com", role="ctb"))

diff --git a/R/clustering.R b/R/clustering.R
@@ -56,7 +56,7 @@ fastcluster <- function( x, k=NULL, rdname="PCA", nstart=3, iter.max=50,
     k <- seq_len(nrow(x))
   }
   if(verbose) message("Building KNN graph and clustering")
-  x <- makeKNNGraph(x, k=min(max(2,floor(sqrt(length(unique(k))))-1),10))
+  x <- makeKNNGraph(as.matrix(x), k=min(max(2,floor(sqrt(length(unique(k))))-1),10))
   if(returnType=="graph") return(list(k=k, graph=x))
   cl <- membership(cluster_louvain(x))
   cl[k]

diff --git a/R/computeDoubletDensity.R b/R/computeDoubletDensity.R
@@ -141,7 +141,7 @@ NULL
     sim.pcs <- .spawn_doublet_pcs(x, size.factors.norm, V=pc.out$rotation, centers=rowMeans(y), niters=niters, block=block)
 
     # Computing densities, using a distance computed from the kth nearest neighbor.
-    pre.pcs <- buildIndex(pcs, BNPARAM=BNPARAM)
+    pre.pcs <- buildIndex(as.matrix(pcs), BNPARAM=BNPARAM)
     self.dist <- findKNN(BNINDEX=pre.pcs, k=k, BPPARAM=BPPARAM, last=1, get.index=FALSE, warn.ties=FALSE)$distance
     if(any(self.dist == 0))
         stop("Duplicate cells detected. These are probably low-quality cells ",

diff --git a/R/recoverDoublets.R b/R/recoverDoublets.R
@@ -102,7 +102,7 @@ NULL
     is.doublet <- logical(nrow(x))
     is.doublet[.subset2index(doublets, x, byrow=TRUE)] <- TRUE
 
-    fout <- findKNN(x, k=k, BNPARAM=BNPARAM, BPPARAM=BPPARAM)
+    fout <- findKNN(as.matrix(x), k=k, BNPARAM=BNPARAM, BPPARAM=BPPARAM)
     neighbors <- fout$index
     neighbors[] <- is.doublet[neighbors]
     P <- rowMeans(neighbors)

diff --git a/R/scDblFinder.R b/R/scDblFinder.R
@@ -513,7 +513,7 @@ scDblFinder <- function(
 
 #' @importFrom BiocNeighbors AnnoyParam
 .evaluateKNN <- function(pca, ctype, origins, expected=NULL, k){
-  knn <- suppressWarnings(findKNN(pca, max(k), BNPARAM=AnnoyParam()))
+  knn <- suppressWarnings(findKNN(as.matrix(pca), max(k), BNPARAM=AnnoyParam()))
   hasOrigins <- length(unique(origins))>1
   knn$type <- matrix(as.integer(ctype)[knn$index]-1L, nrow=nrow(knn$index))
   if(hasOrigins) knn$orig <- matrix(origins[knn$index], nrow=nrow(knn[[1]]))