关于火山图，绘制的教程有很多也有不少专门绘制火山图的包，说到底火山图无非就是散点图的变形，本节来介绍如何通过ggpotl2绘制火山图
安装&加载R包
package.list=c("tidyverse","ggrepel")
for (package in package.list) {
if (!require(package,character.only=T, quietly=T)) {
install.packages(package)
library(package, character.only=T)
}
}
ctrl+shift+M 即可打出 管道符号 %>%
数据清洗
根据padj & log2FoldChange判断差异是否显著
df <- read_tsv("genes.counts..DESeq2.xls") %>%
mutate(gene_type=if_else(
padj > 0.05,"ns",if_else(
abs(log2FoldChange) < 1,"ns",
if_else(log2FoldChange >=1,"up","down"))),
FC=2**log2FoldChange)
统计上下调基因个数
df %>% group_by(gene_type) %>%
summarise(count=n())
自定义颜色
cols <- c("up [1395]"="#FF0000","down [1463]"="#00A08A","ns [28078]"="grey")
数据可视化
ggplot(df %>% mutate(gene_type=case_when(
gene_type =="up" ~ "up [1395]",
gene_type =="down" ~ "down [1463]",
gene_type =="ns" ~ "ns [28078]")),aes(log2FoldChange,-log10(pvalue))) +
geom_point(aes(color=gene_type,size=abs(log2FoldChange)))+
geom_hline(yintercept = -log10(0.05),linetype ="dashed") +
geom_vline(xintercept = c(-1,1),linetype = "dashed")+
geom_label_repel(data=df %>%
filter(abs(log2FoldChange) >3,padj < 1e-100,
id %in% c("TF31923","TF00970","TF26429")),
aes(label=id))+
scale_color_manual(values = cols) +
scale_size(range=c(0.1,3))+
guides(size="none")+
scale_x_continuous(breaks=c(seq(-10,10,2)),limits = c(-10,10))+
theme(panel.grid.major=element_blank(), # 移除主网格线
panel.grid.minor=element_blank(), # 移除次网格线
panel.background = element_blank(), # 设置背景为空
axis.title.x=element_text(color="black",size=11,margin = margin(t = 5)),
axis.title.y=element_text(color="black",size=11,margin = margin(t = 5)),
axis.text.x=element_text(color="black",margin = margin(t = 5)), # 设置X轴文本颜色
axis.text.y=element_text(color="black",margin = margin(r = 5)), # 设置y轴文本颜色
panel.border = element_rect(linetype = "solid",fill = NA), # 定义边框线条类型
plot.margin=unit(c(0.5,0.5,0.5,0.5),units=,"cm"),
legend.title = element_blank(),
legend.key=element_blank(), # 图例键为空
legend.text = element_text(color="black",size=10), # 定义图例文本
legend.spacing.x=unit(0,'cm'), # 定义文本书平距离
legend.background=element_blank(), # 设置背景为空
legend.box.background=element_rect(colour = "black"), # 图例绘制边框
legend.box.margin = margin(1,1,1,1),
legend.position = c(0,1),legend.justification = c(0,1))
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R语言数据分析指南，持续分享数据可视化的经典案例及一些生信知识，希望对大家
