跟着Nature学作图：R语言ggridges包绘制山脊图

跟着Nature学作图：R语言ggridges包绘制山脊图

论文是

Environmental factors shaping the gut microbiome in a Dutch population

数据和代码的github主页链接

​​figureS3a山脊图和S3b小提琴图加箱线图

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因为论文中提供的不是真实数据集，是一个模拟数据集，所以出图和论文原图相差比较大

首先是山脊图的数据

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读取数据集

dag3_species_plot<-readr::read_csv("newdataset/FigureS3a.csv")head(dag3_species_plot)

赋予因子水平

主要是用来调节Y轴的顺序

dag3_species_plot$Level <- factor(dag3_species_plot$Level, levels = c("Bacteroides_vulgatus", "Bacteroidales_bacterium_ph8", "Alistipes_shahii", "Sutterella_wadsworthensis", "Alistipes_onderdonkii", "Bacteroides_uniformis", "Subdoligranulum_unclassified", "Prevotella_copri", "Faecalibacterium_prausnitzii", "Alistipes_putredinis"))

对数值进行-log2转化

dag3_species_plot$Relative=-log2(dag3_species_plot$Relative)

生成配色

library(randomcoloR)palette <- distinctColorPalette(10)

这里​​randomcoloR​​这个R包是第一次使用，主要作用是生成比较容易区分的颜色

作图

library(ggridges)library(ggplot2)ggplot(dag3_species_plot, aes(x = Relative, y = Level,fill=Level,color=Level)) + theme_classic() + geom_density_ridges(alpha=0.8,scale = 2,show.legend = FALSE)+ scale_fill_manual(values = palette) + scale_color_manual(values = palette)+ ylab("")+ xlab("Norm. Rel. Abundance (-log2)")

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这个图可能是因为数据分布的原因看起来不是很美观，重新构造一份数据集画个图

Level<-rep(c("Bacteroides_vulgatus", "Bacteroidales_bacterium_ph8", "Alistipes_shahii", "Sutterella_wadsworthensis", "Alistipes_onderdonkii", "Bacteroides_uniformis", "Subdoligranulum_unclassified", "Prevotella_copri", "Faecalibacterium_prausnitzii", "Alistipes_putredinis"), rep(2000,10))library(tidyverse)Relative<-10:19 %>% map(function(x)rnorm(n=2000,mean=10,sd=x)) %>% unlist()dat01<-data.frame(Level,Relative)head(dat01)dat01$Level<- factor(dat01$Level, levels = c("Bacteroides_vulgatus", "Bacteroidales_bacterium_ph8", "Alistipes_shahii", "Sutterella_wadsworthensis", "Alistipes_onderdonkii", "Bacteroides_uniformis", "Subdoligranulum_unclassified", "Prevotella_copri", "Faecalibacterium_prausnitzii", "Alistipes_putredinis"))ggplot(dat01, aes(x = Relative, y = Level,fill=Level,color=Level)) + theme_classic() + geom_density_ridges(alpha=0.8,scale = 2,show.legend = FALSE)+ scale_fill_manual(values = palette) + scale_color_manual(values = palette)+ ylab("")+ xlab("Norm. Rel. Abundance (-log2)")+ theme(axis.text.y = element_text(face="italic"), axis.text.x = element_text(face="bold"))

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这个就看起来好看了很多

接下来是小提琴图

library(ggsci)library(ggplot2)cluster_plot<-readr::read_csv("newdataset/cluster_plot.csv", col_types = "ccd")g <- ggplot(cluster_plot, aes(x=Cluster, y=Prevotella_copri,fill=Cluster)) + geom_violin()+ geom_boxplot(width=0.1, fill="white")+ scale_fill_npg()+theme_classic()+ ylab("Prevotella Copri, Norm. Rel. Abundance (-log2)")print(g)

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制作封面图

library(patchwork)g+theme(legend.position = "none")+figureS3A

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小明的数据分析笔记本

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