From c06317c800dca736a239771ced527429ef2de3ca Mon Sep 17 00:00:00 2001
From: CJ Yetman <cyetman@rmi.org>
Date: Sat, 16 Dec 2023 15:36:14 +0100
Subject: [PATCH 1/2] change sankey default display to "internal"

---
 R/sankey_network.R     | 2 +-
 inst/sankey_network.js | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/sankey_network.R b/R/sankey_network.R
index 523eae4..0398937 100644
--- a/R/sankey_network.R
+++ b/R/sankey_network.R
@@ -13,7 +13,7 @@
 #' @md
 #' @export
 
-sankey_network <- function(data, width = NULL, height = NULL, ..., viewer = "browser") {
+sankey_network <- function(data, width = NULL, height = NULL, ..., viewer = "internal") {
   data <- as_sankey_data(data, ...)
 
   data <- jsonlite::toJSON(data, null = "null", na = "null", auto_unbox = TRUE,
diff --git a/inst/sankey_network.js b/inst/sankey_network.js
index 132495c..7bb9f93 100644
--- a/inst/sankey_network.js
+++ b/inst/sankey_network.js
@@ -1,4 +1,4 @@
-// !preview r2d3 data = jsonlite::toJSON(list(nodes=data.frame(id=c(0,1,2,3,4,5,6),name=c("node0","node1","node2","node3","node4","node5","node6"),group=c("grp1","grp1","grp2","grp2","grp2","grp3","grp3")),links=data.frame(source=c(0,1,1,1,0,2,2,3,5),target=c(2,2,3,5,4,3,4,4,6),value=c(2,2,2,2,2,2,2,4,4)))), dependencies = "inst/lib/d3-sankey/d3-sankey.min.js", d3_version = 6, width = 600, height = 300, options = list(linkStrokeOpacity=0.3,linkMixBlendMode="multiply",linkPath="d3.sankeyLinkHorizontal()",linkColor="source-target",nodeAlign="justify",nodeGroup="group",nodeWidth=15,nodePadding=10,nodeLabelPadding=6,nodeLabelFontFamily="sans-serif",nodeLabelFontSize=10,colors="d3.schemeCategory10"), viewer = "browser"
+// !preview r2d3 data = jsonlite::toJSON(list(nodes=data.frame(id=c(0,1,2,3,4,5,6),name=c("node0","node1","node2","node3","node4","node5","node6"),group=c("grp1","grp1","grp2","grp2","grp2","grp3","grp3")),links=data.frame(source=c(0,1,1,1,0,2,2,3,5),target=c(2,2,3,5,4,3,4,4,6),value=c(2,2,2,2,2,2,2,4,4)))), dependencies = "inst/lib/d3-sankey/d3-sankey.min.js", d3_version = 6, width = 600, height = 300, options = list(linkStrokeOpacity=0.3,linkMixBlendMode="multiply",linkPath="d3.sankeyLinkHorizontal()",linkColor="source-target",nodeAlign="justify",nodeGroup="group",nodeWidth=15,nodePadding=10,nodeLabelPadding=6,nodeLabelFontFamily="sans-serif",nodeLabelFontSize=10,colors="d3.schemeCategory10"), viewer = "internal"
 
 r2d3.onRender(function(data, svg, width, height, options) {
   let linkStrokeOpacity = options.linkStrokeOpacity;

From 20c144c5da78647df22ccb3b665fc07d448858e7 Mon Sep 17 00:00:00 2001
From: CJ Yetman <cyetman@rmi.org>
Date: Sat, 16 Dec 2023 15:44:02 +0100
Subject: [PATCH 2/2] update docs

---
 DESCRIPTION           |  2 +-
 man/as_tree_data.Rd   | 18 +++++++++---------
 man/sankey_network.Rd |  2 +-
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 37ac459..70cc61c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -16,7 +16,7 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Imports: 
     jsonlite (>= 0.9.6),
     methods,
diff --git a/man/as_tree_data.Rd b/man/as_tree_data.Rd
index dcc40d9..56ad53b 100644
--- a/man/as_tree_data.Rd
+++ b/man/as_tree_data.Rd
@@ -91,23 +91,23 @@ addressed by adding columns for formatting of the incoming link
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{character}: Convert JSON from URL to \code{treenetdf}
+\item \code{as_tree_data(character)}: Convert JSON from URL to \code{treenetdf}
 
-\item \code{hclust}: Convert hclust objects to \code{treenetdf}
+\item \code{as_tree_data(hclust)}: Convert hclust objects to \code{treenetdf}
 
-\item \code{list}: Convert a nested list to \code{treenetdf}
+\item \code{as_tree_data(list)}: Convert a nested list to \code{treenetdf}
 
-\item \code{Node}: data.tree to \code{treenetdf}
+\item \code{as_tree_data(Node)}: data.tree to \code{treenetdf}
 
-\item \code{phylo}: Phylo tree to \code{treenetdf}
+\item \code{as_tree_data(phylo)}: Phylo tree to \code{treenetdf}
 
-\item \code{tbl_graph}: tbl_graph_to_treenetdf
+\item \code{as_tree_data(tbl_graph)}: tbl_graph_to_treenetdf
 
-\item \code{igraph}: Convert igraph tree to \code{treenetdf}
+\item \code{as_tree_data(igraph)}: Convert igraph tree to \code{treenetdf}
 
-\item \code{data.frame}: Convert a data.frame to a \code{treenetdf}
-}}
+\item \code{as_tree_data(data.frame)}: Convert a data.frame to a \code{treenetdf}
 
+}}
 \examples{
 links <- read.csv(header = TRUE, stringsAsFactors = FALSE, text = '
                    source,target,name
diff --git a/man/sankey_network.Rd b/man/sankey_network.Rd
index 57d19af..e7d29da 100644
--- a/man/sankey_network.Rd
+++ b/man/sankey_network.Rd
@@ -4,7 +4,7 @@
 \alias{sankey_network}
 \title{Create an interactive sankey network plot in a htmlwidget}
 \usage{
-sankey_network(data, width = NULL, height = NULL, ..., viewer = "browser")
+sankey_network(data, width = NULL, height = NULL, ..., viewer = "internal")
 }
 \arguments{
 \item{data}{a network description in one of numerous forms (see details)}