Robust fallback mechanism

R/scvelo.R

@@ -108,7 +108,7 @@
 #' containing the velocity vectors for each cell.
 #' }
 #' The output will always have number of columns equal to the number of cells supplied in \code{x},
-#' though the number of rows will depend on whether any subsetting (if \code{subset.row} is supplied) 
+#' though the number of rows will depend on whether any subsetting (if \code{subset.row} is supplied)
 #' or feature selection (if \code{use.theirs=TRUE}) was performed.
 #'
 #' @examples
@@ -123,8 +123,8 @@
 #' out <- scvelo(list(X=spliced, spliced=spliced, unspliced=unspliced))
 #'
 #' # make scvelo use 10 rather than the default 30 neighbors to compute moments for velocity estimation:
-#' out <- scvelo(list(X=spliced, spliced=spliced, unspliced=unspliced), 
-#'               scvelo.params=list(moments=list(n_neighbors=10L))) 
+#' out <- scvelo(list(X=spliced, spliced=spliced, unspliced=unspliced),
+#'               scvelo.params=list(moments=list(n_neighbors=10L)))
 #'
 #' @references
 #' Bergen, V., Lange, M., Peidli, S. et al. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat Biotechnol 38, 1408–1414 (2020). \url{https://doi.org/10.1038/s41587-020-0591-3}
@@ -175,28 +175,25 @@ NULL
         X=X, spliced=spliced, unspliced=unspliced,
         use.theirs=use.theirs, mode=mode,
         scvelo.params=scvelo.params,
-        dimred=dimred)
+        dimred=dimred, testload = c("scvelo", "anndata"))
 
     output
 }
 
-#' @importFrom reticulate import
-#' @importFrom DelayedArray is_sparse t
-#' @importFrom zellkonverter AnnData2SCE
 .run_scvelo <- function(X, spliced, unspliced, use.theirs=FALSE, mode='dynamical', scvelo.params=list(), dimred=NULL) {
-    X <- t(.make_np_friendly(X))
-    spliced <- t(.make_np_friendly(spliced))
-    unspliced <- t(.make_np_friendly(unspliced))
+    X <- t(velociraptor:::.make_np_friendly(X))
+    spliced <- t(velociraptor:::.make_np_friendly(spliced))
+    unspliced <- t(velociraptor:::.make_np_friendly(unspliced))
 
-    and <- import("anndata")
-    scv <- import("scvelo")
+    and <- reticulate::import("anndata")
+    scv <- reticulate::import("scvelo")
     adata <- and$AnnData(X, layers=list(spliced=spliced, unspliced=unspliced))
     adata$obs_names <- rownames(spliced)
     adata$var_names <- colnames(spliced)
 
     ## A supplied dimred will be used even if use.theirs=TRUE
     if (!is.null(dimred)) {
-        dimred <- .make_np_friendly(dimred)
+        dimred <- velociraptor:::.make_np_friendly(dimred)
         adata$obsm <- list(X_pca = dimred)
     }
 
@@ -223,7 +220,7 @@ NULL
 
     do.call(scv$tl$velocity_confidence, c(list(data=adata), scvelo.params$velocity_confidence))
 
-    AnnData2SCE(adata)
+    zellkonverter::AnnData2SCE(adata)
 }
 
 #' @export