...

R/Seurat.Utils.R

@@ -74,7 +74,7 @@ parallel.computing.by.future <- function(cores = 4, maxMemSize = 4000 * 1024^2)
 #'
 #' @export
 IntersectGeneLsWithObject <- function(genes, obj = combined.obj, n_genes_shown = 10, strict = TRUE) {
-  message("IntersectGeneLsWithObject()")
+  message(">>> Running IntersectGeneLsWithObject(), formerly IntersectWithExpressed()")
 
   stopifnot(
     is.character(genes),

R/Seurat.Utils.Visualization.R

@@ -707,29 +707,34 @@ qFeatureScatter <- function(
 
 
 # _________________________________________________________________________________________________
-#' qSeuViolin
+#' @title qSeuViolin
 #'
-#' This function creates a violin plot of a single feature in a Seurat object, split by a grouping variable.
+#' @description This function creates a violin plot of a single feature in a Seurat object,
+#' split by a grouping variable.
 #' @param object A Seurat object.
 #' @param suffix A string to append to the title of the plot.
 #' @param features The name of the feature to plot.
+#' @param hline hline
+#' @param caption caption
 #' @param split.by The grouping variable to split the plot by.
 #' @param logY Whether to plot the y-axis on a log scale.
 #'
 #' @return A ggplot object.
 #'
 #' @export
-
 qSeuViolin <- function(
     object = ls.Seurat[[1]], suffix = GEX_library,
-    features = "nFeature_RNA", split.by = "orig.ident", logY = TRUE) {
-  # Create a violin plot of the feature, split by the grouping variable.
-  p <- VlnPlot(object = object, features = features, split.by = split.by) +
+    features = "nFeature_RNA", split.by = "orig.ident", logY = TRUE, hline = FALSE, caption = FALSE
+    , ...) {
+
+  p <- VlnPlot(object = object, features = features, split.by = split.by, ...) +
     ggtitle(label = features, subtitle = paste(suffix, "by", split.by)) +
     theme(axis.title.x = element_blank()) + labs(y = "Top UVI's depth")
 
   # If `logY` is TRUE, plot the y-axis on a log scale.
   if (logY) p <- p + ggplot2::scale_y_log10()
+  if (hline) p <- p + ggplot2::geom_hline(yintercept = hline)
+  if (!isFALSE(caption)) p <- p + ggplot2::labs(caption = caption)
 
   # Save the plot.
   title_ <- ppp(as.character(features), suffix, flag.nameiftrue(logY))