From 899a2eebc32af2d9d57d1183032b51f42759360d Mon Sep 17 00:00:00 2001
From: Chris Sobczak <chris@sobczak.family>
Date: Mon, 6 Jul 2026 15:52:27 -0700
Subject: Add sorting for heatmap

---
 R/heatmap.R | 34 +++++++++++++++++++---------------
 1 file changed, 19 insertions(+), 15 deletions(-)

(limited to 'R/heatmap.R')

diff --git a/R/heatmap.R b/R/heatmap.R
index cb6c8f8..3351045 100644
--- a/R/heatmap.R
+++ b/R/heatmap.R
@@ -21,23 +21,34 @@ heatmap <- function(R, title = NULL, labels = FALSE, order = NULL){
 	R_list <- tryCatch({
 		if(is.matrix(R)){
 			Rm <- R
-			cnames <- colnames(Rm)
-			rnames <- rownames(Rm)
 		}else{
 			Rm <- as.matrix(R)
-			cnames <- colnames(Rm)
-			rnames <- rownames(Rm)
 		}
+
+		cnames <- colnames(Rm)
+		rnames <- rownames(Rm)
+		if(is.null(cnames)){
+			cnames <- as.character(seq_len(ncol(Rm)))
+		}
+		if(is.null(rnames)){
+			rnames <- as.character(seq_len(nrow(Rm)))
+		}
+
 		if(nrow(Rm) == ncol(Rm)){
 			if(!is.null(order)){
-				order <- get_order(Rm)
-				M <- Rm[order, order]
+				if(length(order) != nrow(Rm)){
+					stop('Provided order is not the same length as the width of R')
+				}else{
+					rownames(Rm) <- rnames
+					colnames(Rm) <- cnames
+					Rm <- Rm[order, order]
+				}
 			}
 			list(
-				M = M[upper.tri(M)],
+				Rm = Rm[upper.tri(Rm)],
 				cnames = cnames,
 				rnames = rnames,
-				p = ncol(M)
+				p = ncol(Rm)
 			)
 		}else{
 			stop('Input must be coercible to a square matrix')
@@ -47,13 +58,6 @@ heatmap <- function(R, title = NULL, labels = FALSE, order = NULL){
 		stop(paste('Invalid input for heatmap:', e$message))
 	})
 
-	if(is.null(R_list$cnames)){
-		R_list$cnames <- as.character(seq_len(R_list$p))
-	}
-	if(is.null(R_list$rnames)){
-		R_list$rnames <- as.character(seq_len(R_list$p))
-	}
-
 	# Now get a df from the upper triangle
 	m <- length(R_list$R)
 	n <- as.integer((1 + sqrt(1 + 8 * m)) / 2)
-- 
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