From 566e6091450489572136cdd38a80e4c452c82708 Mon Sep 17 00:00:00 2001
From: pfgherardini <federico.gherardini@gmail.com>
Date: Tue, 19 Feb 2019 17:01:31 -0800
Subject: [PATCH] fixed problem with write_graph

---
 DESCRIPTION                              | 4 ++--
 inst/shinyGUI/server.R                   | 2 +-
 man/get_scaffold_map.Rd                  | 8 ++++----
 man/get_unsupervised_graph_from_files.Rd | 5 +++--
 4 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e108e34..a1ff196 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: vite
 Type: Package
 Title: Analyzing single-cell data using graphs
-Version: 0.4.4
+Version: 0.4.5
 Authors@R: "Pier Federico Gherardini <pfgherardini@parkerici.org> [aut, cre]"
 Description: This is a package for visualization and analysis of high-dimensional
     single-cell data using graphs
@@ -13,4 +13,4 @@ LinkingTo: Rcpp
 License: GPL v3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0
diff --git a/inst/shinyGUI/server.R b/inst/shinyGUI/server.R
index e115244..f6e180c 100644
--- a/inst/shinyGUI/server.R
+++ b/inst/shinyGUI/server.R
@@ -130,7 +130,7 @@ shinyServer(function(input, output, session) {
             )
 
             out.name <- file.path(working.directory, sprintf("%s.graphml", input$unsupervisedui_out_name))
-            write_graph(G, out.name)
+            vite::write_graph(G, out.name)
 
             showModal(modalDialog(
                 "Analysis Finished", br(),
diff --git a/man/get_scaffold_map.Rd b/man/get_scaffold_map.Rd
index 4439176..eaa5412 100644
--- a/man/get_scaffold_map.Rd
+++ b/man/get_scaffold_map.Rd
@@ -4,10 +4,10 @@
 \alias{get_scaffold_map}
 \title{Creates a Scaffold map}
 \usage{
-get_scaffold_map(tab.clustered, col.names, tab.landmarks, G.landmarks = NULL,
-  ew.influence = ceiling(length(col.names)/3), min.similarity = 0.5,
-  inter.cluster.col.names = col.names, inter.cluster.weight.factor = 0.7,
-  overlap.method = "repel")
+get_scaffold_map(tab.clustered, col.names, tab.landmarks,
+  G.landmarks = NULL, ew.influence = ceiling(length(col.names)/3),
+  min.similarity = 0.5, inter.cluster.col.names = col.names,
+  inter.cluster.weight.factor = 0.7, overlap.method = "repel")
 }
 \arguments{
 \item{tab.clustered}{A \code{data.frame} containing the clusters to be represented in the Scaffold map. Each
diff --git a/man/get_unsupervised_graph_from_files.Rd b/man/get_unsupervised_graph_from_files.Rd
index 662a745..5f2f926 100644
--- a/man/get_unsupervised_graph_from_files.Rd
+++ b/man/get_unsupervised_graph_from_files.Rd
@@ -4,8 +4,9 @@
 \alias{get_unsupervised_graph_from_files}
 \title{Builds an unsupervised graph starting from a list of input files}
 \usage{
-get_unsupervised_graph_from_files(files.list, col.names, filtering.threshold,
-  metadata.tab = NULL, metadata.filename.col = NULL, use.basename = TRUE,
+get_unsupervised_graph_from_files(files.list, col.names,
+  filtering.threshold, metadata.tab = NULL,
+  metadata.filename.col = NULL, use.basename = TRUE,
   process.clusters.data = TRUE, clusters.data.out.dir = "./",
   downsample.to = 1000)
 }