Adjust network

2 files changed, 11 insertions, 7 deletions

diff --git a/R/networkplot.R b/R/networkplot.R
index 1055b08..2401cb1 100644
--- a/R/networkplot.R
+++ b/R/networkplot.R
@@ -133,7 +133,7 @@ networkplot <- function(R, groups = NULL, title = NULL){
 	ggraph::geom_conn_bundle(
 		data = con,
 		ggplot2::aes(
-			edge_alpha = abs(.data$value),
+			edge_alpha = abs(.data$value)^2,
 			edge_colour = .data$value
 		),
 		tension = 0.5
@@ -153,20 +153,18 @@ networkplot <- function(R, groups = NULL, title = NULL){
 	ggraph::geom_node_point(
 		ggplot2::aes(
 			filter = .data$leaf,
-			colour = .data$group,
 			fill = .data$group
 		),
-		size = 3
+		size = 1
 	) +
 	# labels nodes and groups
 	ggraph::geom_node_text(
 		ggplot2::aes(label = .data$name),
 		# prevents text labels from overlapping
 		repel = TRUE,
-		size = 3
+		size = 1
 	) +
-	ggplot2::theme_void() +
-	ggplot2::theme(legend.position = 'none')
+	ggplot2::theme_void()
 
 	if(!is.null(title)){
 		p <- p +
@@ -175,6 +173,11 @@ networkplot <- function(R, groups = NULL, title = NULL){
 			plot.title = ggplot2::element_text(hjust = 0.5)
 		)
 	}
+	
+	if(!is.null(groups)){
+		p <- p +
+		ggplot2::scale_fill_discrete(name = 'Superpathway')
+	}
 
 	return(p)
 }
diff --git a/man/networkplot.Rd b/man/networkplot.Rd
index a4a622d..4337a31 100644
--- a/man/networkplot.Rd
+++ b/man/networkplot.Rd
@@ -20,7 +20,8 @@ A ggraph object
 Draw an undirected graph from a square matrix
 where each variable is a node and the pairwise
 entries are the strength of the relationship
-(ex: correlation, partial correlation)
+(ex: correlation, partial correlation).
+Based on https://r-graph-gallery.com/310-custom-hierarchical-edge-bundling.html
 }
 \examples{
 X <- matrix(data = rnorm(100), nrow = 10)