From ff6ac698d895a370a1996f02adcf03886601e6cb Mon Sep 17 00:00:00 2001
From: Bingxin Lu <soulsophia@gmail.com>
Date: Mon, 13 Mar 2023 15:22:41 +0000
Subject: [PATCH] add option to adjust font size in heatmap

---
 util/plot-trees-all.R | 24 ++++++++++++++++++++++++
 util/plot-util.R      | 23 +----------------------
 2 files changed, 25 insertions(+), 22 deletions(-)

diff --git a/util/plot-trees-all.R b/util/plot-trees-all.R
index 1b94730..f7e6016 100644
--- a/util/plot-trees-all.R
+++ b/util/plot-trees-all.R
@@ -63,6 +63,8 @@ option_list = list(
               help="The width for the plot [default=%default]", metavar="numeric"),              
   make_option(c("", "--height"), type="numeric", default = 5,
               help="The height for the plot [default=%default]", metavar="numeric"),
+  make_option(c("", "--font_size"), type="numeric", default = 6,
+              help="The font size for labels on the heatmap plot [default=%default]", metavar="numeric"),              
   make_option(c("-m", "--mut_rate"), type="numeric", default = 0,
               help="The rate of somatic chromosomal aberrations [default=%default]", metavar="numeric"),
   make_option(c("-u", "--dup_rate"), type="numeric", default = 0,
@@ -127,6 +129,28 @@ title = opt$title
 seed = opt$seed
 height = opt$height
 width = opt$width
+font_size = opt$font_size
+
+theme1 = theme(legend.position = "none",
+               #strip.text.x = element_blank(),
+               #strip.text.y = element_blank(),
+               strip.text.y.left = element_text(size=font_size, angle=0),
+               strip.background = element_blank(),
+               axis.line.x = element_blank(),
+               axis.line.y = element_blank(),
+               axis.text.x = element_blank(),
+               axis.text.y = element_blank(),
+               axis.title.y = element_blank(),
+               axis.title.x = element_blank(),
+               axis.ticks.x = element_blank(),
+               axis.ticks.y = element_blank(),
+               panel.grid.minor = element_blank(),
+               panel.grid.major = element_blank(),
+               panel.spacing.y = unit(0, "lines"),
+               panel.spacing.x = unit(0, "lines"),
+               panel.border = element_rect(color = "#d8d8d8", fill = NA, size = .2),
+               panel.background = element_rect(fill = "#f0f0f0")
+)
 
 if(!is.na(seed)) set.seed(seed)
 
diff --git a/util/plot-util.R b/util/plot-util.R
index f7effb5..e33c6e2 100644
--- a/util/plot-util.R
+++ b/util/plot-util.R
@@ -20,27 +20,6 @@ suppressMessages(library(ggpubr))
 # 3) plotting all tree files in a directory
 
 
-theme1 = theme(legend.position = "none",
-               #strip.text.x = element_blank(),
-               #strip.text.y = element_blank(),
-               strip.text.y.left = element_text(size=6, angle = 0),
-               strip.background = element_blank(),
-               axis.line.x = element_blank(),
-               axis.line.y = element_blank(),
-               axis.text.x = element_blank(),
-               axis.text.y = element_blank(),
-               axis.title.y = element_blank(),
-               axis.title.x = element_blank(),
-               axis.ticks.x = element_blank(),
-               axis.ticks.y = element_blank(),
-               panel.grid.minor = element_blank(),
-               panel.grid.major = element_blank(),
-               panel.spacing.y = unit(0, "lines"),
-               panel.spacing.x = unit(0, "lines"),
-               panel.border = element_rect(color = "#d8d8d8", fill = NA, size = .2),
-               panel.background = element_rect(fill = "#f0f0f0")
-)
-
 # cn_colors1 = c("#6283A9","#bdd7e7","#f0f0f0","#FCAE91", "#B9574E", "#76000D", "#8B0000", "#000000")
 # Max CN to show in heatmap
 MAX_CN = 6
@@ -966,7 +945,7 @@ plot.tree.ci.node.mut.smpl <- function(tree_ci, title = "", lextra = 0, rextra =
   xl = 0 - lextra
 
   p <- ggtree(tree_ci)
-  p <- p + geom_tiplab() + ggtitle(title)
+  p <- p + geom_tiplab() + ggtitle(title) + geom_treescale()
 
   if(has_inode_label){
     p <- p + geom_text2(aes(subset = !isTip, label = label), hjust = -0.3)