Nothing
##plot hairpin loops
stemPlot <- 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=19,
desc="stems"
)
RNAPlot(co,ranges,labTF=F,main = "RNA secondary structure")
print("------------------------------------------------------")
print("* *")
print("* what print below is the information of result *")
print("* *")
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
length_loop <- length(unlist(loops))
max_length <- length(loops[[1]])
min_length <- length(loops[[1]])
for (i in 1:length(loops)) {
if(length(loops[[i]]) > max_length){
max_length <- length(loops[[i]])
}
if(length(loops[[i]]) < min_length){
min_length <- length(loops[[i]])
}
}
attr(loops,"1.Number of base pairs in stems") <- length_loop
attr(loops,"2.Number of stems") <- length(loops)
attr(loops,"3.Average length of a stem") <- length_loop/length(loops)
attr(loops,"4.Maximum length of a stem") <- max_length
attr(loops,"5.Minimum length of a stem") <- min_length
attr(loops,"6.Base positions in stems") <- paste(unlist(loops),collapse = " ",sep = "")
return(loops)
}else{
print("------------------------------------------------------")
print("* *")
print("* what print below is the information of result *")
print("* *")
print("------------------------------------------------------")
print("There is no stem")
}
}
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