什么是倾斜45度的火山图？-技术圈

今天是转录组培训最后一天，剩下一点时间自由探索。朋友们来自山南海北，还是北京的最多。

一位老师聊起火山图（Volcano plot | 别再问我这为什么是火山图（在线轻松绘制）），说见过倾斜45度的类似图，可否演示怎么画？想了下，可能是下面这种图，绘起来看看。

检查和安装包

a = rownames(installed.packages())
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager", repos = site)

a = rownames(installed.packages())

install_bioc <-
  c(
    "egg",
    "ggpubr",
    "ggplot2"
  )

for (i in install_bioc) {
  if (!i %in% a)
    BiocManager::install(i, update = F)
}

if (!"ImageGP" %in% a){
  # devtools::install_github("Tong-Chen/ImageGP")
  devtools::install_git("https://gitee.com/ct5869/ImageGP.git")
}

library(ImageGP)
library(ggplot2)
library(ggpubr)
library(egg)

读入数据并标记差异基因

数据是基于DESeq2分析的差异基因数据。

file <- "data/ehbio.simplier.DESeq2.trt._vs_.untrt.results.txt"

diffexpr <- sp_readTable(file, row.names=1)

# 做一个log转换
diffexpr$trt <- log2(diffexpr$trt+1)
diffexpr$untrt <- log2(diffexpr$untrt+1)

head(diffexpr)

##                      trt     untrt baseMean log2FoldChange    pvalue      padj
## ENSG00000152583 10.88130  6.354646  983.042          4.546 1.219e-91 2.149e-87
## ENSG00000189221 12.09256  8.706410 2391.559          3.387 9.955e-61 8.779e-57
## ENSG00000179094 10.40316  7.343044  757.249          3.065 2.435e-54 1.432e-50
## ENSG00000116584 10.50370 11.567470 2242.427         -1.064 3.957e-49 1.745e-45
## ENSG00000120129 12.55314  9.579082 3386.426          2.975 1.930e-48 6.807e-45
## ENSG00000134686 12.04738 10.587715 2884.847          1.460 1.846e-45 5.427e-42

标记差异基因

diffexpr$level <- ifelse(diffexpr$padj<0.05, 
                         ifelse(diffexpr$log2FoldChange>=1, "trt up", 
                                ifelse(diffexpr$log2FoldChange<=-1, "untrt up", "NoSig")),"NoSig")
head(diffexpr)

##                      trt     untrt baseMean log2FoldChange    pvalue      padj    level
## ENSG00000152583 10.88130  6.354646  983.042          4.546 1.219e-91 2.149e-87   trt up
## ENSG00000189221 12.09256  8.706410 2391.559          3.387 9.955e-61 8.779e-57   trt up
## ENSG00000179094 10.40316  7.343044  757.249          3.065 2.435e-54 1.432e-50   trt up
## ENSG00000116584 10.50370 11.567470 2242.427         -1.064 3.957e-49 1.745e-45 untrt up
## ENSG00000120129 12.55314  9.579082 3386.426          2.975 1.930e-48 6.807e-45   trt up
## ENSG00000134686 12.04738 10.587715 2884.847          1.460 1.846e-45 5.427e-42   trt up

基于ImageGP绘图

p <- sp_scatterplot(diffexpr, xvariable = "trt", yvariable = "untrt", 
               color_variable = "level",
               color_variable_order = c("NoSig","trt up", "untrt up"),
               manual_color_vector = c("grey","firebrick","dodgerblue"),
               legend.position = c(0.8,0.3)) + coord_fixed(1)
p

到这满足需求了，又有老师说能不能加上数据分布展示？

拼上Marginal plot

xplot <- ggplot(diffexpr, aes(x=trt)) + geom_histogram(fill="firebrick") +
  theme_classic() + 
  theme(axis.line.x=element_blank(), 
        axis.ticks.x=element_blank(), 
        axis.text.x = element_blank(), 
        axis.title.x = element_blank(),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank(),
        panel.border = element_blank(),
        panel.background = element_blank(),
        legend.title = element_blank(),
        legend.position = c(0.75,0.85),
        #legend.title = element_text(size = 5), 
        legend.text  = element_text(size = 8),
        legend.key.size = unit(0.5, "lines"),
        legend.spacing = unit(0.3, "cm"),
  ) + ylab("Density")
xplot

yplot <- ggplot(diffexpr, aes(x=untrt)) + geom_histogram(fill="dodgerblue") +
  theme_classic() +
  theme(axis.line.y=element_blank(),  
        axis.ticks.y=element_blank(), 
        axis.text.y = element_blank(), 
        axis.title.y=element_blank(),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank(),
        panel.border = element_blank(),
        panel.background = element_blank(),
        legend.title = element_blank(),
        legend.position = c(0.7,0.8),
        #legend.title = element_text(size = 5), 
        legend.text  = element_text(size = 8),
        legend.key.size = unit(0.5, "lines"),
        legend.spacing = unit(0.3, "cm"),
        ) + ylab("Density") +
  rotate()
yplot

合并起来

white <- ggplot() + theme_void()

egg::ggarrange(xplot, white, p, yplot, 
               widths=c(5,2),heights = c(2,5),padding=unit(0,"line"))

也可以用现成的工具

用ggpubr绘制

ggscatterhist(diffexpr, x="trt", y="untrt", color="level",
              palette=c("grey","firebrick","dodgerblue"), margin.plot="histogram" )

输出数据用在线工具绘制

见次条

高颜值免费在线绘图工具

http://www.ehbio.com/Cloud_Platform/front/#/analysis?page=b%27MTI%3D%27

sp_writeTable(diffexpr, file="DE_gene_label.txt")

数据和代码见 https://gitee.com/ct5869/shengxin-baodian/Plot

往期精品(点击图片直达文字对应教程)

机器学习

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