From 3adf21d5f19ef9e9ff0976edcda5a67d42c2cfba Mon Sep 17 00:00:00 2001
From: theHumanBorch <ncborch@gmail.com>
Date: Wed, 8 Nov 2023 12:07:54 -0600
Subject: [PATCH] importing ggraph

---
 DESCRIPTION                         | 2 +-
 NAMESPACE                           | 1 +
 R/clonalBias.R                      | 2 +-
 R/global.R                          | 1 +
 tests/testthat/test-clonalNetwork.R | 2 +-
 5 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 67b01271..bca66487 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -25,11 +25,11 @@ Imports:
     iNEXT,
     methods,
     plyr,
+    quantreg,
     Rcpp,
     reshape2,
     rjson,
     rlang,
-    rqss,
     S4Vectors,
     SeuratObject,
     SingleCellExperiment,
diff --git a/NAMESPACE b/NAMESPACE
index 178ba6d5..b211c862 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -86,6 +86,7 @@ importFrom(igraph,set_vertex_attr)
 importFrom(methods,slot)
 importFrom(plyr,join)
 importFrom(plyr,llply)
+importFrom(quantreg,rqss)
 importFrom(reshape2,dcast)
 importFrom(reshape2,melt)
 importFrom(rjson,fromJSON)
diff --git a/R/clonalBias.R b/R/clonalBias.R
index af33142c..758cb07d 100644
--- a/R/clonalBias.R
+++ b/R/clonalBias.R
@@ -42,7 +42,7 @@
 #' @param exportTable Returns the data frame used for forming the graph.
 #' @param palette Colors to use in visualization - input any \link[grDevices]{hcl.pals}.
 #' @import ggplot2
-#' @importClassesFrom quantreg rqss
+#' @importFrom quantreg rqss
 #' @importFrom stringr str_sort
 #' @export
 #' @concept SC_Functions
diff --git a/R/global.R b/R/global.R
index a4de2616..198815ff 100644
--- a/R/global.R
+++ b/R/global.R
@@ -42,5 +42,6 @@
     utils::globalVariables ("group.by")
     utils::globalVariables ("group")
     utils::globalVariables ("chain2_aa")
+    utils::globalVariables ("dotSize")
     invisible ()
 }
diff --git a/tests/testthat/test-clonalNetwork.R b/tests/testthat/test-clonalNetwork.R
index f392e46f..a9b188ac 100644
--- a/tests/testthat/test-clonalNetwork.R
+++ b/tests/testthat/test-clonalNetwork.R
@@ -3,7 +3,7 @@
 # library(ggraph) # Qile: I believe libraries shouldn't need to be loaded in scripts? Correct me if im wrong.
 
 test_that("clonalNetwork works", {
-
+  library(ggraph)
   data("scRep_example")
   test_obj <- combineExpression(getCombined(), scRep_example)