有了R語(yǔ)言的基礎(chǔ),以及ggplot2繪圖基礎(chǔ)三幻,我們的生信常用分析圖形的繪制就可以提上日程了!本系列呐能,師兄就開始帶著大家一起學(xué)習(xí)如何用R語(yǔ)言繪制我們自己的各種分析圖吧念搬!
由于本系列的所有分析代碼均為師兄細(xì)心整理和詳細(xì)注釋而成的!歡迎點(diǎn)贊摆出、收藏朗徊、轉(zhuǎn)發(fā)!
您的支持是我持續(xù)更新的最大動(dòng)力偎漫!
系列內(nèi)容包括:
- 各種類型的熱圖你學(xué)會(huì)了嗎爷恳?
- 普通熱圖
- 環(huán)形熱圖
- 解鎖火山圖真諦!
- plot函數(shù)就能畫火山圖象踊?
- 高級(jí)函數(shù)繪制火山圖--ggplot2温亲、ggpurb
- 經(jīng)典富集分析及氣泡圖、柱狀圖繪制
- 氣泡圖繪制
- 柱狀圖繪制
- 富集分析圈圖
- 富集分析弦圖
- 繪制一張可以打動(dòng)審稿人的杀兀基圖
- 生存分析 -- KM曲線圖
- 基礎(chǔ)PCA圖
- 云雨圖
- 韋恩圖
- 環(huán)形互作網(wǎng)絡(luò)圖
- 相互作用網(wǎng)絡(luò)圖
- 聚類樹美化
- 富集分析氣泡圖進(jìn)階版
- mantel test相關(guān)性圖
- 詞云圖
- 瀑布圖
- 森林圖
- 曼哈頓圖
- 啞鈴圖
- 三線表
- 嵌套圈圖
- 列線圖
- 蜂群圖
- 箱線圖+貝塞爾曲線
- 矩陣散點(diǎn)圖
- 等等栈虚,想到再繼續(xù)補(bǔ)充!J仿 节芥!
本期火山圖效果展示
R自帶函數(shù)plot就能畫火山圖?
##############
data <- read.csv("DEG.csv",row.names = 1)
color <- rep("#999999",nrow(data))
color[data$pvalue <0.05 & data$log2FoldChange > 1] <- "#FC4E07"
color[data$pvalue <0.05 & data$log2FoldChange < -1] <- "#00AFBB"
par(oma = c(0,2,0,0))
plot(data$log2FoldChange,-log10(data$pvalue),pch = 16,cex = 0.5,
xlim = c(-4,4), ylim = c(0,32), col = color, frame.plot = F,
xlab = "log2FC", ylab = "-log10(Pvalue)", cex.axis = 1, cex.lab = 1.3)
# 添加參考線:
abline(h = -log10(0.05),lwd = 2, lty = 3) # lwd設(shè)置線的寬度,lty設(shè)置線的類型头镊;
abline(v = c(-1,1),lwd = 2, lty = 3) # lwd設(shè)置線的寬度蚣驼,lty設(shè)置線的類型;
# 添加圖例
legend(x = 3, y = 32, legend = c("Up","Normal","Down"),
bty = "n", # 去除邊框
pch = 19,cex = 1, # 設(shè)置點(diǎn)的樣式和大小
x.intersp = 0.3, # 設(shè)置字與點(diǎn)之間的距離相艇;
y.intersp = 0.3, # 設(shè)置點(diǎn)與點(diǎn)的高度差颖杏,相當(dāng)于行距;
col = c("#FC4E07","#999999","#00AFBB"))
# 添加標(biāo)簽:
color = c()
color[which(data[1:10,]$regulate == "Up")] = "#FC4E07"
color[which(data[1:10,]$regulate != "Up")] = "#00AFBB"
text(data$log2FoldChange[1:10],-log10(data$pvalue)[1:10],
labels = data$row[1:10],
adj = c(0,1.5),
cex = 0.6,
col = color)
- 將上述代碼封裝成函數(shù)坛芽,以后調(diào)用留储,就可以一鍵出圖:
# 包裝函數(shù):
# 調(diào)整1: xlim和ylim得去掉
# 調(diào)整2: 修改圖例的位置
plotVoc <- function(data){
color <- rep("#999999",nrow(data))
color[data$pvalue <0.05 & data$log2FoldChange > 1] <- "#FC4E07"
color[data$pvalue <0.05 & data$log2FoldChange < -1] <- "#00AFBB"
par(oma = c(0,2,0,0))
plot(data$log2FoldChange,-log10(data$pvalue),pch = 16,cex = 0.5,
col = color, frame.plot = F,
xlab = "log2FC", ylab = "-log10(Pvalue)", cex.axis = 1, cex.lab = 1.3)
# 添加參考線:
abline(h = -log10(0.05),lwd = 2, lty = 3) # lwd設(shè)置線的寬度,lty設(shè)置線的類型咙轩;
abline(v = c(-1,1),lwd = 2, lty = 3) # lwd設(shè)置線的寬度获讳,lty設(shè)置線的類型;
# 添加圖例
legend(x = 3, y = max(-log10(data$pvalue)), legend = c("Up","Normal","Down"),
bty = "n", # 去除邊框
pch = 19,cex = 1, # 設(shè)置點(diǎn)的樣式和大小
x.intersp = 0.3, # 設(shè)置字與點(diǎn)之間的距離活喊;
y.intersp = 0.3, # 設(shè)置點(diǎn)與點(diǎn)的高度差丐膝,相當(dāng)于行距;
col = c("#999999", "#FC4E07","#00AFBB"))
# 添加標(biāo)簽:
color = c()
color[which(data[1:10,]$regulate == "Up")] = "#FC4E07"
color[which(data[1:10,]$regulate != "Up")] = "#00AFBB"
text(data$log2FoldChange[1:10],-log10(data$pvalue)[1:10],
labels = data$row[1:10],
adj = c(0,1.5),
cex = 0.6,
col = color)
}
data <- read.csv("DEG2.csv",row.names = 1)
plotVoc(data)
高級(jí)函數(shù)繪制火山圖--ggplot2钾菊、ggpurb
- 使用ggplot2繪制:
library(ggplot2)
data <- read.csv("DEG.csv",row.names = 1)
#################
# ggplot2繪制火山圖
data$label <- c(rownames(data)[1:10],rep(NA,nrow(data) - 10))
ggplot(data,aes(log2FoldChange,-log10(pvalue),color = regulate)) +
xlab("log2FC") +
geom_point(size = 0.6) +
scale_color_manual(values=c("#00AFBB","#999999","#FC4E07")) +
geom_vline(xintercept = c(-1,1), linetype ="dashed") +
geom_hline(yintercept = -log10(0.05), linetype ="dashed") +
theme(title = element_text(size = 15), text = element_text(size = 15)) +
theme_classic() +
geom_text(aes(label = label),size = 3, vjust = 1,hjust = -0.1)
- 使用ggpurb的scatter函數(shù)也可以畫:
#############
# 使用ggpurb繪制火山圖:
library(ggpubr)
data$pvalue <- -log10(data$pvalue)
ggscatter(data,
x = "log2FoldChange",
y = "pvalue",
ylab="-log10(P.value)",
size=0.6,
color = "regulate",
label = rownames(data),
label.select = rownames(data)[1:10],
repel = T,
palette = c("#00AFBB", "#999999", "#FC4E07")) +
geom_hline(yintercept = 1.30,linetype ="dashed") +
geom_vline(xintercept = c(-1,1),linetype ="dashed")
往期優(yōu)秀圖形目錄
以上內(nèi)容僅為群內(nèi)部分內(nèi)容帅矗,不代表全部。詳細(xì)目錄請(qǐng)看下鏈接煞烫!