From b6c336d9c4070e703fc023e260c1fc0b3e3c79fe Mon Sep 17 00:00:00 2001
From: Jieun Oh <jieunoh@mednet.ucla.edu>
Date: Fri, 22 Nov 2024 16:12:27 -0800
Subject: [PATCH 01/15] create.cluster.heatmap.R - single sample compatibility

---
 R/create.cluster.heatmap.R | 33 +++++++++++++++++++++++++--------
 1 file changed, 25 insertions(+), 8 deletions(-)

diff --git a/R/create.cluster.heatmap.R b/R/create.cluster.heatmap.R
index 131b81d..6e50f34 100644
--- a/R/create.cluster.heatmap.R
+++ b/R/create.cluster.heatmap.R
@@ -44,14 +44,31 @@ create.cluster.heatmap <- function(
         arr[arr > ccf.limits[2]] <- ccf.limits[2];
         }
 
-    hm <- create.ccf.heatmap(
-        x = arr,
-        cluster.dimensions = 'none',
-        xlab.label = '',
-        xaxis.lab = xaxis.label,
-        colour.scheme = colour.scheme,
-        ...
-        );
+    if(is.numeric(arr)) {
+        arr <- as.data.frame(arr)
+        colnames(arr) <- as.character(unique(DF$ID))
+
+        hm <- create.ccf.heatmap(
+            x = arr,
+            cluster.dimensions = 'none',
+            xlab.label = '',
+            xaxis.lab = xaxis.label,
+            colour.scheme = colour.scheme,
+            same.as.matrix = TRUE,
+            yat = 1.5,
+            ...
+            );
+            
+    } else {
+        hm <- create.ccf.heatmap(
+            x = arr,
+            cluster.dimensions = 'none',
+            xlab.label = '',
+            xaxis.lab = xaxis.label,
+            colour.scheme = colour.scheme,
+            ...
+            );
+    }
 
     cov <- BoutrosLab.plotting.general::create.heatmap(
         x = t(clone.colours[snv.order$clone.id]),

From ef849192bbfe8382083beb510c36fd9c28f92e85 Mon Sep 17 00:00:00 2001
From: Jieun Oh <jieunoh@mednet.ucla.edu>
Date: Fri, 22 Nov 2024 16:14:10 -0800
Subject: [PATCH 02/15] create.ccf.summary.heatmap.R - single sample
 compatibility

---
 R/create.ccf.summary.heatmap.R | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/R/create.ccf.summary.heatmap.R b/R/create.ccf.summary.heatmap.R
index ec5c4b0..35b4696 100644
--- a/R/create.ccf.summary.heatmap.R
+++ b/R/create.ccf.summary.heatmap.R
@@ -52,6 +52,12 @@ create.ccf.summary.heatmap <- function(
         sample.df$ID        <- factor(sample.df$ID, levels = rev(sample.order));
         }
 
+    if(is.numeric(arr)) {
+        arr <- as.data.frame(arr)
+        colnames(arr) <- as.character(unique(DF$ID))
+        arr <- as.matrix(arr)
+        }
+
     clone.yaxis <- auto.axis(
         x = clone.df$nsnv,
         log.scaled = FALSE,

From 9652a4bac2274757ee740ddc4f9a4e68a7372960 Mon Sep 17 00:00:00 2001
From: Jieun Oh <jieunoh@mednet.ucla.edu>
Date: Fri, 22 Nov 2024 16:43:56 -0800
Subject: [PATCH 03/15] create.ccf.summary.heatmap - single sample
 compatibility

---
 R/create.ccf.summary.heatmap.R | 21 +++++++++++++++++++--
 1 file changed, 19 insertions(+), 2 deletions(-)

diff --git a/R/create.ccf.summary.heatmap.R b/R/create.ccf.summary.heatmap.R
index 35b4696..d705f4d 100644
--- a/R/create.ccf.summary.heatmap.R
+++ b/R/create.ccf.summary.heatmap.R
@@ -98,8 +98,19 @@ create.ccf.summary.heatmap <- function(
         xat = sample.xaxis$at
         );
 
+    #edit start
+    same.as.matrix <- is.numeric(arr)
+    if(is.numeric(arr)) {
+        arr <- as.data.frame(arr)
+        colnames(arr) <- as.character(unique(DF$ID))
+        arr <- as.matrix(arr)
+        hm.args.x <- as.data.frame(arr)
+        } else {
+        hm.args.x <- arr
+        }
+
     hm.args <- list(
-        x = arr,
+        x = hm.args.x,
         cluster.dimensions = 'none',
         xlab.label = 'Clone',
         xlab.cex = ifelse(is.null(clone.colours), subplot.xlab.cex, 0),
@@ -113,7 +124,8 @@ create.ccf.summary.heatmap <- function(
         yaxis.cex = subplot.yaxis.cex,
         yaxis.fontface = subplot.yaxis.fontface,
         print.colour.key = FALSE,
-        colour.scheme = hm.col.scheme
+        colour.scheme = hm.col.scheme,
+        same.as.matrix = same.as.matrix
         );
 
     if (add.median.text) {
@@ -124,6 +136,11 @@ create.ccf.summary.heatmap <- function(
         hm.args$text.col <- ifelse(arr > contrast.thres, 'white', 'black');
         }
 
+    if(same.as.matrix) {
+        hm.args$yat = 1.5
+        hm.args$row.pos = 1.5
+        }
+
     hm <- do.call(BoutrosLab.plotting.general::create.heatmap, hm.args);
 
     legend.ccf <- BoutrosLab.plotting.general::legend.grob(

From 50c9f743e231cdc4123d256fabfee96eca086fbd Mon Sep 17 00:00:00 2001
From: Jieun Oh <jieunoh@mednet.ucla.edu>
Date: Fri, 22 Nov 2024 16:44:20 -0800
Subject: [PATCH 04/15] create.ccf.summary.heatmap - single sample
 compatibility

---
 R/create.ccf.summary.heatmap.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/create.ccf.summary.heatmap.R b/R/create.ccf.summary.heatmap.R
index d705f4d..3bc1b1f 100644
--- a/R/create.ccf.summary.heatmap.R
+++ b/R/create.ccf.summary.heatmap.R
@@ -98,7 +98,6 @@ create.ccf.summary.heatmap <- function(
         xat = sample.xaxis$at
         );
 
-    #edit start
     same.as.matrix <- is.numeric(arr)
     if(is.numeric(arr)) {
         arr <- as.data.frame(arr)

From 2fe34a98c8550a966f13ed2ccd1e56ae523095d3 Mon Sep 17 00:00:00 2001
From: Jieun Oh <jieunoh@mednet.ucla.edu>
Date: Fri, 22 Nov 2024 16:47:09 -0800
Subject: [PATCH 05/15] create.ccf.summary.heatmap - single sample
 compatibility

---
 R/create.ccf.summary.heatmap.R | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/R/create.ccf.summary.heatmap.R b/R/create.ccf.summary.heatmap.R
index 3bc1b1f..7d4f444 100644
--- a/R/create.ccf.summary.heatmap.R
+++ b/R/create.ccf.summary.heatmap.R
@@ -52,12 +52,6 @@ create.ccf.summary.heatmap <- function(
         sample.df$ID        <- factor(sample.df$ID, levels = rev(sample.order));
         }
 
-    if(is.numeric(arr)) {
-        arr <- as.data.frame(arr)
-        colnames(arr) <- as.character(unique(DF$ID))
-        arr <- as.matrix(arr)
-        }
-
     clone.yaxis <- auto.axis(
         x = clone.df$nsnv,
         log.scaled = FALSE,

From 2fa6e380c42e069dec4cd99e1eea4617aff7a543 Mon Sep 17 00:00:00 2001
From: Jieun Oh <jieunoh@mednet.ucla.edu>
Date: Fri, 22 Nov 2024 16:57:42 -0800
Subject: [PATCH 06/15] lintr

---
 R/create.ccf.summary.heatmap.R | 8 ++++----
 R/create.cluster.heatmap.R     | 3 +--
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/R/create.ccf.summary.heatmap.R b/R/create.ccf.summary.heatmap.R
index 7d4f444..a95b4ce 100644
--- a/R/create.ccf.summary.heatmap.R
+++ b/R/create.ccf.summary.heatmap.R
@@ -93,7 +93,7 @@ create.ccf.summary.heatmap <- function(
         );
 
     same.as.matrix <- is.numeric(arr)
-    if(is.numeric(arr)) {
+    if (is.numeric(arr)) {
         arr <- as.data.frame(arr)
         colnames(arr) <- as.character(unique(DF$ID))
         arr <- as.matrix(arr)
@@ -129,9 +129,9 @@ create.ccf.summary.heatmap <- function(
         hm.args$text.col <- ifelse(arr > contrast.thres, 'white', 'black');
         }
 
-    if(same.as.matrix) {
-        hm.args$yat = 1.5
-        hm.args$row.pos = 1.5
+    if (same.as.matrix) {
+        hm.args$yat <- 1.5
+        hm.args$row.pos <- 1.5
         }
 
     hm <- do.call(BoutrosLab.plotting.general::create.heatmap, hm.args);
diff --git a/R/create.cluster.heatmap.R b/R/create.cluster.heatmap.R
index 6e50f34..645d743 100644
--- a/R/create.cluster.heatmap.R
+++ b/R/create.cluster.heatmap.R
@@ -44,7 +44,7 @@ create.cluster.heatmap <- function(
         arr[arr > ccf.limits[2]] <- ccf.limits[2];
         }
 
-    if(is.numeric(arr)) {
+    if (is.numeric(arr)) {
         arr <- as.data.frame(arr)
         colnames(arr) <- as.character(unique(DF$ID))
 
@@ -58,7 +58,6 @@ create.cluster.heatmap <- function(
             yat = 1.5,
             ...
             );
-            
     } else {
         hm <- create.ccf.heatmap(
             x = arr,

From 2023c83f50ad69f02bb54502607f708a94f8cfc2 Mon Sep 17 00:00:00 2001
From: Jieun Oh <jieunoh@mednet.ucla.edu>
Date: Fri, 22 Nov 2024 19:02:26 -0800
Subject: [PATCH 07/15] support monoclonal for single ssample

---
 R/create.ccf.summary.heatmap.R | 30 +++++++++++++++++++++++++++---
 R/create.cluster.heatmap.R     |  2 +-
 2 files changed, 28 insertions(+), 4 deletions(-)

diff --git a/R/create.ccf.summary.heatmap.R b/R/create.ccf.summary.heatmap.R
index a95b4ce..5e6dac8 100644
--- a/R/create.ccf.summary.heatmap.R
+++ b/R/create.ccf.summary.heatmap.R
@@ -92,8 +92,8 @@ create.ccf.summary.heatmap <- function(
         xat = sample.xaxis$at
         );
 
-    same.as.matrix <- is.numeric(arr)
-    if (is.numeric(arr)) {
+    same.as.matrix <- !is.matrix(arr)
+    if (same.as.matrix) {
         arr <- as.data.frame(arr)
         colnames(arr) <- as.character(unique(DF$ID))
         arr <- as.matrix(arr)
@@ -134,6 +134,19 @@ create.ccf.summary.heatmap <- function(
         hm.args$row.pos <- 1.5
         }
 
+    if(nrow(hm.args.x) == 1 & ncol(hm.args.x) == 1) {
+        legend.colour.change <- hm.col.scheme[length(hm.col.scheme)]
+        hm.args$x <- as.data.frame(hm.col.scheme[length(hm.col.scheme)])
+        hm.args$input.colours <- TRUE
+        hm.args$clustering.method <- 'none'
+        hm.args$yat <- 1
+        hm.args$col.pos <- 1.5
+        hm.args$row.pos <- 1
+        legend.col <- hm.col.scheme[length(hm.col.scheme)]
+        } else {
+        legend.col <- hm.col.scheme
+        }
+
     hm <- do.call(BoutrosLab.plotting.general::create.heatmap, hm.args);
 
     legend.ccf <- BoutrosLab.plotting.general::legend.grob(
@@ -141,7 +154,7 @@ create.ccf.summary.heatmap <- function(
             legend = list(
                 title = 'CCF',
                 labels = c(signif(min(arr), 2), rep('', legend.size), signif(max(arr), 2)),
-                colours = c('white', 'blue'),
+                colours = legend.col,
                 border = 'black',
                 continuous = TRUE,
                 cex = legend.label.cex
@@ -153,6 +166,16 @@ create.ccf.summary.heatmap <- function(
         );
 
     if (!is.null(clone.colours)) {
+        if(length(clone.colours) == 1) {
+        clone.cov <- BoutrosLab.plotting.general::create.heatmap(
+            x = as.data.frame(clone.colours),
+            xlab.label = 'Clone',
+            input.colours = TRUE,
+            clustering.method = 'none',
+            print.colour.key = FALSE,
+            yaxis.tck = 0
+            );
+        } else {
         clone.cov <- BoutrosLab.plotting.general::create.heatmap(
             x = t(clone.colours[rownames(arr)]),
             xlab.label = 'Clone',
@@ -167,6 +190,7 @@ create.ccf.summary.heatmap <- function(
             print.colour.key = FALSE,
             yaxis.tck = 0
             );
+            }
         plot.list <- list(clone.bar, hm, sample.bar, clone.cov);
         layout.skip <- c(FALSE, TRUE, FALSE, FALSE, FALSE, TRUE);
         layout.height <- 3;
diff --git a/R/create.cluster.heatmap.R b/R/create.cluster.heatmap.R
index 645d743..7ccc55b 100644
--- a/R/create.cluster.heatmap.R
+++ b/R/create.cluster.heatmap.R
@@ -44,7 +44,7 @@ create.cluster.heatmap <- function(
         arr[arr > ccf.limits[2]] <- ccf.limits[2];
         }
 
-    if (is.numeric(arr)) {
+    if (!is.matrix(arr)) {
         arr <- as.data.frame(arr)
         colnames(arr) <- as.character(unique(DF$ID))
 

From e974d66900fc9c54540a50b012ee766180b2a89d Mon Sep 17 00:00:00 2001
From: Jieun Oh <jieunoh@mednet.ucla.edu>
Date: Fri, 22 Nov 2024 19:05:21 -0800
Subject: [PATCH 08/15] lintr

---
 R/create.ccf.summary.heatmap.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/create.ccf.summary.heatmap.R b/R/create.ccf.summary.heatmap.R
index 5e6dac8..9571e46 100644
--- a/R/create.ccf.summary.heatmap.R
+++ b/R/create.ccf.summary.heatmap.R
@@ -134,7 +134,7 @@ create.ccf.summary.heatmap <- function(
         hm.args$row.pos <- 1.5
         }
 
-    if(nrow(hm.args.x) == 1 & ncol(hm.args.x) == 1) {
+    if (nrow(hm.args.x) == 1 & ncol(hm.args.x) == 1) {
         legend.colour.change <- hm.col.scheme[length(hm.col.scheme)]
         hm.args$x <- as.data.frame(hm.col.scheme[length(hm.col.scheme)])
         hm.args$input.colours <- TRUE
@@ -166,7 +166,7 @@ create.ccf.summary.heatmap <- function(
         );
 
     if (!is.null(clone.colours)) {
-        if(length(clone.colours) == 1) {
+        if (length(clone.colours) == 1) {
         clone.cov <- BoutrosLab.plotting.general::create.heatmap(
             x = as.data.frame(clone.colours),
             xlab.label = 'Clone',

From b0d24b27c4c4a7096c53625f9ec6aa022e7453ba Mon Sep 17 00:00:00 2001
From: whelena <hwinata@mednet.ucla.edu>
Date: Thu, 20 Feb 2025 17:54:15 -0800
Subject: [PATCH 09/15] make yaxis.lab modifiable

---
 R/create.ccf.heatmap.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/create.ccf.heatmap.R b/R/create.ccf.heatmap.R
index e9893b3..17ff16b 100644
--- a/R/create.ccf.heatmap.R
+++ b/R/create.ccf.heatmap.R
@@ -5,6 +5,7 @@ create.ccf.heatmap <- function(
     distance.method = 'euclidean',
     xaxis.lab = '',
     xlab.label = 'SNVs',
+    yaxis.lab = colnames(x),
     print.colour.key = FALSE,
     colour.scheme = c('white', 'blue'),
     ...
@@ -21,7 +22,7 @@ create.ccf.heatmap <- function(
         cols.distance.method = distance.method,
         xaxis.lab = xaxis.lab,
         xlab.label = xlab.label,
-        yaxis.lab = colnames(x),
+        yaxis.lab = yaxis.lab,
         print.colour.key = print.colour.key,
         colourkey.labels.at = col.labels,
         colour.scheme = colour.scheme,

From 1ba7ee89c25daf0ff8d99a51da6550ce2a6aadc7 Mon Sep 17 00:00:00 2001
From: whelena <hwinata@mednet.ucla.edu>
Date: Thu, 20 Feb 2025 18:35:51 -0800
Subject: [PATCH 10/15] make heatmaps compatible with single sample

---
 R/create.ccf.summary.heatmap.R | 25 +++++++-----------
 R/create.cluster.heatmap.R     | 48 ++++++++++++++--------------------
 2 files changed, 29 insertions(+), 44 deletions(-)

diff --git a/R/create.ccf.summary.heatmap.R b/R/create.ccf.summary.heatmap.R
index b537d05..7b8b840 100644
--- a/R/create.ccf.summary.heatmap.R
+++ b/R/create.ccf.summary.heatmap.R
@@ -94,6 +94,7 @@ create.ccf.summary.heatmap <- function(
 
     same.as.matrix <- !is.matrix(arr)
     if (same.as.matrix) {
+        # I don't know why this sequence works but simply setting as.data.frame does not work
         arr <- as.data.frame(arr)
         colnames(arr) <- as.character(unique(DF$ID))
         arr <- as.matrix(arr)
@@ -105,6 +106,7 @@ create.ccf.summary.heatmap <- function(
     hm.args <- list(
         x = hm.args.x,
         cluster.dimensions = 'none',
+        clustering.method = 'none',
         xlab.label = 'Clone',
         xlab.cex = ifelse(is.null(clone.colours), subplot.xlab.cex, 0),
         xaxis.lab = rownames(arr),
@@ -129,22 +131,13 @@ create.ccf.summary.heatmap <- function(
         hm.args$text.col <- ifelse(arr > contrast.thres, 'white', 'black');
         }
 
-    if (same.as.matrix) {
-        hm.args$yat <- 1.5
-        hm.args$row.pos <- 1.5
-        }
-
     if (nrow(hm.args.x) == 1 & ncol(hm.args.x) == 1) {
-        legend.colour.change <- hm.col.scheme[length(hm.col.scheme)]
-        hm.args$x <- as.data.frame(hm.col.scheme[length(hm.col.scheme)])
-        hm.args$input.colours <- TRUE
-        hm.args$clustering.method <- 'none'
-        hm.args$yat <- 1
-        hm.args$col.pos <- 1.5
-        hm.args$row.pos <- 1
-        legend.col <- hm.col.scheme[length(hm.col.scheme)]
-        } else {
-        legend.col <- hm.col.scheme
+        colour.scheme <- colour.scheme[length(colour.scheme)];
+        hm.args$x <- as.data.frame(colour.scheme);
+        hm.args$input.colours <- TRUE;
+        hm.args$yat <- 1;
+        hm.args$col.pos <- 1.5;
+        hm.args$row.pos <- 1;
         }
 
     hm <- do.call(BoutrosLab.plotting.general::create.heatmap, hm.args);
@@ -154,7 +147,7 @@ create.ccf.summary.heatmap <- function(
             legend = list(
                 title = 'CCF',
                 labels = c(signif(min(arr), 2), rep('', legend.size), signif(max(arr), 2)),
-                colours = legend.col,
+                colours = colour.scheme,
                 border = 'black',
                 continuous = TRUE,
                 cex = legend.label.cex
diff --git a/R/create.cluster.heatmap.R b/R/create.cluster.heatmap.R
index 7ccc55b..d24d698 100644
--- a/R/create.cluster.heatmap.R
+++ b/R/create.cluster.heatmap.R
@@ -25,10 +25,10 @@ create.cluster.heatmap <- function(
     if (is.null(clone.colours)) {
         clone.colours <- get.colours(DF$clone.id, return.names = TRUE);
         }
-    DF              <- droplevels(DF)[order(DF$clone.id, -abs(DF$CCF)), ];
-    snv.order       <- unique(DF[, c('SNV.id', 'clone.id')]);
-    arr             <- data.frame.to.array(DF);
-    arr             <- arr[snv.order$SNV.id, rev(levels(DF$ID))];
+    DF        <- droplevels(DF)[order(DF$clone.id, -abs(DF$CCF)), ];
+    snv.order <- unique(DF[, c('SNV.id', 'clone.id')]);
+    arr       <- data.frame.to.array(DF);
+    arr       <- arr[snv.order$SNV.id, rev(levels(DF$ID))];
 
     if (!is.null(xaxis.col)) {
         xaxis.label <- unique(DF[DF$SNV.id %in% rownames(arr), xaxis.col]);
@@ -36,6 +36,13 @@ create.cluster.heatmap <- function(
         xaxis.label <- NULL;
         }
 
+    if (!is.matrix(arr)) {
+        arr <- t(arr);
+        yaxis.label <- levels(DF$ID);
+    } else {
+        yaxis.label <- colnames(arr);
+        }
+
     if (!is.null(ccf.limits)) {
         if (length(ccf.limits) != 2) {
             stop('ccf.limits must be a vector of length 2');
@@ -44,30 +51,15 @@ create.cluster.heatmap <- function(
         arr[arr > ccf.limits[2]] <- ccf.limits[2];
         }
 
-    if (!is.matrix(arr)) {
-        arr <- as.data.frame(arr)
-        colnames(arr) <- as.character(unique(DF$ID))
-
-        hm <- create.ccf.heatmap(
-            x = arr,
-            cluster.dimensions = 'none',
-            xlab.label = '',
-            xaxis.lab = xaxis.label,
-            colour.scheme = colour.scheme,
-            same.as.matrix = TRUE,
-            yat = 1.5,
-            ...
-            );
-    } else {
-        hm <- create.ccf.heatmap(
-            x = arr,
-            cluster.dimensions = 'none',
-            xlab.label = '',
-            xaxis.lab = xaxis.label,
-            colour.scheme = colour.scheme,
-            ...
-            );
-    }
+    hm <- create.ccf.heatmap(
+        x = arr,
+        cluster.dimensions = 'none',
+        xlab.label = '',
+        xaxis.lab = xaxis.label,
+        yaxis.lab = yaxis.label,
+        colour.scheme = colour.scheme,
+        ...
+        );
 
     cov <- BoutrosLab.plotting.general::create.heatmap(
         x = t(clone.colours[snv.order$clone.id]),

From 30d23f944e23d060f0f7b144d7a0f8a8ea4caf02 Mon Sep 17 00:00:00 2001
From: whelena <hwinata@mednet.ucla.edu>
Date: Fri, 21 Feb 2025 13:13:27 -0800
Subject: [PATCH 11/15] update NEWS.md

---
 NEWS.md                   | 1 +
 man/create.ccf.heatmap.Rd | 2 ++
 2 files changed, 3 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 64ddc85..5194d6f 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -12,6 +12,7 @@
 * Add option to use scale bars instead of y-axes.
 * Wrapper function for `SRCgrob` to automatically save plots to file
 * Add option to annotate the CCF summary heatmap with the cell values.
+* Add support for 1xn and 1x1 heatmaps.
 
 ## Update
 * Fixed angle calculation bug where child angles do not follow
diff --git a/man/create.ccf.heatmap.Rd b/man/create.ccf.heatmap.Rd
index 094748f..50ce5b4 100644
--- a/man/create.ccf.heatmap.Rd
+++ b/man/create.ccf.heatmap.Rd
@@ -12,6 +12,7 @@ create.ccf.heatmap(
     distance.method = 'euclidean',
     xaxis.lab = '',
     xlab.label = 'SNVs',
+    yaxis.lab = colnames(x),
     print.colour.key = FALSE,
     colour.scheme = c('white', 'blue'),
     ...
@@ -24,6 +25,7 @@ create.ccf.heatmap(
     \item{distance.method}{Defaults to \dQuote{euclidean}.}
     \item{xaxis.lab}{Defaults to an empty string.}
     \item{xlab.label}{Defaults to \dQuote{SNVs}.}
+    \item{xaxis.lab}{Defaults to the column names of array \code{x}.}
     \item{print.colour.key}{Defaults to \code{FALSE}.}
     \item{colour.scheme}{Defaults to \code{c('white', 'blue')}.}
     \item{...}{Pass through argument. See BoutrosLab.plotting.general::create.heatmap() for further details.}

From 97370ab856a06b3a2b207b79d0c96ef5a02897c1 Mon Sep 17 00:00:00 2001
From: whelena <hwinata@mednet.ucla.edu>
Date: Fri, 21 Feb 2025 13:25:17 -0800
Subject: [PATCH 12/15] fix documentation

---
 man/create.ccf.heatmap.Rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/man/create.ccf.heatmap.Rd b/man/create.ccf.heatmap.Rd
index 50ce5b4..763f67d 100644
--- a/man/create.ccf.heatmap.Rd
+++ b/man/create.ccf.heatmap.Rd
@@ -25,7 +25,7 @@ create.ccf.heatmap(
     \item{distance.method}{Defaults to \dQuote{euclidean}.}
     \item{xaxis.lab}{Defaults to an empty string.}
     \item{xlab.label}{Defaults to \dQuote{SNVs}.}
-    \item{xaxis.lab}{Defaults to the column names of array \code{x}.}
+    \item{yaxis.lab}{Defaults to the column names of array \code{x}.}
     \item{print.colour.key}{Defaults to \code{FALSE}.}
     \item{colour.scheme}{Defaults to \code{c('white', 'blue')}.}
     \item{...}{Pass through argument. See BoutrosLab.plotting.general::create.heatmap() for further details.}

From 0827db2a2c2d8a324736b5285183438a1196f168 Mon Sep 17 00:00:00 2001
From: whelena <hwinata@mednet.ucla.edu>
Date: Mon, 10 Mar 2025 16:01:44 -0700
Subject: [PATCH 13/15] address comments

---
 R/create.ccf.heatmap.R | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/R/create.ccf.heatmap.R b/R/create.ccf.heatmap.R
index 17ff16b..dcbcd4c 100644
--- a/R/create.ccf.heatmap.R
+++ b/R/create.ccf.heatmap.R
@@ -5,12 +5,16 @@ create.ccf.heatmap <- function(
     distance.method = 'euclidean',
     xaxis.lab = '',
     xlab.label = 'SNVs',
-    yaxis.lab = colnames(x),
+    yaxis.lab = NULL,
     print.colour.key = FALSE,
     colour.scheme = c('white', 'blue'),
     ...
     ) {
 
+    if (is.null(yaxis.lab)) {
+        yaxis.lab <- colnames(x);
+        }
+
     col.labels <- seq(min(x), max(x), length.out = 5);
 
     return(BoutrosLab.plotting.general::create.heatmap(

From 13221c2da28e4bd078de5264a6ef721a6f419ff4 Mon Sep 17 00:00:00 2001
From: whelena <hwinata@mednet.ucla.edu>
Date: Mon, 10 Mar 2025 16:39:16 -0700
Subject: [PATCH 14/15] fix documentation

---
 man/create.ccf.heatmap.Rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/man/create.ccf.heatmap.Rd b/man/create.ccf.heatmap.Rd
index 763f67d..0d82675 100644
--- a/man/create.ccf.heatmap.Rd
+++ b/man/create.ccf.heatmap.Rd
@@ -12,7 +12,7 @@ create.ccf.heatmap(
     distance.method = 'euclidean',
     xaxis.lab = '',
     xlab.label = 'SNVs',
-    yaxis.lab = colnames(x),
+    yaxis.lab = NULL,
     print.colour.key = FALSE,
     colour.scheme = c('white', 'blue'),
     ...

From 6f568d4da9f0858fff2aea32ac9c51f19156c024 Mon Sep 17 00:00:00 2001
From: Dan Knight <danknight@mednet.ucla.edu>
Date: Wed, 12 Mar 2025 13:41:47 -0700
Subject: [PATCH 15/15] Update date

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ab9d683..2d7e41c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: CancerEvolutionVisualization
 Title: Publication Quality Phylogenetic Tree Plots
 Version: 3.0.0
-Date: 2025-01-06
+Date: 2025-03-12
 Authors@R: c(
 	person("Paul Boutros", role = "cre", email = "PBoutros@mednet.ucla.edu"),
 	person("Adriana Salcedo", role = "aut"),
diff --git a/NEWS.md b/NEWS.md
index 5194d6f..74e7676 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# CancerEvolutionVisualization 3.0.0 (2025-01-06)
+# CancerEvolutionVisualization 3.0.0 (2025-03-12)
 
 ## Added
 * Dendrogram mode