Update 2.0.1-dev-stable

DESCRIPTION

@@ -2,7 +2,7 @@ Type: Package
 Package: SCpubr
 Title: Generate Publication Ready Visualizations of Single Cell
     Transcriptomics Data
-Version: 2.0.1
+Version: 2.0.1.9000
 Authors@R: 
     person("Enrique", "Blanco-Carmona", , "scpubr@gmail.com", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0002-1208-1691"))

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(do_AffinityAnalysisPlot)
 export(do_AlluvialPlot)
 export(do_BarPlot)
 export(do_BeeSwarmPlot)
@@ -9,6 +10,7 @@ export(do_ChordDiagramPlot)
 export(do_ColorPalette)
 export(do_CopyNumberVariantPlot)
 export(do_CorrelationPlot)
+export(do_DiffusionMapPlot)
 export(do_DimPlot)
 export(do_DotPlot)
 export(do_EnrichmentHeatmap)
@@ -18,11 +20,17 @@ export(do_FunctionalAnnotationPlot)
 export(do_GeyserPlot)
 export(do_GroupedGOTermPlot)
 export(do_GroupwiseDEPlot)
+export(do_LigandReceptorPlot)
+export(do_LoadingsPlot)
+export(do_MetadataPlot)
 export(do_NebulosaPlot)
 export(do_PathwayActivityPlot)
 export(do_RidgePlot)
+export(do_SCEnrichmentHeatmap)
+export(do_SCExpressionHeatmap)
 export(do_TFActivityPlot)
 export(do_TermEnrichmentPlot)
 export(do_ViolinPlot)
 export(do_VolcanoPlot)
 export(package_report)
+export(save_Plot)

R/save_Plot.R

@@ -0,0 +1,203 @@
+#' Save a plot as png, pdf and svg.
+#'
+#'
+#' @param plot Plot to save.
+#' @param figure_path \strong{\code{\link[base]{character}}} | Path where the figure will be stored.
+#' @param create_path \strong{\code{\link[base]{logical}}} | Whether to create the path.
+#' @param file_name \strong{\code{\link[base]{character}}} | Name of the file (without extension, it will be added automatically).
+#' @param output_format \strong{\code{\link[base]{character}}} | Output format of the saved figure.  One of:
+#' \itemize{
+#'   \item \emph{\code{pdf}}: Saves the figure as a PDF file.
+#'   \item \emph{\code{png}}: Saves the figure as a PNG file.
+#'   \item \emph{\code{jpeg}}: Saves the figure as a JPEG file.
+#'   \item \emph{\code{tiff}}: Saves the figure as a TIFF file.
+#'   \item \emph{\code{svg}}: Saves the figure as a SVG file.
+#'   \item \emph{\code{publication}}: Saves the figure as PDF, PNG and SVG files.
+#'   \item \emph{\code{all}}: Saves the figure in all possible formats.
+#' }
+#' @param dpi \strong{\code{\link[base]{numeric}}} | Dpi to use.
+#' @param width,height \strong{\code{\link[base]{numeric}}} | Width and height of the figure (inches).
+#'
+#' @return Nothing.
+#' @export
+#'
+#' @example /man/examples/examples_save_Plot.R
+save_Plot <- function(plot,
+                      figure_path = NULL,
+                      create_path = TRUE,
+                      file_name = NULL,
+                      dpi = 300,
+                      output_format = "publication",
+                      width = 8,
+                      height = 8){
+  # nocov start
+
+  # Checks for packages.
+  check_suggests(function_name = "save_Plot")
+
+  # Check logical parameters.
+  logical_list <- list("create_path" = create_path)
+  check_type(parameters = logical_list, required_type = "logical", test_function = is.logical)
+  # Check numeric parameters.
+  numeric_list <- list("dpi" = dpi,
+                       "width" = width,
+                       "height" = height)
+  check_type(parameters = numeric_list, required_type = "numeric", test_function = is.numeric)
+  # Check character parameters.
+  character_list <- list("figure_path" = figure_path,
+                         "file_name" = file_name)
+  check_type(parameters = character_list, required_type = "character", test_function = is.character)
+
+  # Null file name?
+  if (is.null(file_name)){file_name <- "output_figure"}
+  # Null figure path?
+  if (is.null(figure_path)){figure_path <- paste0(".", .Platform$file.sep)}
+
+  # Create directory.
+  if (!(dir.exists(figure_path))){
+    if (isTRUE(create_path)){dir.create(figure_path, recursive = TRUE)}
+  }
+
+
+
+
+  # Handle devices:
+  output_options <- c("all", "publication", "pdf", "png", "jpeg", "svg", "tiff")
+
+  assertthat::assert_that(sum(output_format %in% output_options) >= 1,
+                          msg = "Please select a valid output format from the available options: all, publication, pdf, png, jpeg, svg, tiff")
+
+  assertthat::assert_that(base::isFALSE("all" %in% output_format & "publication" %in% output_format),
+                          msg = "Please select either `all` or `publication`.")
+
+  if (output_format == "publication"){
+    devices_use <- c("pdf", "png", "svg")
+  } else if (output_format == "all"){
+    devices_use <- c("pdf", "png", "jpeg", "svg", "tiff")
+  } else {
+    possible_options <- c("pdf", "png", "jpeg", "svg", "tiff")
+    devices_use <- output_format[output_format %in% possible_options]
+  }
+
+  # is ggplot?
+
+  if (sum(class(plot) %in% "ggplot") >= 1){
+    # Having width = NULL and height = NULL will make the ggsave() function crash.
+    for (device in devices_use){
+        suppressMessages({
+          ggplot2::ggsave(filename = sprintf("%s.%s", file_name, device),
+                          plot = plot,
+                          path = figure_path,
+                          dpi = dpi,
+                          width = width,
+                          height = height,
+                          device = device)
+        })
+    }
+  # Is it a heatmap?
+  } else if (sum(class(plot) %in% c("HeatmapList", "ComplexHeatmap")) >= 1) {
+    suppressMessages({
+      filename <- paste0(figure_path, "/", file_name)
+      if ("png" %in% devices_use){
+        grDevices::png(filename = paste0(filename, ".png"), units = "in", height = height, width = width, res = dpi)
+        ComplexHeatmap::draw(plot, show_heatmap_legend = TRUE, padding = ggplot2::unit(c(20, 20, 2, 20), "mm"))
+        grDevices::dev.off()
+      }
+
+      if ("pdf" %in% devices_use){
+        grDevices::pdf(file = paste0(filename, ".pdf"), height = height, width = width)
+        ComplexHeatmap::draw(plot, show_heatmap_legend = TRUE, padding = ggplot2::unit(c(20, 20, 2, 20), "mm"))
+        grDevices::dev.off()
+      }
+
+      if ("jpeg" %in% devices_use){
+        grDevices::jpeg(file = paste0(filename, ".jpeg"), units = "in", height = height, width = width, res = dpi)
+        ComplexHeatmap::draw(plot, show_heatmap_legend = TRUE, padding = ggplot2::unit(c(20, 20, 2, 20), "mm"))
+        grDevices::dev.off()
+      }
+
+      if ("tiff" %in% devices_use){
+        grDevices::jpeg(file = paste0(filename, ".tiff"), units = "in", height = height, width = width, res = dpi)
+        ComplexHeatmap::draw(plot, show_heatmap_legend = TRUE, padding = ggplot2::unit(c(20, 20, 2, 20), "mm"))
+        grDevices::dev.off()
+      }
+
+      if ("svg" %in% devices_use){
+        svglite::svglite(filename = paste0(filename, ".svg"), height = height, width = width)
+        ComplexHeatmap::draw(plot, show_heatmap_legend = TRUE, padding = ggplot2::unit(c(20, 20, 2, 20), "mm"))
+        grDevices::dev.off()
+      }
+
+    })
+
+  } else if (sum(class(plot) %in% "pheatmap") >= 1){
+    suppressMessages({
+      filename <- paste0(figure_path, "/", file_name)
+      if ("png" %in% devices_use){
+        grDevices::png(filename = paste0(filename, ".png"), units = "in", height = height, width = width, res = dpi)
+        print(plot)
+        grDevices::dev.off()
+
+      }
+
+      if ("pdf" %in% devices_use){
+        grDevices::pdf(file = paste0(filename, ".pdf"), height = height, width = width)
+        print(plot)
+        grDevices::dev.off()
+      }
+
+      if ("jpeg" %in% devices_use){
+        grDevices::jpeg(file = paste0(filename, ".jpeg"), units = "in", height = height, width = width, res = dpi)
+        print(plot)
+        grDevices::dev.off()
+      }
+
+      if ("tiff" %in% devices_use){
+        grDevices::jpeg(file = paste0(filename, ".tiff"), units = "in", height = height, width = width, res = dpi)
+        print(plot)
+        grDevices::dev.off()
+      }
+
+      if ("svg" %in% devices_use){
+        svglite::svglite(filename = paste0(filename, ".svg"), height = height, width = width)
+        print(plot)
+        grDevices::dev.off()
+      }
+    })
+  } else if (sum(class(plot) %in% "recordedplot") >= 1){
+    suppressMessages({
+      filename <- paste0(figure_path, "/", file_name)
+      if ("png" %in% devices_use){
+        grDevices::png(filename = paste0(filename, ".png"), units = "in", height = height, width = width, res = dpi)
+        grDevices::replayPlot(plot)
+        grDevices::dev.off()
+
+      }
+
+      if ("pdf" %in% devices_use){
+        grDevices::pdf(file = paste0(filename, ".pdf"), height = height, width = width)
+        grDevices::replayPlot(plot)
+        grDevices::dev.off()
+      }
+
+      if ("jpeg" %in% devices_use){
+        grDevices::jpeg(file = paste0(filename, ".jpeg"), units = "in", height = height, width = width, res = dpi)
+        grDevices::replayPlot(plot)
+        grDevices::dev.off()
+      }
+
+      if ("tiff" %in% devices_use){
+        grDevices::jpeg(file = paste0(filename, ".tiff"), units = "in", height = height, width = width, res = dpi)
+        grDevices::replayPlot(plot)
+        grDevices::dev.off()
+      }
+
+      if ("svg" %in% devices_use){
+        svglite::svglite(filename = paste0(filename, ".svg"), height = height, width = width)
+        grDevices::replayPlot(plot)
+        grDevices::dev.off()
+      }
+    })
+  }
+  # nocov end
+}