论文

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

image.png

本地文件 s41564-020-0771-4.pdf

代码和数据下载链接

https://github.com/plemey/SARSCoV2origins

今天的推文我们来重复一下论文中的 Figure5b

image.png

他这个图是先用密码子的RSCU值做主成分分析，然后做散点图展示结果

加载需要用到的R包

library(tidyverse)
library(ggplot2)
library(ggrepel)

读取数据

all_rscu <- read_csv('all_rscu_codonBiasReanalysis.csv')

all_df <- as.data.frame(all_rscu[,2:26])
row.names(all_df) <- all_rscu$codon

主成分分析

df_pca <- prcomp(t(all_df))

给主成分分析的结果添加分组信息

subset_viruses <- c('MG772934','MG772933','GU190215','KP886808','KP886809','MN908947')

df_out <- as.data.frame(df_pca$x)
df_out$group <- ifelse(row.names(df_out) %in% subset_viruses,'virus','vertebrate')
df_out$species <- row.names(df_out)

论文中提供的代码作图

ggplot(df_out,aes(x=PC1,y=PC2,color=group)) +
  geom_point(show.legend = F) +
  scale_color_manual(values = c('dodgerblue4','firebrick')) +
  geom_label_repel(aes(label = species),show.legend = F) +
  theme_bw() + theme(aspect.ratio = 1, panel.grid = element_blank())

image.png

但是这个图和论文中最终呈现的图还是有些细节不太一样的，我们对代码进行修改，尽量重复原图

增加箭头

ggplot(df_out,aes(x=PC1,y=PC2)) +
  geom_point(show.legend = F)+ 
  geom_label_repel(aes(label = species,
                       color=group),
                   show.legend = F) +
  scale_color_manual(values = c('black','#6a9a97')) +
  theme_bw() + 
  theme(aspect.ratio = 1, 
        panel.grid = element_blank())+
  geom_segment(aes(x=1.5,y=0,xend=0,yend=1),
               arrow = arrow(type="closed"),
               lty="dashed",
               color="grey")+
  geom_segment(aes(x=1.5,y=0,xend=3,yend=-1),
               arrow = arrow(type="closed"),
               lty="dashed",
               color="grey")

image.png

增加注释的文字

ggplot(df_out,aes(x=PC1,y=PC2)) +
  geom_point(show.legend = F)+ 
  geom_label_repel(aes(label = species,
                       color=group),
                   show.legend = F) +
  scale_color_manual(values = c('black','#6a9a97')) +
  theme_bw() + 
  theme(aspect.ratio = 1, 
        panel.grid = element_blank())+
  geom_segment(aes(x=1.5,y=0,xend=0,yend=1),
               arrow = arrow(type="closed"),
               lty="dashed",
               color="grey")+
  geom_segment(aes(x=1.5,y=0,xend=3,yend=-1),
               arrow = arrow(type="closed"),
               lty="dashed",
               color="grey")+
  annotate(geom = "text",
           x=-2,y=-1,
           label="Eukaryotes",
           fontface="bold")+
  annotate(geom = "text",
           x=1.6,y=0.5,
           label="Coronaviruses",
           fontface="bold",
           color='#6a9a97')+
  annotate(geom = "text",
           x=0,y=1.2,
           label="High GC")+
  annotate(geom = "text",
           x=3,y=-1.2,
           label="Low GC")

image.png

论文中最终呈现的图还对其中一个点的文字标签进行了更改，这个出图后借助其他软件来更改了

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