From 3858af647d49944911c903b71a1972712ace7a0f Mon Sep 17 00:00:00 2001
From: vertesy <abel.vertesy@imba.oeaw.ac.at>
Date: Fri, 21 Jun 2024 12:35:57 +0200
Subject: [PATCH] v2.8.0

---
 CITATION.cff                   | 2 +-
 DESCRIPTION                    | 4 ++--
 Development/config.R           | 2 +-
 R/Seurat.Utils.Visualization.R | 1 -
 man/filterNcGenes.Rd           | 4 ++--
 man/qSeuViolin.Rd              | 9 ++++++++-
 6 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index 94e0cf6..07c10d6 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -1,6 +1,6 @@
 cff-version: 1.2.0
 title: vertesy/Seurat.utils
-version: v2.7.5
+version: v2.8.0
 message: >-
   If you use this software, please cite it using these metadata.
 type: software
diff --git a/DESCRIPTION b/DESCRIPTION
index c23a063..ad64f8c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Seurat.utils
 Title: Seurat.utils - utility functions for Seurat
-Version: 2.7.5
+Version: 2.8.0
 Authors@R: 
     person("Abel", "Vertesy", , "av@imba.oeaw.ac.at", role = c("aut", "cre"))
 Author: Abel Vertesy <av@imba.oeaw.ac.at> [aut, cre]
@@ -59,6 +59,6 @@ Suggests:
     RColorBrewer,
     SoupX
 Encoding: UTF-8
-Packaged: 2024-05-27 16:35:31.283439
+Packaged: 2024-06-21 12:31:42.585143
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
diff --git a/Development/config.R b/Development/config.R
index 5dbba55..80eaa19 100644
--- a/Development/config.R
+++ b/Development/config.R
@@ -1,7 +1,7 @@
 # Configuration for the Package
 DESCRIPTION <- list(
   package.name = "Seurat.utils",
-  version = "2.7.5",
+  version = "2.8.0",
   title = "Seurat.utils - utility functions for Seurat",
   description = "Seurat.utils Is a collection of utility functions for Seurat single cell analysis.
     Functions allow 3D plotting, visualisation of statistics & QC,
diff --git a/R/Seurat.Utils.Visualization.R b/R/Seurat.Utils.Visualization.R
index 9e45aa0..db62c3e 100644
--- a/R/Seurat.Utils.Visualization.R
+++ b/R/Seurat.Utils.Visualization.R
@@ -1780,7 +1780,6 @@ qSeuViolin <- function(
   if(exists('features')) warning("Use arg. feature instead of features!\n", immediate. = TRUE)
 
   split_col <- unlist(obj[[ident]])
-  # browser()
   if(is.null(w)) w <- ceiling(length(unique(split_col))/6) + 6
   message("Plot width: ", w)
 
diff --git a/man/filterNcGenes.Rd b/man/filterNcGenes.Rd
index 76826a2..5fca658 100644
--- a/man/filterNcGenes.Rd
+++ b/man/filterNcGenes.Rd
@@ -6,8 +6,8 @@
 \usage{
 filterNcGenes(
   genes,
-  pattern_NC = c("^AC[0-9].+", "^AL[0-9].+", "^AP[0-9].+", "^AF[0-9].+", "^Z[0-9]+.+",
-    "^LINC0.+", "^C[1-9]orf.+", "^MIR[1-9].+", ".+\\\\.AS[1-9]$", ".+\\\\.DT[1-9]$"),
+  pattern_NC = c("^A[CFLP][0-9]{6}", "^Z[0-9]{5}", "^LINC0[0-9]{4}", "^C[1-9]+orf[1-9]+",
+    "[-|\\\\.]AS[1-9]*$", "[-|\\\\.]DT[1-9]*$", "^MIR[1-9]", "^SNHG[1-9]"),
   unique = TRUE,
   ...
 )
diff --git a/man/qSeuViolin.Rd b/man/qSeuViolin.Rd
index 11aea9a..88efcfa 100644
--- a/man/qSeuViolin.Rd
+++ b/man/qSeuViolin.Rd
@@ -9,6 +9,7 @@ qSeuViolin(
   feature = "nFeature_RNA",
   ident = GetNamedClusteringRuns(obj)[1],
   split.by = NULL,
+  colors = NULL,
   replace.na = FALSE,
   pt.size = 0.5,
   sub = NULL,
@@ -19,8 +20,10 @@ qSeuViolin(
   hline = FALSE,
   ylab = "Expression",
   ylimit = NULL,
+  legend = TRUE,
+  legend.pos = NULL,
   show_plot = TRUE,
-  w = 9,
+  w = NULL,
   h = 5,
   ...
 )
@@ -54,6 +57,10 @@ qSeuViolin(
 
 \item{ylimit}{A numeric vector specifying the limits of the y-axis.}
 
+\item{legend}{Show legend; Default: opposite of \code{label}.}
+
+\item{legend.pos}{Position of legend; Default: 'NULL'.}
+
 \item{show_plot}{A logical indicating whether to display the plot.}
 
 \item{w}{Width of the plot.}