rasterises plots

DESCRIPTION

@@ -16,7 +16,6 @@ URL: https://github.com/powellgenomicslab/Nebulosa
 BugReports: https://github.com/powellgenomicslab/Nebulosa/issues
 License: GPL-3
 Encoding: UTF-8
-LazyData: true
 Depends:
     R (>= 4.0),
     ggplot2,
@@ -25,12 +24,12 @@ Imports:
     Seurat,
     SingleCellExperiment,
     SummarizedExperiment,
-    SeuratObject,
     ks,
     Matrix,
     stats, 
-    methods
-RoxygenNote: 7.1.1
+    methods,
+    ggrastr
+RoxygenNote: 7.2.3
 VignetteBuilder: knitr
 Suggests: 
     testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils,

NAMESPACE

@@ -28,6 +28,7 @@ importFrom(ggplot2,scale_color_viridis_c)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,xlab)
 importFrom(ggplot2,ylab)
+importFrom(ggrastr,rasterise)
 importFrom(ks,hpi)
 importFrom(ks,kde)
 importFrom(methods,is)

R/helpers.R

@@ -37,14 +37,14 @@
 
 #' @importFrom patchwork wrap_plots
 .plot_final_density <- function(vars, cell_embeddings, features, joint, method,
-                                adjust, shape, size, pal, combine, ...) {
+                                adjust, shape, size, pal, combine, raster, ...) {
     dim_names <- colnames(cell_embeddings)
     if (ncol(vars) > 1) {
         res <- apply(vars, 2, calculate_density, 
                      cell_embeddings, method, adjust)
         p <- mapply(plot_density_, as.list(as.data.frame(res)), colnames(res),
                     MoreArgs = list(cell_embeddings, dim_names, shape, size,
-                                    "Density", pal = pal, ...), 
+                                    "Density", pal = pal, raster, ...), 
                     SIMPLIFY = FALSE)
 
         if(joint){
@@ -58,6 +58,7 @@
                                 size,
                                 "Joint density",
                                 pal = pal,
+                                raster,
                                 ...
             )
 
@@ -86,6 +87,7 @@
                            size,
                            "Density",
                            pal = pal,
+                           raster,
                            ...
         )
     }

R/methods.R

@@ -26,6 +26,7 @@
 #' @param combine Create a single plot? If \code{FALSE}, a list with ggplot
 #'  objects is returned
 #' @param pal String specifying the viridis color palette to use.
+#' @param raster Rasterise plot
 #' @param ... Further scale arguments passed to scale_color_viridis_c
 #' Options:
 #' \itemize{
@@ -48,6 +49,7 @@ setGeneric("plot_density", function(object, features, slot = NULL,
                                     method = c("ks", "wkde"),
                                     adjust = 1, size = 1, shape = 16,
                                     combine = TRUE, pal = "viridis",
+                                    raster = TRUE,
                                     ...)
     standardGeneric("plot_density"))
 
@@ -59,7 +61,7 @@ setMethod("plot_density", signature("Seurat"),
                    features, slot = NULL, joint = FALSE, reduction = NULL,
                    dims = c(1, 2), method = c("ks", "wkde"), adjust = 1,
                    size = 1, shape = 16, combine = TRUE, pal = "viridis",
-                   ...) {
+                   raster = TRUE, ...) {
 
               # Validate dimensions -----
               .validate_dimensions(dims)
@@ -102,7 +104,7 @@ setMethod("plot_density", signature("Seurat"),
               }
               .plot_final_density(vars, cell_embeddings, features, joint,
                                   method, adjust, shape, size, pal, combine,
-                                  ...)
+                                  raster, ...)
           })
 
 
@@ -117,7 +119,7 @@ setMethod("plot_density", signature("SingleCellExperiment"),
                    features, slot = NULL, joint = FALSE, reduction = NULL,
                    dims = c(1, 2), method = c("ks", "wkde"), adjust = 1,
                    size = 1, shape = 16, combine = TRUE, pal = "viridis",
-                   ...) {
+                   raster = TRUE, ...) {
 
               # Validate dimensions -----
               .validate_dimensions(dims)
@@ -167,5 +169,6 @@ setMethod("plot_density", signature("SingleCellExperiment"),
               }
               .plot_final_density(vars, cell_embeddings, features, joint,
                                   method, adjust, shape, size, pal, combine,
+                                  raster,
                                   ...)
           })

R/plotting.R

@@ -8,17 +8,21 @@
 #' @param size Geom size
 #' @param legend_title String used as legend title
 #' @param pal String specifying the viridis color palette to use
+#' @param raster Rasterise plot
 #' @param ... Further scale arguments passed to scale_color_viridis_c
 #' @return A ggplot object
 #' @importFrom ggplot2 ggplot aes_string geom_point xlab ylab ggtitle labs
 #' guide_legend theme element_text element_line element_rect element_blank
 #' scale_color_viridis_c scale_color_gradientn
+#' @importFrom ggrastr rasterise
 plot_density_ <- function(z, feature, cell_embeddings, dim_names, shape, size,
                           legend_title,
                           pal = c(
                               "viridis", "magma", "cividis",
                               "inferno", "plasma"
-                          ), ...) {
+                          ), 
+                          raster, 
+                          ...) {
     p <- ggplot(data.frame(cell_embeddings, feature = z)) +
         aes_string(dim_names[1], dim_names[2], color = "feature") +
         geom_point(shape = shape, size = size) +
@@ -36,6 +40,12 @@ plot_density_ <- function(z, feature, cell_embeddings, dim_names, shape, size,
         )
 
     pal <- match.arg(pal)
-    p + scale_color_viridis_c(option = pal, ...)
+    p <- p + scale_color_viridis_c(option = pal, ...)
+
+    if(raster){
+      rasterise(p, dpi = 300)
+    }else{
+      p
+    }
 
 }