From 252872b4ac9f09cc08655208cd7e87e0ceb42846 Mon Sep 17 00:00:00 2001 From: Matthew Jones Date: Thu, 3 Mar 2022 09:16:18 -0800 Subject: [PATCH 1/2] added seurat import in data handler --- R/methods-Vision.R | 2 ++ 1 file changed, 2 insertions(+) diff --git a/R/methods-Vision.R b/R/methods-Vision.R index 7f8dc990..d7e38630 100644 --- a/R/methods-Vision.R +++ b/R/methods-Vision.R @@ -596,6 +596,8 @@ setMethod("Vision", signature(data = "Seurat"), call. = FALSE) } + library(Seurat) + obj <- data args <- list(...) From 45b15212f6c1cee6a8fb2a72846d276c8ec0820f Mon Sep 17 00:00:00 2001 From: Matthew Jones Date: Sat, 5 Mar 2022 07:46:46 -0800 Subject: [PATCH 2/2] moved to Seurat:: for imports --- R/methods-Vision.R | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/R/methods-Vision.R b/R/methods-Vision.R index d7e38630..44b689f3 100644 --- a/R/methods-Vision.R +++ b/R/methods-Vision.R @@ -595,8 +595,6 @@ setMethod("Vision", signature(data = "Seurat"), stop("Package \"Seurat\" needed to load this data object. Please install it.", call. = FALSE) } - - library(Seurat) obj <- data args <- list(...) @@ -623,13 +621,13 @@ setMethod("Vision", signature(data = "Seurat"), } # Get latent space - if (is.null(dimRed) && "pca" %in% Reductions(obj)) { + if (is.null(dimRed) && "pca" %in% Seurat:Reductions(obj)) { dimRed <- "pca" } if (!("latentSpace" %in% names(args))){ - latentSpace <- Embeddings(obj, + latentSpace <- Seurat::Embeddings(obj, reduction = dimRed ) @@ -655,7 +653,7 @@ setMethod("Vision", signature(data = "Seurat"), message(sprintf("Adding Visualization: %s", name)) - coordinates <- Embeddings(obj, + coordinates <- Seurat:Embeddings(obj, reduction = method) vis <- addProjection(vis,