各位同学,大家好!
想必大家在安装R包的时候会遇到
Warning in install.packages :
package ‘ggscatter’ is not available (for R version 3.6.1)
上述的状况,这里主要说的是ggscatter包无法匹配R的3.6.1版本,所以我查看了一下自己的R版本(Tool>Global Options),确实是3.6.1。用如下程序进行更新(在R中操作):
install.packages("installr")
require(installr)
updateR()
在弹出的选择框里选择China(Lanzhou),如果用方法的话,下载的速度较快。
接下来,打开Rstudio>help>Check for Updates,如果这里有需要更新版本,就会有提示,点击后会直接跳转到Rstudio的更新界面。
完成了Rstudio版本的更新后,再次尝试下载ggscatter包,出现
Warning in install.packages :
package ‘ggscatter’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
我们打开此链接,没有发现有用的信息。在网上查到如下代码:
library(ggplot2)
diff <- read.csv("DEG.Out.csv",header = T)
logFC <-diff$logFC
adj <- diff$FDR
data <- data.frame(logFC=logFC,padj=padj)
data$sig[(data$padj > 0.05|data$padj=="NA")|(data$logFC < 0.5)& data$logFC > -0.5] <- "no"
data$sig[data$padj <= 0.05 & data$logFC >= 0.5] <- "up"
data$sig[data$padj <= 0.05 & data$logFC <= -0.5] <- "down"
# 选最大值作为xlim的上下边界
x_lim <- max(logFC,-logFC)
# 绘制火山图
library(ggplot2)
library(RColorBrewer)
pdf(file = "miRNA_volcano.pdf",width=8,height=8)
theme_set(theme_bw())
p <- ggplot(data,aes(logFC,-1*log10(padj),
color = sig))+geom_point()+
xlim(-5,5) + labs(x="log2(FoldChange)",y="-log10(FDR)")
p <- p + scale_color_manual(values =c("#0072B5","grey","#BC3C28"))+
geom_hline(yintercept=-log10(0.05),linetype=4)+
geom_vline(xintercept=c(-0.5,0.5),linetype=4)
p <- p +theme(panel.grid =element_blank())+
theme(axis.line = element_line(size=0))+ylim(0,15)
p <- p +guides(colour = FALSE)
p <- p +theme(axis.text=element_text(size=20),axis.title=element_text(size=20))
p
dev.off()
print(p)
下一步,就是去尝试一下了。