use explicit 'ggplot2' imports

Author: CATALYST-project

NAMESPACE

@@ -9,13 +9,33 @@ exportMethods(rotate)
 exportMethods(scale)
 exportMethods(translation)
 import(SpatialData)
-import(ggplot2)
 importFrom(DelayedArray,realize)
 importFrom(S4Vectors,metadata)
 importFrom(SingleCellExperiment,int_metadata)
 importFrom(dplyr,mutate)
 importFrom(dplyr,select)
 importFrom(ggforce,geom_circle)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,annotation_raster)
+importFrom(ggplot2,coord_equal)
+importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_line)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_polygon)
+importFrom(ggplot2,geom_tile)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,guide_legend)
+importFrom(ggplot2,guides)
+importFrom(ggplot2,scale_color_gradientn)
+importFrom(ggplot2,scale_fill_gradientn)
+importFrom(ggplot2,scale_fill_manual)
+importFrom(ggplot2,scale_type)
+importFrom(ggplot2,scale_x_continuous)
+importFrom(ggplot2,scale_y_reverse)
+importFrom(ggplot2,theme)
+importFrom(ggplot2,theme_bw)
+importFrom(ggplot2,unit)
 importFrom(grDevices,col2rgb)
 importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,hcl.colors)

R/plot.R

@@ -29,6 +29,9 @@ NULL
 #' @importFrom grDevices col2rgb
 .str_is_col <- \(x) !inherits(tryCatch(error=\(e) e, col2rgb(x)), "error")
 
+#' @importFrom ggplot2 
+#'   coord_equal theme_bw theme 
+#'   element_blank element_text element_line
 .theme <- list(
     coord_equal(), theme_bw(), theme(
         panel.grid=element_blank(),
@@ -40,6 +43,7 @@ NULL
 )
 
 #' @rdname plotImage
+#' @importFrom ggplot2 ggplot scale_y_reverse
 #' @export
 plotSpatialData <- \() ggplot() + scale_y_reverse() + .theme 
 
@@ -77,7 +81,10 @@ plotSpatialData <- \() ggplot() + scale_y_reverse() + .theme
     list(w=wh[, 1], h=wh[, 2])
 }
 
-#' @import ggplot2
+#' @importFrom ggplot2 
+#'   scale_x_continuous
+#'   scale_x_continuous
+#'   annotation_raster
 .gg_i <- \(x, w, h, dpi) list(
     scale_x_continuous(limits=w), scale_y_reverse(limits=rev(h)),
     annotation_raster(x, w[2],w[1], -h[1],-h[2], interpolate=FALSE))

R/plotLabel.R

@@ -36,6 +36,9 @@ NULL
 #' @importFrom S4Vectors metadata
 #' @importFrom rlang .data
 #' @importFrom methods as
+#' @importFrom ggplot2 
+#'   scale_fill_manual scale_fill_gradientn
+#'   aes geom_tile theme unit guides guide_legend
 #' @export
 setMethod("plotLabel", "SpatialData", \(x, i=1, c=NULL, 
     a=0.5, pal=c("red", "green"), nan=NA, assay=1) {

R/plotPoint.R

@@ -33,6 +33,9 @@ NULL
 #' @importFrom methods is
 #' @importFrom grDevices hcl.colors
 #' @importFrom SingleCellExperiment int_metadata
+#' @importFrom ggplot2 
+#'   geom_point scale_color_gradientn
+#'   aes theme guides guide_legend scale_type
 .gg_p <- \(x, c, s, a, ...) {
     dots <- list(...)
     i <- dots$i

R/plotShape.R

@@ -32,6 +32,7 @@ NULL
 
 #' @rdname plotShape
 #' @importFrom sf st_as_sf st_coordinates st_geometry_type
+#' @importFrom ggplot2 aes theme scale_type geom_polygon
 #' @importFrom ggforce geom_circle
 #' @importFrom utils tail
 #' @export