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R绘图(6): 拯救初学者
install.packages("ggpubr")
library(ggpubr)
1. 单变量——连续型
1.1 密度图
#创建数据框
set.seed(0330)
mydata = data.frame(
group = rep(c("A", "B","C","D"), each=200),
value = c(rnorm(200, mean = 2), rnorm(200, 6),rnorm(200,2,4),rnorm(200,6,4))
)
ggdensity(mydata, x = "value", y="..density..", #或者"..count.."，默认为"..density.."
fill = "lightgray",
add = "mean", #或者"median",
rug = TRUE #在图形下方添加密度线
)
ggsave("density1.pdf",width = 10,height = 10,units = "cm")
分组绘制 ggdensity(mydata, x = "value", color = "group", fill="group", #分组 palette = "Dark2",#或者"aaas"这种ggsci包的配色形式,或者"#00AFBB"这种编码形式 add = "mean", rug = TRUE, alpha=0.2, #调整透明度 xlab=F,ylab = "Density", facet.by="group", #分面 panel.labs=list(group = c("1", "2", "3", "4")), #修改每个panel的名字 title="density plot", ggtheme=theme_bw() #可以是ggplot2中的主题类型 ) ggsave("density2.pdf",width = 13,height = 12,units = "cm")
1.2 密度图叠加正态分布
set.seed(0330)
mydata = data.frame(
group = rep(c("A", "B"), each=200),
value = c(rnorm(200, 2), rnorm(200, 6, 4))
)
ggdensity(mydata, x = "value", fill = "red") +
stat_overlay_normal_density(color = "red", linetype = "dashed")+
scale_x_continuous(limits = c(-5,20))
ggsave("density3.pdf",width = 10,height = 10,units = "cm")
分组绘制 ggdensity(mydata, x = "value", fill = "group") + stat_overlay_normal_density(aes(color=group), linetype = "dashed")+ scale_x_continuous(limits = c(-5,20)) ggsave("density4.pdf",width = 10,height = 10,units = "cm")
分组+分面 ggdensity(mydata, x = "value", fill = "group", facet.by = "group") + stat_overlay_normal_density(aes(color=group), linetype = "dashed")+ scale_x_continuous(limits = c(-5,20)) ggsave("density5.pdf",width = 16,height = 10,units = "cm")
1.3 直方图
gghistogram(mydata, x = "value", fill = "lightgray",
add = "mean", rug = TRUE)
ggsave("hist1.pdf",width = 10,height = 10,units = "cm")
分组绘制 gghistogram(mydata, x = "value", fill = "group", add = "mean", rug = TRUE, palette = c("#00AFBB", "#E7B800")) ggsave("hist2.pdf",width = 10,height = 10,units = "cm")
添加核密度图 gghistogram(mydata, x = "value", fill = "group", rug = TRUE, palette = c("#00AFBB", "#E7B800"), add_density = TRUE) ggsave("hist3.pdf",width = 10,height = 10,units = "cm")
2. 双变量——x离散，y连续
2.1 箱型图
library(patchwork)
set.seed(0330)
mydata = data.frame(
group = rep(c("A", "B"), each=100),
group2 = rep(c("g1","g2","g1","g2"),each=50),
value = c(rnorm(100, 2), rnorm(100, 6, 4))
)
#下面的加号表示拼接图形
ggboxplot(mydata, x = "group", y = "value", width = 0.8)+
ggboxplot(mydata, x = "group", y = "value", width = 0.8, orientation = "horizontal")+
ggboxplot(mydata, x = "group", y = "value", width = 0.8, notch = TRUE,order = c("B","A"))+
ggboxplot(mydata, x = "group", y = "value", width = 0.8, select = c("A"))
ggsave("box1.pdf",width = 10,height = 10,units = "cm")
orientation调整图形方向；notch添加缺口；order调整顺序；select选择特定的水平来画图 
ggboxplot(mydata, x = "group", y = "value", width = 0.8, add = "jitter",add.params=list(color = "lightblue",size=1, shape = 17))+
ggboxplot(mydata, x = "group", y = "value", width = 0.8, add = "dotplot",add.params=list(color = "lightblue",size=0.5))
ggsave("box2.pdf",width = 16,height = 10,units = "cm")
上面的add添加额外图形add.params对附加图形的参数进行调整，shape表示点的形状，可以参加下图 
内部分组 ggboxplot(mydata, x = "group", y = "value", width = 0.6, color = "black",fill="group2",palette = c("#00AFBB", "#E7B800"), xlab = F, #不显示x轴的label bxp.errorbar=T,bxp.errorbar.width=0.4, #添加errorbar size=1, #箱型图边线的粗细 outlier.shape=NA, #不显示outlier legend = "right") #图例放右边 ggsave("box3.pdf",width = 10,height = 10,units = "cm")
2.1.1 箱型图添加配对连线
可以接受两种数据框 mydata2=mydata mydata2$group2=NULL head(mydata2) # group value # 1 A 3.551687 # 2 A 3.664068 # 3 A 2.194454 # 4 A 2.569605 # 5 A 2.579997 # 6 A 1.837967 ggpaired(mydata2, x = "group", y = "value", color = "group", line.color = "gray", line.size = 0.4, palette = "npg") mydata2$id=rep(1:100,2) mydata2=mydata2%>%reshape2::dcast(id~group) head(mydata2) # id A B # 1 1 3.551687 4.720074 # 2 2 3.664068 7.821049 # 3 3 2.194454 8.956841 # 4 4 2.569605 -4.450063 # 5 5 2.579997 7.568216 # 6 6 1.837967 5.133688 ggpaired(mydata2, cond1 = "A", cond2 = "B", color = "condition", line.color = "gray", line.size = 0.4, palette = "npg") ggsave("box4.pdf",width = 10,height = 10,units = "cm")上面两种数据框得到的图是一模一样的 
2.1.2 添加p值
一般用法 ggboxplot(mydata, x = "group", y = "value", width = 0.8, add = "dotplot",add.params=list(color = "lightblue",size=0.5))+ stat_compare_means(method = "t.test") ggsave("box5.pdf",width = 10,height = 10,units = "cm")
成对数据 ggpaired(mydata2, cond1 = "A", cond2 = "B", color = "condition", line.color = "gray", line.size = 0.4, palette = "npg")+ stat_compare_means(paired = TRUE) ggsave("box6.pdf",width = 10,height = 10,units = "cm")
多于两个组时，定义想检验的配对 my_comparisons |
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