跟着Science Advances学画图：R语言ggplot2

今天的推文是昨天推文的延续。在昨天的推文中模仿了论文 Landscapes of bacterial and metabolic signatures and their interaction in major depressive disorders中的 figure2B

image.png

但是有一个细节没有能够实现，就是让坐标轴以上图样子的科学计数法显示，昨天的推文发出后有读者留言了对应的解决办法，今天在推文中记录一下

首先是构造一份数据

df<-data.frame(x=c("A","B","C","D"),
               y=c(0.001,0.002,0.003,0.004))
df

最基本的柱形图

ggplot(df,aes(x=x,y=y))+
  geom_col()

image.png

默认是以小数形式

加上如下函数

ggplot(df,aes(x=x,y=y))+
  geom_col()+
  scale_y_continuous(labels = scales::scientific)

image.png

能够修改成上图的科学计数法

另外的方式是

ggplot(df,aes(x=x,y=y))+
  geom_col()+
  scale_y_continuous(labels = c(expression(italic(0)),
                                expression(1%*%10^-10),
                                expression(2%*%10^-10),
                                expression(3%*%10^-10),
                                expression(4%*%10^-10)),
                     #position = "right",
                     expand = c(0,0),
                     breaks = c(0,0.001,0.002,0.003,0.004),
                     limits = c(0,0.005))

image.png

这个expression（）函数还真好用，得花时间学习一下他的用法

接下来简单的美化一下

ggplot(df,aes(x=x,y=y))+
  geom_col(aes(fill=x))+
  scale_y_continuous(labels = c(expression(italic(0)),
                                expression(1%*%10^-10),
                                expression(2%*%10^-10),
                                expression(3%*%10^-10),
                                expression(4%*%10^-10)),
                     position = "right",
                     expand = c(0,0),
                     breaks = c(0,0.001,0.002,0.003,0.004),
                     limits = c(0,0.005))+
  labs(y=NULL)+
  coord_flip()+
  theme_bw()

image.png

昨天放到推文里的代码稍微有点错误，今天放一个完整的代码

library(ggplot2)
library(dplyr)
library(patchwork)
set.seed(1234)
x<-seq(5,10,by=0.5)
 
df<-data.frame(`s__Klebsiella_phage_vB_KpnP_SU552A` = sample(x,10,replace = T),
               `s__Escherichia_phage_ECBP5` = sample(x,10,replace = T),
               `s__Clostridium_phage_phi8074-B1` = sample(x,10,replace = T),
               check.names = F)
head(df)
df%>%
  reshape2::melt()%>%
  group_by(variable)%>%
  summarise(mean_value=mean(value),
            sd_value=sd(value)) -> df2

df%>%
  reshape2::melt() -> df1

p1<-ggplot()+
  geom_col(data=df2,aes(x=variable,y=mean_value),
           fill="#8babd3",
           color="black",
           width = 0.2)+
  geom_errorbar(data=df2,aes(x=variable,
                             ymin=mean_value-sd_value,
                             ymax=mean_value+sd_value),
                width=0.1)+
  geom_jitter(data=df1,aes(x=variable,y=value),
              width = 0.2,color="grey")+
  #scale_y_continuous(expand = c(0,0))+
  theme_bw()+
  coord_flip()+
  scale_y_reverse(expand=c(0,0),
                  position="right")+
  labs(x=NULL,y=NULL)
p1
p2<-ggplot()+
  geom_col(data=df2,aes(x=variable,y=mean_value),
           fill="#ffc080",
           color="black",
           width=0.2)+
  geom_errorbar(data=df2,aes(x=variable,
                             ymin=mean_value-sd_value,
                             ymax=mean_value+sd_value),
                width=0.1)+
  geom_jitter(data=df1,aes(x=variable,y=value),
              width = 0.2,color="grey")+
  scale_y_continuous(expand = c(0,0),
                     position = "right")+
  theme_bw()+
  coord_flip()+
  labs(x=NULL,y=NULL)+
  theme(axis.text.y = element_blank(),
        axis.ticks.y = element_blank())
p2
df3<-data.frame(x="A",
                y=c("s__Klebsiella_phage_vB_KpnP_SU552A",
                    "s__Escherichia_phage_ECBP5",
                    "s__Clostridium_phage_phi8074-B1"),
                group=c("f__Siphoviridae",
                        "f__Podoviridae",
                        "f__Podoviridae"))

p3<-ggplot(df3,aes(x=x,y=y))+
  geom_tile(aes(fill=group),show.legend = F)+
  labs(x=NULL,y=NULL)+
  scale_x_discrete(expand = c(0,0))+
  scale_y_discrete(expand = c(0,0),
                   position = "right",
                   labels=c("f__Podoviridae",
                            "",
                            "f__Siphoviridae"))+
  theme(panel.background = element_blank(),
        axis.ticks = element_blank(),
        axis.text.x = element_blank())+
  scale_fill_manual(values = c("#c65911","#ffd965"))


p1+p2+p3+ggtitle("Bacteriophages")+
  theme(plot.title = element_text(hjust=5))+
  plot_layout(widths = c(1.2,1,0.2)) -> p
ggsave(filename = "Rplot11.pdf",
       p,
       width = 10,height = 3)

最终的结果如下

image.png

再次感谢昨天推文读者的留言。

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