GO圈图

作者

[编辑] 郑虎;

[审核] .

GO圈图用于显示圆图结合了基因表达和基因注释富集数据。术语的子集与GOBar图一起显示与基因表达数据的散点图结合使用。整个图都在特定的坐标系上绘制，以实现圆形布局。该段标记为术语ID。

环境配置

  • 系统: Cross-platform (Linux/MacOS/Windows)

  • 编程语言: R

  • 依赖包: GOplot; ggplotify

# 安装包
if (!requireNamespace("GOplot", quietly = TRUE)) {
  install.packages("GOplot")
}
if (!requireNamespace("ggplotify", quietly = TRUE)) {
  install.packages("ggplotify")
}

# 加载包
library(GOplot)
library(ggplotify)

数据准备

加载的数据是具有七个列的GO富集的结果：category, GO id, GO term, gene count, gene name, logFC, adjust pvalue and zscore。

# 加载数据
data <- read.delim("files/Hiplot/079-gocircle-data.txt", header = T)

# 整理数据格式
colnames(data) <- c("category","ID","term","count","genes","logFC","adj_pval","zscore")
data <- data[!is.na(data$adj_pval),]
data$adj_pval <- as.numeric(data$adj_pval)
data$zscore <- as.numeric(data$zscore)
data$count <- as.numeric(data$count)

# 查看数据
head(data)
  category         ID              term count  genes      logFC adj_pval
1       BP GO:0007507 heart development    54   DLC1 -0.9707875 2.17e-06
2       BP GO:0007507 heart development    54   NRP2 -1.5153173 2.17e-06
3       BP GO:0007507 heart development    54   NRP1 -1.1412315 2.17e-06
4       BP GO:0007507 heart development    54   EDN1  1.3813006 2.17e-06
5       BP GO:0007507 heart development    54 PDLIM3 -0.8876939 2.17e-06
6       BP GO:0007507 heart development    54   GJA1 -0.8179480 2.17e-06
      zscore
1 -0.8164966
2 -0.8164966
3 -0.8164966
4 -0.8164966
5 -0.8164966
6 -0.8164966

可视化

# GO圈图
p <- function () {
  GOCircle(data, title = "GO Enrichment Circleplot",
           nsub = 10, rad1 = 2, rad2 = 3, table.legend = T, label.size = 5,
           zsc.col = c("#FC8D59","#FFFFBF","#99D594")) + 
    theme(plot.title = element_text(hjust = 0.5))
}
p <- as.ggplot(p)

p
图 1: GO圈图

如示例图所示，外圈显示了分配基因的logFC的每个项的散点图。默认情况下，红色圆圈显示上调和蓝色的下调。