Create networkplot

7 files changed, 134 insertions, 39 deletions

diff --git a/.Rbuildignore b/.Rbuildignore
index 2a2cb83..d74dc1d 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,2 +1,3 @@
 ^LICENSE\.md$
 ^README\.Rmd$
+^R/saveplot\.R$
diff --git a/DESCRIPTION b/DESCRIPTION
index 0152b88..186479f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -10,7 +10,8 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 8.0.0.9000
 Imports: 
     ggplot2,
-    ragg,
+    ggraph,
+    igraph,
     reshape2
 Suggests: 
     testthat (>= 3.0.0)
diff --git a/NAMESPACE b/NAMESPACE
index 6f4e5ca..1a107ff 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,7 +2,8 @@
 
 export(corplot)
 export(gg_csobczak)
-export(saveplot)
+export(networkplot)
 import(ggplot2)
-import(ragg)
+import(ggraph)
+import(igraph)
 importFrom(reshape2,melt)
diff --git a/R/corplot.R b/R/corplot.R
index 4a9335e..08221a4 100644
--- a/R/corplot.R
+++ b/R/corplot.R
@@ -1,4 +1,3 @@
-utils::globalVariables(c('i', 'j', 'value'))
 #' Correlation Plot (Upper Triangle)
 #'
 #' Minimal ggplot2 correlation plot showing the upper triangle
@@ -51,7 +50,7 @@ corplot <- function(R, title = NULL){
 	# And plot it
 	p <- ggplot2::ggplot(
 		data = df,
-		ggplot2::aes(x = j, y = i, fill = value)
+		ggplot2::aes(x = .data$j, y = .data$i, fill = .data$value)
 	) +
 	ggplot2::geom_tile() +
 	ggplot2::scale_fill_gradient2(
diff --git a/R/networkplot.R b/R/networkplot.R
new file mode 100644
index 0000000..cb6aad8
--- /dev/null
+++ b/R/networkplot.R
@@ -0,0 +1,99 @@
+#' Network Plot
+#'
+#' Draw an undirected graph from a square matrix
+#' where each variable is a node and the pairwise
+#' entries are the strength of the relationship
+#' (ex: correlation, partial correlation)
+#'
+#' @param R A square numeric matrix with names columns and rows
+#' @param title Optional plot title
+#'
+#' @return A ggraph object
+#'
+#' @examples
+#' X <- matrix(data = rnorm(100), nrow = 10)
+#' R <- cor(X)
+#' networkplot(R, title = 'Example Correlation Plot')
+#'
+#' @import ggraph
+#' @import igraph
+#'
+#' @export
+networkplot <- function(R, title = NULL){
+	Rm <- tryCatch({
+		if(is.matrix(R)){
+			if(nrow(R) != ncol(R)) stop('R must be square')
+			Rm <- R
+		}else if(is.vector(R)){
+			m <- length(R)
+			n <- (1 + sqrt(1 + 8 * m)) / 2
+			if(n != floor(n)) stop('Vector length not compatible with upper triangle')
+			n <- as.integer(n)
+			Rm <- matrix(0, n, n)
+			Rm[upper.tri(Rm)] <- R
+			Rm <- Rm + t(Rm)
+			diag(Rm) <- 1
+		}else{
+			Rm <- as.matrix(R)
+			if(nrow(Rm) != ncol(Rm)) stop('R must be square')
+		}
+
+		if(is.null(rownames(Rm))){
+			rownames(Rm) <- as.character(seq_len(nrow(Rm)))
+		}
+
+		if(is.null(colnames(Rm))){
+			colnames(Rm) <- as.character(seq_len(ncol(Rm)))
+		}
+
+		Rm
+	}, error = function(e){
+		stop(paste('Invalid input for networkplot:', e$message))
+	})
+
+	idx <- which(upper.tri(Rm), arr.ind = TRUE)
+	edges <- data.frame(
+		from = rownames(Rm)[idx[,1]],
+		to = colnames(Rm)[idx[,2]],
+		r = Rm[idx]
+	)
+	g <- igraph::graph_from_data_frame(
+		edges,
+		directed = FALSE
+	)
+
+	p <- ggraph::ggraph(graph = g, layout = 'circle') +
+	ggraph::geom_edge_arc(
+		ggplot2::aes(
+			edge_alpha = abs(.data$r),
+			edge_color = .data$r
+		),
+		strength = 0.5
+	) +
+	ggraph::scale_edge_color_gradient2(
+		low = 'red',
+		mid = 'white',
+		high = 'blue',
+		midpoint = 0,
+		limits = c(-1, 1),
+		guide = 'none'
+	) +
+	ggraph::geom_node_point(size = 3) +
+	ggraph::geom_node_text(
+		ggplot2::aes(label = .data$name),
+		repel = TRUE,
+		size = 3
+	) +
+	ggplot2::theme_void() +
+	ggplot2::theme(legend.position = 'none')
+
+	if(!is.null(title)){
+		p <- p +
+		ggplot2::ggtitle(title) +
+		ggplot2::theme(
+			plot.title = ggplot2::element_text(hjust = 0.5)
+		)
+	}
+
+	return(p)
+}
diff --git a/man/networkplot.Rd b/man/networkplot.Rd
new file mode 100644
index 0000000..055bc46
--- /dev/null
+++ b/man/networkplot.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/networkplot.R
+\name{networkplot}
+\alias{networkplot}
+\title{Network Plot}
+\usage{
+networkplot(R, title = NULL)
+}
+\arguments{
+\item{R}{A square numeric matrix with names columns and rows}
+
+\item{title}{Optional plot title}
+}
+\value{
+A ggraph object
+}
+\description{
+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)
+}
+\examples{
+X <- matrix(data = rnorm(100), nrow = 10)
+R <- cor(X)
+networkplot(R, title = 'Example Correlation Plot')
+
+}
diff --git a/man/saveplot.Rd b/man/saveplot.Rd
deleted file mode 100644
index 170e077..0000000
--- a/man/saveplot.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/saveplot.R
-\name{saveplot}
-\alias{saveplot}
-\title{Save a ggplot object}
-\usage{
-saveplot(p, filename, units = "in", width = 10, height = 10, dpi = 600)
-}
-\arguments{
-\item{p}{ggplot object you want to save}
-
-\item{filename}{The name of the file you want to export to}
-
-\item{units}{The units for dimensions of the plot (default inches)}
-
-\item{width}{Width of the plot in units (default 10)}
-
-\item{height}{Height of the plot in units (default 10)}
-
-\item{dpi}{Dots per inch (detault 300)}
-}
-\value{
-No return value
-}
-\description{
-Standard method for saving ggplot objects for best
-quality for the desired use case
-}
-\examples{
-df <- data.frame(x = rnorm(100))
-p <- ggplot2::ggplot(data = df, ggplot2::aes(x = x)) + ggplot2::geom_histogram()
-saveplot(p, filename = 'plot.png')
-
-}