使用UpSetR绘制个性化UpSet图的技术问题求助

一、UpSetR 三大需求实现 #

1. 解决条形图上方数字重叠问题 #

直接调整text.scale参数缩小标签字号，针对性优化条形上方的计数标签，避免重叠：

# text.scale参数顺序：标题、横轴标签、纵轴标签、集合标签、条形上方数字、图例文字
upsetPlot <- upset(
  fromList(combined),
  text.scale = c(1.2, 1.2, 1, 1, 0.8, 1),
  order.by = "freq", 
  keep.order = T, 
  sets = rev(c("c0_prt", "c0_24h", "c4_12w", "c5_12w", "c7_12w"))
)

2. 坐标轴刻度改为科学计数法 #

利用你定义的fancy_scientific()函数，通过mainbar.y.scale参数替换纵轴刻度：

# 保留你的科学计数法转换函数
fancy_scientific <- function(l) {
  l <- gsub("^0","0", l)
  l <- format(l, scientific = TRUE)
  l <- gsub("^(.*)e", "'\\1'e", l)
  l <- gsub("e", "%*%10^", l)
  parse(text=l)
}

# 绘图时指定纵轴刻度转换
upsetPlot <- upset(
  fromList(combined),
  mainbar.y.scale = fancy_scientific,
  text.scale = c(1.2, 1.2, 1, 1, 0.8, 1),
  order.by = "freq", 
  keep.order = T, 
  sets = rev(c("c0_prt", "c0_24h", "c4_12w", "c5_12w", "c7_12w"))
)

3. 修改集合条形和交集点的颜色 #

给sets.bar.color传颜色向量设置每个集合的条形颜色，用point.color自定义交集点颜色：

# 自定义5个集合的条形颜色
set_colors <- c("#E69F00", "#56B4E9", "#009E73", "#F0E442", "#D55E00")

upsetPlot <- upset(
  fromList(combined),
  sets.bar.color = set_colors,
  point.color = "#CC79A7", # 交集点统一颜色，也可传向量对应不同交集
  mainbar.y.scale = fancy_scientific,
  text.scale = c(1.2, 1.2, 1, 1, 0.8, 1),
  order.by = "freq", 
  keep.order = T, 
  sets = rev(c("c0_prt", "c0_24h", "c4_12w", "c5_12w", "c7_12w"))
)
upsetPlot

二、ComplexUpset 用法及集合标签加粗 #

ComplexUpset基于ggplot2，灵活性更强，实现步骤如下：

1. 数据格式转换 #

先将列表转成tidy格式的data.frame：

library(ComplexUpset)
library(tidyr)
library(ggplot2)

# 转换为适合ComplexUpset的格式
combined_df <- enframe(combined, name = "set", value = "element") %>%
  unnest(value) %>%
  pivot_wider(names_from = set, values_from = set, values_fn = ~!is.na(.x), values_fill = FALSE)

2. 绘图并设置集合标签加粗 #

通过theme()中的axis.text.y设置集合标签为加粗字体，同时支持自定义颜色等样式：

upset(
  combined_df,
  intersect = colnames(combined_df)[-1], # 指定集合列
  set_order = rev(c("c0_prt", "c0_24h", "c4_12w", "c5_12w", "c7_12w")),
  sort_intersections_by = 'cardinality',
  # 设置集合条形颜色
  set_sizes = aes(fill = set),
  geom_set_size = geom_bar(show.legend = FALSE),
  fill = set_colors,
  # 设置交集点颜色
  geom_point = geom_point(color = "#CC79A7", size = 3),
  # 集合标签加粗
  theme = theme(
    axis.text.y = element_text(face = "bold", size = 11),
    # 可选：调整横轴标签字号避免重叠
    axis.text.x = element_text(size = 9)
  )
)

内容的提问来源于stack exchange，提问作者Matteo