R语言编程

20231005_利用 UpSetR 包进行高效的交集数据可视化

Song Wei 2023年10月5日 22:31

352

UpSetR 是一个 R 语言的包，用于创建 UpSet 图，这是一种用于可视化交集的创新图形。传统的维恩图（Venn图）在处理超过5个集合的交集时会变得复杂且难以阅读。相比之下，UpSetR 通过垂直的条形图来表示交集的大小，可以更好地处理大量的集合交集。

BiocManager::install("UpSetR")
#载入UpSetR包
library(UpSetR)
data <- read.table("final_result_for_upset_plot-ok-2.txt", header=TRUE, sep="\t",row.names = 1 )
head(data)

> head(data)
                   circbase circpedia riboCIRC transcirc
chr1_24737_24891          1         0        0         0
chr1_324438_324686        1         0        0         0
chr1_586820_586955        0         1        0         0
chr1_632324_632413        0         1        0         0
chr1_667396_667587        1         0        0         0
chr1_667396_675566        1         0        0         0



upset(data, sets = colnames(data), order.by = "freq")
bar_colors = c("red", "black", "black", "red")
upset(data, sets = colnames(data), order.by = "freq",sets.bar.color = bar_colors)

queries = list(
  list(
    query = intersects,
    params = list("circbase","circpedia","riboCIRC","transcirc"),
    color = "orange",  
    active = T
  )
)
upset(data,
      sets = colnames(data),  
      order.by = "freq",
      sets.bar.color = bar_colors,
      queries = queries)



queries = list(
  list(
    query = intersects,
    params = list("circbase","circpedia","riboCIRC","transcirc"),
    color = "orange",
    active = T
  ),
  list(
    query=intersects, 
    params=c("riboCIRC","transcirc"),
    color = "orange",  
    active = T
  )  
)
upset(data,
      sets = colnames(data),  
      order.by = "freq",
      sets.bar.color = bar_colors,
      queries = queries)
upset(data, sets = colnames(data), order.by = "freq", sets.bar.color = bar_colors, queries = queries, point.size = 4, line.size = 1, text.scale = c(1.3, 1.3, 1.3, 1.3, 1.3, 1.5) ,mb.ratio = c(0.65, 0.35) )  
# 开始PDF设备
pdf("my_upset_plot.pdf", width = 12, height = 8)
upset(data, sets = colnames(data), order.by = "freq", sets.bar.color = bar_colors, queries = queries, point.size = 4, line.size = 1, text.scale = c(1.3, 1.3, 1.3, 1.3, 1.3, 1.5) ,mb.ratio = c(0.65, 0.35) )  
# 关闭PDF设备
dev.off()