Clean up imports by importing individual functions where possible

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)

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, ...) {

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) {

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
 #'