跟着Nature学作图：R语言ggplot2分组折线图添加误差线

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发布于 2022-05-23 15:54:31

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发布于 2022-05-23 15:54:31

文章被收录于专栏：小明的数据分析笔记本小明的数据分析笔记本

论文是

Environmental factors shaping the gut microbiome in a Dutch population

数据和代码的github主页链接

https://github.com/GRONINGEN-MICROBIOME-CENTRE/DMP

这个也是数据代码的下载链接，可以看目录结构

https://zenodo.org/record/5910709#.YmAcp4VBzic

今天的推文重复一下论文中的figure1b

image.png

数据集

image.png

这里误差线的范围是平均值加减标准差，数据提前算好，整理到csv文件中

读取数据

library(readr)
dat01<-read_csv("newdataset/MockData_Fig_1B_microbiome_rarefaction_datatable.csv")
head(dat01)

分组折线图

library(ggplot2)

ggplot(data=dat01,aes(x=nr,y=spec.nr.mn,color=Taxon))+
  geom_line(size=1.5,linetype=dat01$linetype)

image.png

添加误差线

ggplot(data=dat01,aes(x=nr,y=spec.nr.mn,color=Taxon))+
  geom_line(size=1.5,linetype=dat01$linetype)+
  geom_errorbar(aes(ymin=spec.nr.mn-spec.nr.sd, 
                    ymax=spec.nr.mn+spec.nr.sd),
                size=1.05, colour="black")

image.png

再叠加一层散点图

ggplot(data=dat01,aes(x=nr,y=spec.nr.mn,color=Taxon))+
  geom_line(size=1.5,linetype=dat01$linetype)+
  geom_errorbar(aes(ymin=spec.nr.mn-spec.nr.sd, 
                    ymax=spec.nr.mn+spec.nr.sd),
                size=1.05, colour="black")+
  geom_point(shape=21,size=1.75,fill="white")

image.png

更改坐标轴标题

ggplot(data=dat01,aes(x=nr,y=spec.nr.mn,color=Taxon))+
  geom_line(size=1.5,linetype=dat01$linetype)+
  geom_errorbar(aes(ymin=spec.nr.mn-spec.nr.sd, 
                    ymax=spec.nr.mn+spec.nr.sd),
                size=1.05, colour="black")+
  geom_point(shape=21,size=1.75,fill="white")+
  xlab("Number of samples") + ylab("Number of features")

最后是美化调整细节

ggplot(data=dat01,aes(x=nr,y=spec.nr.mn,color=Taxon))+
  geom_line(size=1.5,linetype=dat01$linetype)+
  geom_errorbar(aes(ymin=spec.nr.mn-spec.nr.sd, 
                    ymax=spec.nr.mn+spec.nr.sd),
                size=1.05, colour="black")+
  geom_point(shape=21,size=1.75,fill="white")+
  xlab("Number of samples") + ylab("Number of features")+
  scale_color_manual(values = c("#56B4E9", "#009E73", "#0072B2", "#D55E00", "#CC79A7", "#E69F00"))+
  theme_bw()+
  theme(text = element_text(size = 17))

image.png

制作封面图

ggplot(data=dat01,aes(x=nr,y=spec.nr.mn,color=Taxon))+
  geom_line(size=1.5,linetype=dat01$linetype)+
  geom_errorbar(aes(ymin=spec.nr.mn-spec.nr.sd, 
                    ymax=spec.nr.mn+spec.nr.sd),
                size=1.05, colour="black")+
  geom_point(shape=21,size=1.75,fill="white")+
  xlab("Number of samples") + ylab("Number of features") -> p1

print(p1)

ggplot(data=dat01,aes(x=nr,y=spec.nr.mn,color=Taxon))+
  geom_line(size=1.5,linetype=dat01$linetype)+
  geom_errorbar(aes(ymin=spec.nr.mn-spec.nr.sd, 
                    ymax=spec.nr.mn+spec.nr.sd),
                size=1.05, colour="black")+
  geom_point(shape=21,size=1.75,fill="white")+
  xlab("Number of samples") + ylab("Number of features")+
  scale_color_manual(values = c("#56B4E9", "#009E73", "#0072B2", "#D55E00", "#CC79A7", "#E69F00"))+
  theme_bw()+
  theme(text = element_text(size = 17)) -> p2
print(p2)

library(patchwork)

p1+p2