From 6732e3cf4d3b569f182c78b1e1e12da8cfc35e90 Mon Sep 17 00:00:00 2001
From: vertesy <abel.vertesy@imba.oeaw.ac.at>
Date: Wed, 3 Jan 2024 19:33:19 +0100
Subject: [PATCH] ...

---
 R/Seurat.Utils.R                      |  2 +-
 R/Seurat.Utils.Visualization.R        | 17 +++++++++++------
 man/AutoLabelTop.logFC.Rd             |  2 +-
 man/plot.clust.size.distr.Rd          |  2 +-
 man/qSeuViolin.Rd                     | 12 ++++++++++--
 man/remove.residual.small.clusters.Rd |  2 +-
 6 files changed, 25 insertions(+), 12 deletions(-)

diff --git a/R/Seurat.Utils.R b/R/Seurat.Utils.R
index 1654aa5..dd7eda0 100644
--- a/R/Seurat.Utils.R
+++ b/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),
diff --git a/R/Seurat.Utils.Visualization.R b/R/Seurat.Utils.Visualization.R
index f2a2679..e60a68b 100644
--- a/R/Seurat.Utils.Visualization.R
+++ b/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))
diff --git a/man/AutoLabelTop.logFC.Rd b/man/AutoLabelTop.logFC.Rd
index 8b9bd5e..9cb2f71 100644
--- a/man/AutoLabelTop.logFC.Rd
+++ b/man/AutoLabelTop.logFC.Rd
@@ -6,7 +6,7 @@
 \usage{
 AutoLabelTop.logFC(
   obj = combined.obj,
-  group.by = GetClusteringRuns()[1],
+  group.by = GetClusteringRuns(obj)[1],
   res = 0.1,
   plot.top.genes = TRUE,
   suffix = res,
diff --git a/man/plot.clust.size.distr.Rd b/man/plot.clust.size.distr.Rd
index 74c6823..3442725 100644
--- a/man/plot.clust.size.distr.Rd
+++ b/man/plot.clust.size.distr.Rd
@@ -6,7 +6,7 @@
 \usage{
 \method{plot}{clust.size.distr}(
   obj = combined.obj,
-  ident = GetClusteringRuns()[2],
+  ident = GetClusteringRuns(obj)[2],
   plot = TRUE,
   thr.hist = 30,
   ...
diff --git a/man/qSeuViolin.Rd b/man/qSeuViolin.Rd
index bcc76a0..f359948 100644
--- a/man/qSeuViolin.Rd
+++ b/man/qSeuViolin.Rd
@@ -9,7 +9,10 @@ qSeuViolin(
   suffix = GEX_library,
   features = "nFeature_RNA",
   split.by = "orig.ident",
-  logY = TRUE
+  logY = TRUE,
+  hline = FALSE,
+  caption = FALSE,
+  ...
 )
 }
 \arguments{
@@ -22,10 +25,15 @@ qSeuViolin(
 \item{split.by}{The grouping variable to split the plot by.}
 
 \item{logY}{Whether to plot the y-axis on a log scale.}
+
+\item{hline}{hline}
+
+\item{caption}{caption}
 }
 \value{
 A ggplot object.
 }
 \description{
-This function creates a violin plot of a single feature in a Seurat object, split by a grouping variable.
+This function creates a violin plot of a single feature in a Seurat object,
+split by a grouping variable.
 }
diff --git a/man/remove.residual.small.clusters.Rd b/man/remove.residual.small.clusters.Rd
index a35eec3..f3586ce 100644
--- a/man/remove.residual.small.clusters.Rd
+++ b/man/remove.residual.small.clusters.Rd
@@ -6,7 +6,7 @@
 \usage{
 remove.residual.small.clusters(
   obj = combined.obj,
-  identitites = GetClusteringRuns(obj = obj),
+  identitites = GetClusteringRuns(obj),
   max.cells = max(round((ncol(obj))/2000), 5)
 )
 }