Create networkplot

1 files changed, 99 insertions, 0 deletions

diff --git a/R/networkplot.R b/R/networkplot.R
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index 0000000..cb6aad8
--- /dev/null
+++ b/R/networkplot.R
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+#' 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)
+}