From 25dc155d0551a0a823a9ef939c86595e86fc92c1 Mon Sep 17 00:00:00 2001
From: Nick-Eagles <nick.eagles@libd.org>
Date: Tue, 7 Nov 2023 14:05:47 -0500
Subject: [PATCH] Clean up imports by importing individual functions where
 possible

---
 NAMESPACE            |  7 ++++---
 R/multi_gene.R       | 15 ++++++++++-----
 R/spe_seurat.R       |  9 +++++----
 R/spot_plot.R        |  4 +++-
 man/spe_to_seurat.Rd |  4 ++--
 5 files changed, 24 insertions(+), 15 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 16c03b0..c1c02ae 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,9 +7,10 @@ export(spot_plot_sparsity)
 export(spot_plot_z_score)
 import(Matrix)
 import(MatrixGenerics)
-import(SummarizedExperiment)
-import(SpatialExperiment)
 import(Seurat)
+import(SpatialExperiment)
 import(ggplot2)
 import(spatialLIBD)
-import(viridisLite)
+importFrom(SummarizedExperiment,colData)
+importFrom(stats,prcomp)
+importFrom(viridisLite,plasma)
diff --git a/R/multi_gene.R b/R/multi_gene.R
index 2d51676..6909d6b 100644
--- a/R/multi_gene.R
+++ b/R/multi_gene.R
@@ -23,7 +23,8 @@
 #'
 #' @export
 #' @author Nicholas J. Eagles
-#' @import SpatialExperiment SummarizedExperiment Matrix MatrixGenerics
+#' @import SpatialExperiment Matrix MatrixGenerics
+#' @importFrom SummarizedExperiment colData
 #' @family Spot plots summarizing expression of multiple genes simultaneously
 #'
 #' @examples
@@ -80,7 +81,8 @@ spot_plot_z_score <- function(spe, genes, sample_id, assayname = "logcounts", mi
 #'
 #' @export
 #' @author Nicholas J. Eagles
-#' @import SpatialExperiment SummarizedExperiment Matrix MatrixGenerics
+#' @import SpatialExperiment Matrix MatrixGenerics
+#' @importFrom SummarizedExperiment colData
 #' @family Spot plots summarizing expression of multiple genes simultaneously
 #'
 #' @examples
@@ -138,7 +140,9 @@ spot_plot_sparsity <- function(spe, genes, sample_id, assayname = "counts", minC
 #'
 #' @export
 #' @author Nicholas J. Eagles
-#' @import SpatialExperiment SummarizedExperiment
+#' @import SpatialExperiment
+#' @importFrom SummarizedExperiment colData
+#' @importFrom stats prcomp
 #' @family Spot plots summarizing expression of multiple genes simultaneously
 #'
 #' @examples
@@ -164,7 +168,7 @@ spot_plot_pca <- function(spe, genes, sample_id, assayname = "logcounts", minCou
         spe, genes, sample_id, assayname, minCount, ...
     )
 
-    pc_exp <- prcomp(t(assays(spe)[[assayname]]), center = TRUE, scale = TRUE)
+    pc_exp <- stats::prcomp(t(assays(spe)[[assayname]]), center = TRUE, scale = TRUE)
     spe$pc_select_genes <- pc_exp$x[, "PC1"]
 
     #   Given that:
@@ -198,7 +202,8 @@ spot_plot_pca <- function(spe, genes, sample_id, assayname = "logcounts", minCou
 #'
 #' @author Nicholas J. Eagles
 #' @inheritParams spot_plot_z_score
-#' @import SpatialExperiment SummarizedExperiment
+#' @import SpatialExperiment
+#' @importFrom SummarizedExperiment colData
 #' @return \code{SpatialExperiment} subsetted to the specified sample and to
 #' each of the non-constant-expression genes
 .multi_gene_validity_check <- function(spe, genes, sample_id, assayname, minCount, ...) {
diff --git a/R/spe_seurat.R b/R/spe_seurat.R
index 43289b2..f15932d 100644
--- a/R/spe_seurat.R
+++ b/R/spe_seurat.R
@@ -15,7 +15,8 @@
 #'
 #' @export
 #' @author Nicholas J. Eagles
-#' @import SummarizedExperiment SpatialExperiment spatialLIBD Seurat
+#' @import SpatialExperiment spatialLIBD Seurat
+#' @importFrom SummarizedExperiment colData
 #'
 #' @examples
 #'
@@ -24,8 +25,8 @@
 #' spe <- spatialLIBD::fetch_data(type = "spatialDLPFC_Visium_example_subset")
 #' spe$array_row_transformed = spe$array_row
 #' spe$array_col_transformed = spe$array_col
-#' spe$pxl_row_in_fullres_transformed = spatialCoords(spe)[,'pxl_row_in_fullres']
-#' spe$pxl_col_in_fullres_transformed = spatialCoords(spe)[,'pxl_col_in_fullres']
+#' spe$pxl_row_in_fullres_transformed = SpatialExperiment::spatialCoords(spe)[,'pxl_row_in_fullres']
+#' spe$pxl_col_in_fullres_transformed = SpatialExperiment::spatialCoords(spe)[,'pxl_col_in_fullres']
 #' colnames(spe) = spe$key
 #'
 #' #   Convert
@@ -59,7 +60,7 @@ spe_to_seurat = function(spe, verbose = TRUE) {
     }
 
     if (verbose) message("Running 'as.Seurat(spe)'...")
-    seur = as.Seurat(spe)
+    seur = Seurat::as.Seurat(spe)
 
     for (sample_id in unique(spe$sample_id)) {
         if (verbose) {
diff --git a/R/spot_plot.R b/R/spot_plot.R
index 00d8158..13d204d 100644
--- a/R/spot_plot.R
+++ b/R/spot_plot.R
@@ -40,7 +40,9 @@
 #'
 #' @export
 #' @author Nicholas J. Eagles
-#' @import viridisLite spatialLIBD ggplot2 SpatialExperiment SummarizedExperiment
+#' @import spatialLIBD ggplot2 SpatialExperiment
+#' @importFrom viridisLite plasma
+#' @importFrom SummarizedExperiment colData
 #'
 #' @examples
 #'
diff --git a/man/spe_to_seurat.Rd b/man/spe_to_seurat.Rd
index b93bf89..2e86dfd 100644
--- a/man/spe_to_seurat.Rd
+++ b/man/spe_to_seurat.Rd
@@ -30,8 +30,8 @@ appearance of images are buggy for now.
 spe <- spatialLIBD::fetch_data(type = "spatialDLPFC_Visium_example_subset")
 spe$array_row_transformed = spe$array_row
 spe$array_col_transformed = spe$array_col
-spe$pxl_row_in_fullres_transformed = spatialCoords(spe)[,'pxl_row_in_fullres']
-spe$pxl_col_in_fullres_transformed = spatialCoords(spe)[,'pxl_col_in_fullres']
+spe$pxl_row_in_fullres_transformed = SpatialExperiment::spatialCoords(spe)[,'pxl_row_in_fullres']
+spe$pxl_col_in_fullres_transformed = SpatialExperiment::spatialCoords(spe)[,'pxl_col_in_fullres']
 colnames(spe) = spe$key
 
 #   Convert