火山图（volcano plot） 是散点图的一种，它将统计学中的显著性度量和变化幅度相结合，从而能够帮助我们快速直观地识别那些变化幅度较大且具有统计学意义的对象。本篇文章将简单介绍应用ggplot2进行火山图的绘制，当然这肯定是不够放在文章上面的，相关的细节调整还需要进行个性化的学习。前面提到火山图可以...
library(volcano3Ddata) # Basic DESeq2 set up library(DESeq2) library(ggplot2) library(kableExtra) 3.5 数据展示 结合示例数据进行准备数据,基本与我们平时做差异分析数据保持一致,或是你直接使用DESep2做差异分析,使用其结果进行绘图。 citation("volcano3D") ## ## To cite package 'volcano3D' in public...
library(ggplot2) ggplot(DEG, aes(x = logFC, y = -log10(PValue), colour=Sig)) + geom_point(alpha=0.4, size=3.5) + scale_color_manual(values=c("#546de5", "#d2dae2","#ff4757"))+ # 辅助线 geom_vline(xintercept=c(-1,1),lty=4,col="black",lwd=0.8) + geom_hline(yinter...
volcano plot ZM3 May 2019 火山图 火山图,它用于展示不同组样本间基因表达水平差异的分布,横轴为Log2 Fold Change;纵轴为(-1)*Log10 Pvalue,纵坐标值越大差异越显著。一般横轴越偏离中心的点其纵轴值也会比较大,因此呈现火山喷发的形状。今天小编为大家介绍下如何用R语言ggplot2包绘制火山图。 数据准备 ...
setwd("C:\\Users\\FengLei\\Desktop\\scatter-plot") library(ggplot2) library(ggthemes) library(Cairo) data=read.csv("control-vs-e7107-deseq2.csv", head=T) ### 火山图 data$threshold = as.factor(ifelse(data$pvalue =1, 'Up', ifelse(data$pvalue < 0.05 & data$log2FoldChange <=...
library(ggplot2) plot1<-ggplot(mtcars,aes(x=factor(cyl),fill=factor(gear)))+ geom_bar(width = 0.5)+ labs(title = "Here is title", subtitle = "Here is subtitle", caption = "R2-12", x = "cyl") plot1 #creat a new theme ...
如果之前提供了fold change列,则可以使用 invoice_trio 函数调查病理类型之间的比较。这将创建 ggplot 输出: 代码语言:javascript 代码运行次数:0 运行 AI代码解释 syn_plots<-volcano_trio(polar=syn_polar,sig_names=c("significant","significant","not significant","not significant"),colours=rep(c("slateblue...
options(repr.plot.width=6, repr.plot.height=6) ggplot(data.df,aes(x=log2FC, y=-log10(p_value))) + geom_hline(aes(yintercept=1), colour="grey50", linetype="dashed", size=0.2) + #geom_vline(aes(xintercept=0.5), colour="red", linetype="dashed", size=0.2) + ...
data.df$gene<-rownames(data.df)## colordata.df$color<-"black"data.df[data.df$gene%in%oxidation.go.genes,]$color<-"red"# prepare annotation data pointmark.df<-subset(data.df,gene%in%oxidation.go.genes)library("ggrepel")options(repr.plot.width=6,repr.plot.height=6)ggplot(data.df,aes(...
By then setting parseLabels = TRUE, these will be parsed by the internal ggplot2 or ggrepel engine and presented as italicised text. Advanced users can encode any expression as the label, which will then also be parsed.To flip the volcano on its side, we just use EnhancedVolcano(…) + ...