From 4450d3957607f8695503c35802ed6bb4d641fda0 Mon Sep 17 00:00:00 2001
From: xiangpin <xshuangbin@163.com>
Date: Tue, 1 Jul 2025 15:00:54 +0800
Subject: [PATCH 1/2] add citation

---
 DESCRIPTION |  3 ++-
 NAMESPACE   |  2 ++
 R/zzz.R     | 30 ++++++++++++++++++++++++++++++
 3 files changed, 34 insertions(+), 1 deletion(-)
 create mode 100644 R/zzz.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 4ad9aba..c6c4997 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -18,7 +18,8 @@ Imports:
   magrittr,
   methods,
   utils,
-  yulab.utils (>= 0.1.9)
+  yulab.utils (>= 0.1.9),
+  pillar
 Suggests:
   ggtree  
 URL: https://github.com/YuLab-SMU/aplot, https://yulab-smu.top/aplot/
diff --git a/NAMESPACE b/NAMESPACE
index a750dee..e424656 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -66,4 +66,6 @@ importFrom(patchwork,patchworkGrob)
 importFrom(patchwork,plot_annotation)
 importFrom(patchwork,plot_layout)
 importFrom(patchwork,plot_spacer)
+importFrom(pillar,style_subtle)
 importFrom(utils,modifyList)
+importFrom(utils,packageDescription)
diff --git a/R/zzz.R b/R/zzz.R
new file mode 100644
index 0000000..cf1cac5
--- /dev/null
+++ b/R/zzz.R
@@ -0,0 +1,30 @@
+#' @importFrom utils packageDescription
+#' @importFrom pillar style_subtle
+.onAttach <- function(libname, pkgname) {
+    pkgVersion <- packageDescription(pkgname, fields="Version")
+    msg <- paste0(pkgname, " v", pkgVersion, "  ",
+                  "For help: https://github.com/YuLab-SMU/aplot/issues", "\n\n")
+
+    citation <- paste0("If you use ", pkgname,
+                       " in published research, please cite the paper:\n\n",
+                       aplot_citations())
+    
+    packageStartupMessage(paste0(strwrap(pillar::style_subtle(paste0(msg, citation, suppressmsg(pkgname)))), collapse="\n"))
+}
+
+aplot_citations <- function(){
+    paste("Shuangbin Xu, Qianwen Wang, Shaodi Wen, Junrui Li, Nan He, Ming Li, Thomas Hackl, Rui Wang,
+          Dongqiang Zeng, Shixiang Wang, Shensuo Li, Chunhui Gao, Lang Zhou, Shaoguo Tao, Zijing Xie,
+          Lin Deng, and Guangchuang Yu.",
+          "aplot: Simplifying the creation of complex graphs to visualize associations across diverse data types.",
+          "The Innovation. 2025, 6(9):100958. doi: 10.1016/j.xinn.2025.100958\n\n",
+          "Export the citation to BibTex by citation('aplot')\n\n"
+    )    
+    
+}
+
+suppressmsg <- function(pkgname){
+    paste0("This message can be suppressed by:\n",
+        "suppressPackageStartupMessages(library(", pkgname ,"))"
+    )
+}

From 87637c90e91b618de5ef3985a56ddda4d9d02e53 Mon Sep 17 00:00:00 2001
From: xushuangbin <xshuangbin@163.com>
Date: Tue, 1 Jul 2025 16:51:39 +0800
Subject: [PATCH 2/2] fixed tag_levels issue of plot_list when ggplot2 > 3.5.2

---
 NAMESPACE     | 2 +-
 R/plot-list.R | 7 +++----
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index e424656..f515726 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -45,6 +45,7 @@ importFrom(ggplot2,element_text)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggplotGrob)
 importFrom(ggplot2,ggplot_add)
+importFrom(ggplot2,ggplot_build)
 importFrom(ggplot2,ggsave)
 importFrom(ggplot2,is.ggplot)
 importFrom(ggplot2,labs)
@@ -67,5 +68,4 @@ importFrom(patchwork,plot_annotation)
 importFrom(patchwork,plot_layout)
 importFrom(patchwork,plot_spacer)
 importFrom(pillar,style_subtle)
-importFrom(utils,modifyList)
 importFrom(utils,packageDescription)
diff --git a/R/plot-list.R b/R/plot-list.R
index 5a6a543..e2a71a1 100644
--- a/R/plot-list.R
+++ b/R/plot-list.R
@@ -22,7 +22,6 @@
 ##' @importFrom ggplot2 theme
 ##' @importFrom ggplot2 element_text
 ##' @importFrom ggplot2 labs
-##' @importFrom utils modifyList
 ##' @importFrom ggfun ggbreak2ggplot
 ##' @export
 ##' @author Guangchuang Yu
@@ -93,7 +92,7 @@ plot_list <- function(..., gglist = NULL,
 
 
 
-
+#' @importFrom ggplot2 ggplot_build
 plot_list2 <- function(gglist = NULL,
                       ncol = NULL, 
                       nrow = NULL, 
@@ -117,11 +116,11 @@ plot_list2 <- function(gglist = NULL,
                     )
 
     if (!is.null(tag_levels) || !is.null(labels)) {
-        pt <- p$theme$plot.tag
+        pt <- ggplot_build(p)$plot$theme$plot.tag
         if (is.null(pt)){
             pt <- ggplot2::element_text()
         }
-        pt <- modifyList(pt, list(size = tag_size))
+        pt$size <- tag_size
         p <- p + plot_annotation(tag_levels=tag_levels) &
             theme(plot.tag = pt)
     }