WT: Bug fix

Author: williamthistle

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: SPEEDI
 Title: Single-cell Pipeline for End to End Data Integration (SPEEDI)
-Version: 1.1.0.0000
+Version: 1.1.1.0000
 Authors@R: c(
     person("Yuan", "Wang", email = "yuanwang@princeton.edu", role = c("aut", "cre")),
     person("William", "Thistlethwaite", email = "wat2@princeton.edu", role = "aut"))

R/process_batches.R

@@ -50,7 +50,11 @@ InferBatches <- function(sc_obj, exit_with_code = FALSE, log_flag = FALSE) {
         tmp <- find_clusters_SPEEDI(sc_obj = sc_obj, resolution = i, method = "Louvain", log_flag = log_flag)
         dims <- 1:30
         clusters <- tmp$seurat_clusters
-        sil.out <- bluster::approxSilhouette(Seurat::Embeddings(tmp@reductions$pca)[, dims], clusters)
+        if ('lsi' %in% SeuratObject::Reductions(sc_obj)) {
+          sil.out <- bluster::approxSilhouette(Seurat::Embeddings(tmp@reductions$lsi)[, dims], clusters)
+        } else {
+          sil.out <- bluster::approxSilhouette(Seurat::Embeddings(tmp@reductions$pca)[, dims], clusters)
+        }
         sil.score <- mean(sil.out$width)
         names(sil.score) <- i
         return(sil.score)