# 安装包
if (!requireNamespace("EnhancedVolcano", quietly = TRUE)) {
install_github('kevinblighe/EnhancedVolcano')
}
# 加载包
library(EnhancedVolcano)
MA 图
注记
Hiplot 网站
本页面为 Hiplot EnhancedMA
插件的源码版本教程,您也可以使用 Hiplot 网站实现无代码绘图,更多信息请查看以下链接:
差异表达基因可视化。
环境配置
系统: Cross-platform (Linux/MacOS/Windows)
编程语言: R
依赖包:
EnhancedVolcano
数据准备
# 加载数据
<- read.delim("files/Hiplot/143-pseudo-enhanced-ma-data.txt", header = T)
data
# 整理数据格式
row.names(data) <- data[,1]
<- data[,-1]
data $baseMeanNew <- 1 / (10^log(data$baseMean + 1))
data
# 查看数据
head(data)
baseMean log2FoldChange lfcSE stat pvalue
COL6A3 8.494143e+04 -0.34453583 0.07607842 -4.5305972 5.881720e-06
ZNF157 2.456747e+00 -0.42976616 0.33693867 -1.2957785 1.950518e-01
RPL23P11 0.000000e+00 NA NA NA NA
SCARNA10 4.406548e-01 -0.05657159 0.15265730 -0.2329492 8.158009e-01
RNU6-857P 0.000000e+00 NA NA NA NA
TOPORS 5.331777e+02 0.10709656 0.12572643 0.8549637 3.925712e-01
padj baseMeanNew
COL6A3 6.207728e-05 4.469624e-12
ZNF157 NA 5.750056e-02
RPL23P11 NA 1.000000e+00
SCARNA10 NA 4.314220e-01
RNU6-857P NA 1.000000e+00
TOPORS 6.148749e-01 5.239278e-07
可视化
# MA 图
<- EnhancedVolcano(
p lab = rownames(data), title = "MA plot", subtitle = "EnhancedMA",
data, x = 'log2FoldChange', y = 'baseMeanNew', xlab = bquote(~Log[2]~ 'fold change'),
ylab = bquote(~Log[e]~ 'base mean + 1'), ylim = c(0,12),
pCutoff = as.numeric(1e-05), FCcutoff = 1, pointSize = 3.5,
labSize = 4, boxedLabels = T, colAlpha = 1,
legendLabels = c('NS', expression(Log[2]~FC),
'Mean expression',
expression(Mean-expression~and~log[2]~FC)),
legendPosition = "bottom", legendLabSize = 16, legendIconSize = 4.0,
encircleCol = 'black', encircleSize = 2.5, encircleFill = 'pink',
encircleAlpha = 1/2) +
coord_flip() +
theme(text = element_text(family = "Arial"),
plot.title = element_text(size = 12,hjust = 0.5),
axis.title = element_text(size = 12),
axis.text = element_text(size = 10),
axis.text.x = element_text(angle = 0, hjust = 0.5,vjust = 1),
legend.title = element_text(size = 10),
legend.text = element_text(size = 10))
p
