R语言GEO数据处理（七）

# 6. 可视化展示 ----------------------------------------------------------------

##6.1 火山图

library(ggplot2)

p <- ggplot(data = deg,

aes(x = logFC,

y = -log10(P.Value))) +

geom_point(alpha=0.4, size=1.5,

aes(color=change)) +

ylab("-log10(Pvalue)")+

scale_color_manual(values=c("blue", "grey","red"))+

geom_vline(xintercept=c(-logFC,logFC),lty=4,col="black",lwd=0.8) +

geom_hline(yintercept = -log10(P.Value),lty=4,col="black",lwd=0.8) +

theme_bw()

p

###添加标签

x1 = deg %>%

filter(change == "up") %>%

head(5)

x2 = deg %>%

filter(change == "down") %>%

head(5)

label = rbind(x1,x2)

volcano_plot <- p +

geom_point(size = 1, shape = 1, data = label) +

ggrepel::geom_label_repel(data = label, aes(label = rownames(label)), color="black")

volcano_plot

##6.2 热图

#全部差异基因

cg = rownames(deg)[deg$change !="not"]

diff=exp2[cg,]

library(pheatmap)

annotation_col=data.frame(group=group_list)

rownames(annotation_col)=colnames(diff)

p3 <-  pheatmap(diff,

annotation_col=annotation_col,

scale = "row",

show_rownames = F,

show_colnames = F,

color = colorRampPalette(c("navy", "white", "red"))(50),

fontsize = 10,

fontsize_row = 3,

fontsize_col = 3)

p3