Add vertical spacing control StackedVlnPlot

R/Plotting_Utilities.R

@@ -67,7 +67,7 @@ PC_Plotting <- function(
 #' @noRd
 #'
 #' @author Ming Tang (Original Code), Sam Marsh (Modified function for use in scCustomtize)
-#' @references https://divingintogeneticsandgenomics.rbind.io/post/stacked-violin-plot-for-visualizing-single-cell-data-in-seurat/
+#' @references https://divingintogeneticsandgenomics.rbind.io/post/stacked-violin-plot-for-visualizing-single-cell-data-in-seurat/.  Solution for re-enabling plot spacing modification by Abdenour ABBAS (comment on original blog post; http://disq.us/p/2b54qh2).
 #' @seealso https://twitter.com/tangming2005
 #'
 
@@ -76,7 +76,7 @@ Modify_VlnPlot <- function(
   features,
   pt.size = 0,
   cols = NULL,
-  plot_margin = unit(c(-0.5, 0, -0.5, 0), "cm"),
+  plot_margin = NULL,
   ...
 ) {
   #remove the x-axis text and tick

R/Seurat_Plotting.R

@@ -642,10 +642,14 @@ Meta_Highlight_Plot <- function(
 #' groups plotted is greater than 36.  Default = 123.
 #' @param ggplot_default_colors logical.  If `colors_use = NULL`, Whether or not to return plot using
 #' default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
+#' @param plot_spacing Numerical value specifying the vertical spacing between each plot in the stack.
+#' Default is 0.15 ("cm").  Spacing dependent on unit provided to `spacing_unit`.
+#' @param spacing_unit Unit to use in specifying vertical spacing between plots.  Default is "cm".
 #' @param ... Extra parameters passed to \code{\link[Seurat]{VlnPlot}}.
 #'
 #' @return A ggplot object
 #'
+#' @import ggplot2
 #' @import patchwork
 #' @importFrom purrr map map_dbl map2
 #' @importFrom Seurat VlnPlot
@@ -674,6 +678,8 @@ Stacked_VlnPlot <- function(
   colors_use = NULL,
   color_seed = 123,
   ggplot_default_colors = FALSE,
+  plot_spacing = 0.15,
+  spacing_unit = "cm",
   ...
 ) {
   # Check Seurat
@@ -722,8 +728,11 @@ Stacked_VlnPlot <- function(
     }
   }
 
+  # Setup plot spacing/margin parameter
+  plot_margin <- margin(t = plot_spacing, r = 0, b = plot_spacing, l = 0, unit = spacing_unit)
+
   # Create plots
-  plot_list <- map(all_found_features, function(x) Modify_VlnPlot(seurat_object = seurat_object, features = x, cols = colors_use, group.by = group.by, split.by = split.by, idents = idents, ...))
+  plot_list <- map(all_found_features, function(x) Modify_VlnPlot(seurat_object = seurat_object, features = x, cols = colors_use, group.by = group.by, split.by = split.by, idents = idents, plot_margin = plot_margin, ...))
 
   # Add back x-axis title to bottom plot. patchwork is going to support this?
   # Add ability to rotate the X axis labels to the function call