From 5bd91e5a718563f10dd8ce9af3ddbb08cff9a103 Mon Sep 17 00:00:00 2001
From: vckraemer <vanessa.kraemer1@online.de>
Date: Fri, 8 Nov 2024 14:11:48 +0100
Subject: [PATCH] upating documentation

---
 .gitignore               | 1 +
 DESCRIPTION              | 2 +-
 R/plot.R                 | 1 +
 man/plot_bar_rankings.Rd | 3 ++-
 4 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/.gitignore b/.gitignore
index a717309..e4b042f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,3 +9,4 @@ omnipathr-log
 .ipynb_checkpoints
 /markdown/.ipynb_checkpoints
 .Rhistory
+/.vscode/
\ No newline at end of file
diff --git a/DESCRIPTION b/DESCRIPTION
index 971b926..011e972 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -36,7 +36,7 @@ biocViews: Network, SystemsBiology, SingleCell, Software, GraphAndNetwork
 Encoding: UTF-8
 LazyData: TRUE
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Imports:
     pals (>= 1.1),
     graphlayouts (>= 0.7.0),
diff --git a/R/plot.R b/R/plot.R
index 3abb410..eca5005 100644
--- a/R/plot.R
+++ b/R/plot.R
@@ -1321,6 +1321,7 @@ plot_bar_rankings_cci <- function(data_object, table_name, ranking = "pagerank",
 #' @param ranking name of the network ranking to use
 #' @param type gene type (L,R,TF, LR/RL, RTF/TFR, LTF/TFL)
 #' @param filter_sign show all (NULL), only positive (pos), or only negativ (neg) results
+#' @param top_num number of top genes to show in positive or negative direction
 #' @import ggplot2
 #' @import ggrepel
 #' @import reshape2
diff --git a/man/plot_bar_rankings.Rd b/man/plot_bar_rankings.Rd
index 09c3262..f4d0022 100644
--- a/man/plot_bar_rankings.Rd
+++ b/man/plot_bar_rankings.Rd
@@ -11,7 +11,8 @@ plot_bar_rankings(
   ranking,
   type = NULL,
   filter_sign = NULL,
-  mode = "cci"
+  mode = "cci",
+  top_num = 10
 )
 }
 \arguments{