绘制基因差异表达泡泡图

今天小果绘制一下基因在不同组织中差异表达的泡泡图，代码如下：

1. 安装所需要的R包

install.packages(“ggplot2”)

install.packages(“tidyverse”)

BiocManager::install(“ComplexHeatmap”)

1. 导入需要的R包

library(ggplot2)

library(tidyverse)

library(ComplexHeatmap)

3读取数据

exprTab<-read.table(“expr.txt”,header=T)

4.代码展示

# 产生泡泡图

orange <- “#E45737”

green <- “#6F8B35”

blue <- “#4577FF”

red <- “#C2151A”

#确定基因因子顺序

exprTab$gene <- factor(exprTab$gene,

levels=rev(c(“CDKN1A”,”HSPA5″,”TTC35″,”SLC7A11″,”NFE2L2″,”MT1G”,”HSPB1″,”GPX4″,”FANCD2″,”CISD1″, “FDFT1″,”SLC1A5″,”SAT1″,”TFRC”,”RPL8″,”NCOA4″,”LPCAT3″,”GLS2″,”DPP4″,”CS”,”CARS”,”ATP5G3″,”ALOX15″,”ACSL4″)))

my_palette <- colorRampPalette(c(green,”white”,orange), alpha=TRUE)(n=128)

p <- ggplot(exprTab, aes(x=tumor,y=gene)) +

geom_point(aes(size=-log10(FDR),color=log2fc)) +

scale_color_gradientn(‘log2(FC)’,

colors=my_palette) +

theme_bw() +

theme(#panel.grid.minor = element_blank(),

#panel.grid.major = element_blank(),

axis.text.x = element_text(angle = 45, size = 12, hjust = 0.3, vjust = 0.5, color = “black”),

axis.text.y = element_text(size = 12, color = rep(c(red,blue),c(14,10))),

axis.title = element_blank(),

panel.border = element_rect(size = 0.7, linetype = “solid”, colour = “black”),

plot.margin = unit(c(0,0,1,1), “lines”))

ggsave( p,file=”Bubbleplot.pdf”, width = 8, height = 8)

泡泡图最终完整的展现出来了，有需要的小伙伴可以借鉴学习奥。