Ks密度曲线分布图绘图

---

Ka(dN)代表每非同义位点的碱基替代数，而 Ks(dS)则代表每同义位点的碱基替代数， Ka/Ks的比值常用于判断某个蛋白编码基因是否受到选择压力的作用。一般认为，当 Ka/Ks>1时，则认为有 正选择效应。当 Ka/Ks=1时，则认为存在 中性选择。当 Ka/Ks<1时，则认为有 纯化选择的作用。常用的选择压力Ka/Ks的计算工具有PAML包中的 yn00程序，或 KaKs_calculator等软件。Ks密度曲线分布图常用于判断某一物种在长期的进化过程中是否发生了基因组加倍事件，根据密度曲线对应峰值的Ks值以及该物种核苷酸碱基的替代速率，可以大致计算出该物种发生加倍的进化时间。

加载所需R包

rm(list=ls())
library(ggplot2)
library(reshape2)

---

设置工作路径并加载数据

setwd("/Users/Davey/Desktop")
data <- read.table("test_ks.txt",header = T,sep="\t")
data <- melt(data,variable.name="Species",value.name =  "Ks")
#去除缺失的行
data = na.omit(data)
head(data)
##             Species     Ks
## 1 SpeciesA_SpeciesB 0.0915
## 2 SpeciesA_SpeciesB 0.2535
## 3 SpeciesA_SpeciesB 0.0386
## 4 SpeciesA_SpeciesB 0.1385
## 5 SpeciesA_SpeciesB 0.1125
## 6 SpeciesA_SpeciesB 0.1960

---

使用ggplot2绘图

p1 <- ggplot(data,aes(Ks,fill=Species,color=Species,alpha=0.8))  +`
geom_density()  + xlim(0,1)  + theme_classic()  + geom_rug()  +
guides(alpha=FALSE)  +
theme(axis.title = element_text(size=16),axis.text=element_text(size=16),legend.position =  "top")
p1
#ggsave("Ks_plot.png",p1)
ggsave("Ks_plot.pdf",p1)

image

---

p2 <- ggplot(data,aes(Ks,color=Species))  +
geom_line(stat="density")  + xlim(0,1)  + theme_bw()  +
theme(axis.title = element_text(size=16),axis.text=element_text(size=16))
p2

image

---

p3 <- ggplot(data,aes(Ks,fill=Species,color=Species))  +
geom_histogram(bins=100)  + geom_rug()  +
xlim(0,1)  + theme_bw()  +
theme(axis.title = element_text(size=16),axis.text=element_text(size=16))
p3

image

---

p4 <- ggplot(data,aes(Ks,..density..,fill=Species))  +
geom_histogram(bins=100)  + geom_line(stat="density")  +
xlim(0,1)  + theme_bw()  + facet_grid(Species~.)  +
theme(axis.title = element_text(size=16),axis.text=element_text(size=16))
p4

image

---

sessionInfo()
## R version 3.5.1 (2018-07-02)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: OS X El Capitan 10.11.3
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
##
## locale:
## [1] zh_CN.UTF-8/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/zh_CN.UTF-8
##
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base
##
## other attached packages:
## [1] ggpubr_0.1.7.999 magrittr_1.5     reshape2_1.4.3   ggplot2_3.0.0
##
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.18     rstudioapi_0.7   bindr_0.1.1      knitr_1.20     
##  [5] tidyselect_0.2.4 munsell_0.5.0    colorspace_1.3-2 R6_2.2.2       
##  [9] rlang_0.2.2      stringr_1.3.1    plyr_1.8.4       dplyr_0.7.6 
## [13] tools_3.5.1      grid_3.5.1       gtable_0.2.0     withr_2.1.2
## [17] htmltools_0.3.6  assertthat_0.2.0 yaml_2.2.0       lazyeval_0.2.1 
## [21] rprojroot_1.3-2  digest_0.6.16    tibble_1.4.2     crayon_1.3.4  
## [25] bindrcpp_0.2.2   purrr_0.2.5      glue_1.3.0       evaluate_0.11
## [29] rmarkdown_1.10   labeling_0.3     stringi_1.2.4    compiler_3.5.1 
## [33] pillar_1.3.0     scales_1.0.0     backports_1.1.2  pkgconfig_2.0.2