Nothing
##plot hairpin loops
plot_stem <- function(ctFile){
dot <- ct2dot(ctFile)
ct <- makeCt(dot[[1]][1],dot[[2]][1])
co <- ct2coord(ct)
loops <- stem(ctFile)
arr_min <- c()
arr_max <- c()
if(length(loops) != 0){
for (i in 1:length(loops)) {
arr_min <- c(arr_min,loops[[i]][1])
if(length(loops[[i]]) > 1){
for (j in 2:length(loops[[i]])) {
if(loops[[i]][j-1] == loops[[i]][j] - 1){
}else{
arr_max <- c(arr_max,loops[[i]][j-1])
arr_min <- c(arr_min,loops[[i]][j])
}
}
arr_max <- c(arr_max,loops[[i]][j])
}else{
arr_max <- c(arr_max,loops[[i]][1])
}
}
ranges=data.frame(min=arr_min,max=arr_max,col=c(2),
desc="stems"
)
RNAPlot(co,ranges,labTF=F)
print("------------------------------------------------------")
print("summary of stems:")
print(paste("the number of stems is:",length(loops)))
print(paste("the bases in stems are:",paste(unlist(loops),collapse = " ",sep = "")))
loops_name <- c()
for (i in 1:length(loops)) {
loops_name <- c(loops_name,paste("bases in stem ",i))
}
names(loops) <- loops_name
return(loops)
}
}
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