使用R绘制简单的序列图

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  • 资料来源

《Building Bioinformatics Solutions with Perl, R and MySQL》（P162-163）

  • 结果展示

seq

  • 程序源码

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    # SSSEQ.R
# Simple R program to display a sequence with structural anotation
 
# define sequence and secondary structure
seq <- "GARVHMDGARLMNAAVALRIPPARLVEHCDSVSFCFSKG"
struct <- c(0,0,2,2,2,2,2,1,1,1,1,0,0,0,0,0,0,0,0,0,0,1,1,1,1,0,0,0,0,0,2,2,2,2,2,0,0,0,0)
residuecount <- 39
 
# set up the window for poltting
x11()
plot.new()
plot.window(c(0,40),c(-20,20))
 
# plot a line representing the length of the sequence
segments(0.5,0,39.5,0)
 
# plot the sequence and feature
for(i in 1:residuecount){
	text(i,-2,substr(seq,i,i))
	if(struct[i] != 0){
		if(struct[i] == 1) boxcolour <- "firebrick" # alpha helix
		if(struct[i] == 2) boxcolour <- "yellow3" # beta sheet
		rect(i-0.5,-1,i+0.5,1,col=boxcolour,border=NA)
	}
}
 
# plot a legend
legend(x=0,y=8,legend=(c("alpha helix","beta sheet")),pch=15,col=c("firebrick","yellow3"),bg="snow")