论文

Environmentally robust cis-regulatory changes underlie rapid climatic adaptation

https://www.biorxiv.org/content/10.1101/2022.08.29.505745v1

2022.08.29.505745v1.full.pdf

还没有发表,论文的数据和代码都公开
https://github.com/malballinger/BallingerMack_NYBZase_2022

今天的推文我们重复一下论文中的Figure3C

image.png

这里桑基图实现是借助R包 ggalluvial

帮助文档

https://cran.r-project.org/web/packages/ggalluvial/vignettes/ggalluvial.html#:~:text=The%20ggalluvial%20package%20is%20a,the%20feedback%20of%20many%20users.

或者直接通过命令查看help(package="ggalluvial")

首先是自己构造数据的一个简单例子

library(ggalluvial)
as.data.frame(Titanic)

dat01<-data.frame(first=c("A","A","C"),
                  second=c("B","D","E"),
                  third=c("F","G","F"),
                  n=c(15,30,20))

dat01$first<-factor(dat01$first,
                    levels = c("C","A"))
ggplot(data=dat01,
       aes(axis1=first,axis2=second,axis3=third,
           y=n))+
  geom_alluvium(aes(fill=second),
                #size=3,
                #color="white",
                width = 0.1,
                aes.bind = "flows")+
  geom_stratum(fill=c("red","blue","green",'yellow',
                           'orange',"blue","green"),
               #color="white",
               #size=3,
               width=0.1)+
  geom_label(stat = "stratum", aes(label = after_stat(stratum)))+
  scale_x_continuous(breaks = c(1,2),
                     labels = c("first","second"),
                     expand = expansion(mult = c(0,0)))+
  theme_void()

image.png

加载需要用到的R包

library(tidyverse)
library(readr)
library(ggplot2)
library(ggalluvial)
library(latex2exp)

论文中的数据和图

fig3c1<-read_csv("figure3c1.csv")
fig3c1

cp2 <- c("#FC7945", "#4AB08C", "#482870",
                  "gray", "#FC7945", "#4AB08C",
                  "#482870", "gray")

fig3c1$category_warm<-factor(fig3c1$category_warm,
                             levels = c("Amb&Conserved",
                                        "TRANS_ONLY",
                                        "Cis&Trans",
                                        "CIS_ONLY"))

fig3c1$category_cold<-factor(fig3c1$category_cold,
                             levels = c("Amb&Conserved",
                                        "TRANS_ONLY",
                                        "Cis&Trans",
                                        "CIS_ONLY"))
fig3c1 %>%
  ggplot(aes(y = n, axis1 = category_warm, axis2 = category_cold)) +
  geom_alluvium(aes(fill= category_warm, color = category_warm), 
                size = 0.7, alpha = 0.6, 
                curve_type = "cubic", width = 1/4, 
                show.legend = FALSE,
                aes.bind = "flows") +
  geom_stratum( 
               color = cp2, fill = cp2, 
               alpha = 0.99, width = 1/4, show.legend = FALSE) +
  scale_fill_manual(breaks = c("Amb&Conserved", "Cis&Trans", "TRANS_ONLY", "CIS_ONLY"),
                    values = c("darkgray", "#29AF7F", "#3B0F6F", "#FC4E07"),
                    labels = c("Conserved", "Cis + Trans", "Trans", "Cis")) +
  scale_color_manual(breaks = c("Amb&Conserved", "Cis&Trans", "TRANS_ONLY", "CIS_ONLY"),
                     values = c("darkgray", "#29AF7F", "#3B0F6F", "#FC4E07"),
                     labels = c("Conserved", "Cis + Trans", "Trans", "Cis")) +
  scale_x_continuous(breaks = 1:2, labels = c("Warm", "Cold"), expand = c(0.025,0.025)) +
  scale_y_continuous(limits = c(0,1400), breaks = seq(0, 1400, 400),
                     expand = c(0,0)) +
  theme_classic() +
  theme(panel.grid = element_blank(),
        axis.title = element_blank(),
        axis.text = element_text (size = 10, 
                                  family = "sans"),
        plot.margin = unit(c(0,1.5,0,0),'cm'))+
  coord_cartesian(clip="off")+
  annotate(geom="text",
           x=2.15,y=225,
           label=TeX(r"(\textit{cis})"),
           hjust=0,
           color="#FC7945")+
  annotate(geom="text",
           x=2.15,y=621.5,
           label=TeX(r"(\textit{cis & trans})"),
           hjust=0,
           color= "#4AB08C")+
  annotate(geom="text",
           x=2.15,y=892,
           label=TeX(r"(\textit{trans})"),
           hjust=0,
           color="#482870")+
  annotate(geom="text",
           x=2.15,y=1186,
           label="conserved\nambiguous",
           hjust=0,
           color="gray")

image.png

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