From 706f4d82a662e80c96c972f7a5b5419fdb158c75 Mon Sep 17 00:00:00 2001
From: Paul Hoffman <mojaveazure@users.noreply.github.com>
Date: Wed, 28 Apr 2021 14:25:03 -0400
Subject: [PATCH] Replace Seurat imports with SeuratObject Replaces all Seurat
 data access imports with SeuratObject This should help decrease install time
 for platforms that utilize source installs as Seurat and all of its
 dependencies are no longer installed All functionality remains intact;
 automated install of Seurat alongside Nebulosa can be achived by passing
 `dependencies = TRUE` to the install command

---
 DESCRIPTION | 3 +--
 NAMESPACE   | 8 ++++----
 R/methods.R | 2 +-
 3 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b0cdf14..aa97a8b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -22,7 +22,6 @@ Depends:
     ggplot2,
     patchwork
 Imports:
-    Seurat,
     SingleCellExperiment,
     SummarizedExperiment,
     SeuratObject,
@@ -34,7 +33,7 @@ RoxygenNote: 7.1.1
 VignetteBuilder: knitr
 Suggests: 
     testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils,
-    igraph, BiocFileCache
+    igraph, BiocFileCache, Seurat
 biocViews: 
     Software, GeneExpression, SingleCell, Visualization, 
     DimensionReduction
diff --git a/NAMESPACE b/NAMESPACE
index db0fb99..b694915 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -4,10 +4,10 @@ export(plot_density)
 exportMethods(plot_density)
 importFrom(Matrix,Matrix)
 importFrom(Matrix,t)
-importFrom(Seurat,Embeddings)
-importFrom(Seurat,FetchData)
-importFrom(Seurat,GetAssayData)
-importFrom(Seurat,Reductions)
+importFrom(SeuratObject,Embeddings)
+importFrom(SeuratObject,FetchData)
+importFrom(SeuratObject,GetAssayData)
+importFrom(SeuratObject,Reductions)
 importFrom(SingleCellExperiment,colData)
 importFrom(SingleCellExperiment,reducedDim)
 importFrom(SingleCellExperiment,reducedDims)
diff --git a/R/methods.R b/R/methods.R
index 87c03b7..818c3a4 100644
--- a/R/methods.R
+++ b/R/methods.R
@@ -51,7 +51,7 @@ setGeneric("plot_density", function(object, features, slot = NULL,
                                     ...)
     standardGeneric("plot_density"))
 
-#' @importFrom Seurat GetAssayData Reductions Embeddings FetchData
+#' @importFrom SeuratObject GetAssayData Reductions Embeddings FetchData
 #' @export
 #' @describeIn plot_density Plot gene-weighted 2D kernel density
 setMethod("plot_density", signature("Seurat"),