MAplot转录组差异基因表达展示

之前有小伙伴咨询一幅差异基因展示的图，我随口就说这类似于火山图，就是点图，ggplot就可以完成，不晓得他最后做出来没有。对了，之前Bulk RNA转录组系列关于DESeq2的帖子，封面图就是这样的。术语叫做MAplot，展示数据分布情况的可视化！

 

最近在文献中看到这样的差异基因展示方式，所以复现一下。这里我们从counts矩阵的转录组差异分析开始做这个图，很简单，原理就是散点图，按照火山图的做法筛选差异基因即可。重试差异分析：

setwd('D:/KS项目/公众号文章/MAplot')
data <- read.csv('counts.csv', header = T, row.names = 1)
genecounts <- data[apply(data, 1, sum) > 0, ]
SampleAnno <- data.frame(condition = factor(rep(c('neg', 'pos'), each = 3),
                                            levels = c('neg', 'pos')))
library(dplyr)
library(ggplot2)
library(RColorBrewer)
library(DESeq2)
library(ggrepel)


dds <- DESeqDataSetFromMatrix(countData=genecounts, colData=SampleAnno, design= ~condition)
dds1 <- dds
dds1 <- DESeq(dds1)
res <- results(dds1, contrast = c('condition', 'pos', 'neg'))
res <- as.data.frame(res)
write.csv(res, file = 'DEGs.csv')#差异分析结果

构建数据：

df <- as.data.frame(counts(dds1, normalized=TRUE))
df_merge = merge(res,df,by ='row.names')
rownames(df_merge) = df_merge$Row.names
df_merge = select(df_merge,-1)
#挑选需要展示的差异基因
genes = c("CLSTN2",
          "MME",
          "SYNPO",
          "ENC1",
          "PDGFRB",
          "TAGLN3",
          "ZFHX4",
          "THY1",
          "CYP26A1",
          "RGS4",
          "CDH10",
          "JAM2",
          "LMX1B",
          "NTRK1",
          "ST8SIA1",
          "FUT9",
          "DOK5",
          "CABP7",
          "APOL6",
          "CHI3L1")

添加label：

df_merge$label = ifelse(rownames(df_merge) %in% genes,rownames(df_merge),"")
df_merge$condition = ifelse(df_merge$log2FoldChange >= 1 & df_merge$padj < 0.01,"UP",
                      ifelse(df_merge$log2FoldChange <= -1 & df_merge$padj < 0.01,"DOWN","none"))
df_merge$condition = ifelse(rownames(df_merge) %in% genes,"label",df_merge$condition)

ggplot2作图：

ggplot(df_merge,aes(x=baseMean,y=log2FoldChange)) +
  geom_point(aes(color=condition,size = condition,alpha = condition),
             show.legend = F) +
  geom_hline(yintercept =  c(-1,1),lty=2,lwd = 1) +
  theme_bw(base_size = 12) + 
  ggtitle("Neg vs Pos") + 
  scale_color_manual(values = c("cadetblue","black","grey","darkorange")) +
  scale_size_manual(values = c(1.5,2,1.5,1.5)) +
  scale_alpha_manual(values = c(0.6,1,0.6,0.6)) +
  scale_x_log10() + 
  theme(panel.grid=element_blank()) +
  scale_y_continuous(limits = c(-10,8),breaks = c(-10,-5,0,4,8)) +
  xlab("Mean Normalized Counts") + 
  ylab("log2FoldChange")+
  geom_text_repel(aes(label=label), color="black",fontface="italic", 
                  size=4, segment.size=0.5,hjust=0,
                  nudge_x=1, nudge_y = 1)

 

效果和火山图差不多，就是一个展现形式而已，萝卜青菜各有所爱！示例数据及代码已上传群文件！更多精彩请至我的公众号---KS科研分享与服务！