跟着Nature microbiology学画图~R语言ggpl

今天要模仿的图片来自于论文 Core gut microbial communities are maintained by beneficial interactions and strain variability in fish。期刊是 Nature microbiology

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今天重复的图片是Figure2中的气泡图

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首先是准备数据

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需要练习数据可以直接在文末留言

读入数据

df<-read.csv("example_data/bubble_plot_example.csv",
             header=T)
df

读入的数据是宽格式，ggplot2作图需要用长格式数据，对宽格式数据进行转化

df1<-reshape2::melt(df)
df1

最基本的散点图

ggplot(df1,aes(x=x,y=variable))+
  geom_point()

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用数值来映射颜色和大小

ggplot(df1,aes(x=x,y=variable))+
  geom_point(aes(color=value,size=value))

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接下来是进行美化

去掉灰色背景

ggplot(df1,aes(x=x,y=variable))+
  geom_point(aes(color=value,size=value))+
  theme(panel.background = element_blank())

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添加网格线

ggplot(df1,aes(x=x,y=variable))+
  geom_point(aes(color=value,size=value))+
  theme(panel.background = element_blank(),
        panel.grid = element_line(color="grey"))

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去掉坐标轴的标题和更改x轴字体的方向和字体的颜色

ggplot(df1,aes(x=x,y=variable))+
  geom_point(aes(color=value,size=value))+
  theme(panel.background = element_blank(),
        panel.grid = element_line(color="grey"),
        axis.title = element_blank(),
        axis.ticks = element_blank(),
        axis.text.x=element_text(angle = 45,hjust = 1,
                                 colour = c("red","red","red","red",
                                            "green","red","yellow")))

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接下来是更改图例的一些操作

首先是去掉颜色的图例

ggplot(df1,aes(x=x,y=variable))+
  geom_point(aes(color=value,size=value))+
  theme(panel.background = element_blank(),
        panel.grid = element_line(color="grey"),
        axis.title = element_blank(),
        axis.ticks = element_blank(),
        axis.text.x=element_text(angle = 45,hjust = 1,
                                 colour = c("red","red","red","red",
                                            "green","red","yellow")))+
  guides(color=FALSE)

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更改图例的位置

ggplot(df1,aes(x=x,y=variable))+
  geom_point(aes(color=value,size=value))+
  theme(panel.background = element_blank(),
        panel.grid = element_line(color="grey"),
        axis.title = element_blank(),
        axis.ticks = element_blank(),
        legend.position = "bottom",
        axis.text.x=element_text(angle = 45,hjust = 1,
                                 colour = c("red","red","red","red",
                                            "green","red","yellow")))+
  guides(color=FALSE)

更改图例的标题和标题的位置

ggplot(df1,aes(x=x,y=variable))+
  geom_point(aes(color=value,size=value))+
  theme(panel.background = element_blank(),
        panel.grid = element_line(color="grey"),
        axis.title = element_blank(),
        axis.ticks = element_blank(),
        legend.position = "bottom",
        axis.text.x=element_text(angle = 45,hjust = 1,
                                 colour = c("red","red","red","red",
                                            "green","red","yellow")))+
  guides(color=FALSE,
         size=guide_legend(title.position = "top",
                           title.hjust = 0.5))+
  labs(size="Relative abundance (%)")

image.png

最后更改一下填充颜色和点的大小

ggplot(df1,aes(x=x,y=variable))+
  geom_point(aes(color=value,size=value))+
  theme(panel.background = element_blank(),
        panel.grid = element_line(color="grey"),
        axis.title = element_blank(),
        axis.ticks = element_blank(),
        legend.position = "bottom",
        axis.text.x=element_text(angle = 45,hjust = 1,
                                 colour = c("red","red","red","red",
                                            "green","red","yellow")))+
  guides(color=FALSE,
         size=guide_legend(title.position = "top",
                           title.hjust = 0.5,
                           override.aes = 
                             list(size=c(1,2,3,4))))+
  labs(size="Relative abundance (%)")+
  scale_color_viridis_c()+
  scale_size_continuous(range = c(1,20))

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