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uco <- function (seq, frame = 0, index = c("eff", "freq", "rscu"),
as.data.frame = FALSE, NA.rscu = NA)
{
choice <- match.arg(index)
if(any(seq%in%LETTERS)){
seq <- tolower(seq)
}
sequence <- splitseq(seq = seq, frame = frame, word = 3)
if( as.data.frame == FALSE ) {
eff <- table(factor(sequence, levels = SEQINR.UTIL$CODON.AA$CODON))
if(choice == "eff") return(eff)
freq <- eff/(floor(length(seq)/3))
if(choice == "freq") return(freq)
T <- split(freq, SEQINR.UTIL$CODON.AA$AA)
rscu <- lapply(T, function(x) {
return(x/((1/length(x)) * sum(x)))
})
names(rscu) <- NULL
rscu <- unlist(rscu)[as.character(SEQINR.UTIL$CODON.AA$CODON)]
is.na(rscu[!is.finite(rscu)]) <- TRUE
rscu[is.na(rscu)] <- NA.rscu
return(rscu)
} else { # return all indices in a data.frame
eff <- table(factor(sequence, levels = SEQINR.UTIL$CODON.AA$CODON))
freq <- eff/(floor(length(seq)/3))
T <- split(freq, SEQINR.UTIL$CODON.AA$AA)
rscu <- lapply(T, function(x) {
return(x/((1/length(x)) * sum(x)))
})
names(rscu) <- NULL
rscu <- unlist(rscu)[as.character(SEQINR.UTIL$CODON.AA$CODON)]
is.na(rscu[!is.finite(rscu)]) <- TRUE
rscu[is.na(rscu)] <- NA.rscu
df <- data.frame(SEQINR.UTIL$CODON.AA$AA, eff = eff, freq = as.vector(freq), RSCU = rscu)
names(df) = c("AA", "codon", "eff", "freq", "RSCU")
return(df)
}
}
dotchart.uco <- function(x, numcode = 1, aa3 = TRUE, cex = 0.7,
alphabet = s2c("tcag"), pch = 21, gpch = 20, bg = par("bg"),
color = par("fg"), gcolor = par("fg"), lcolor = "gray", xlim, ...)
{
if( is.null(names(x)) ) names(x) <- words( alphabet = alphabet )
#
# General sorting
#
x <- sort(x)
labels <- names(x)
stringlabel = paste(labels, sep="", collapse="")
groups <- as.factor(translate(s2c(stringlabel), numcode = numcode))
gdata <- sapply(split(x, groups), sum)
#
# Now, sorting by aa order
#
gordered <- rank(gdata)
xidx <- numeric(64)
for( i in seq_len(64) )
{
xidx[i] <- -0.01*i + gordered[groups[i]]
}
x <- x[order(xidx)]
labels <- names(x)
stringlabel = paste(labels, sep="", collapse="")
aa <- translate(s2c(stringlabel), numcode = numcode)
groups <- factor(aa, levels = unique(aa))
gdata <- sapply(split(x, groups), sum)
if( missing(xlim) ) xlim <- c(0, max(gdata))
if( aa3 )
{
levels(groups) <- aaa(levels(groups))
}
dotchart(x = x, labels = labels, groups = groups, gdata = gdata,
cex = cex, pch = pch, gpch = gpch, bg = bg, color = color,
gcolor = gcolor, lcolor = lcolor, xlim, ...)
#
# Return invisibly for further plots
#
result <- list(0)
result$x <- x
result$labels <- labels
result$groups <- groups
result$gdata <- gdata
ypg <- numeric( length(levels(groups)) )
i <- 1
for( aa in levels(groups) )
{
ypg[i] <- length(which(groups == aa)) + 2
i <- i + 1
}
ypg <- rev(cumsum(rev(ypg))) - 1
names(ypg) <- levels(groups)
result$ypg <- ypg
ypi <- numeric( length(x) )
for( i in seq_len(length(x)) )
{
ypi[i] <- ypg[groups[i]]
}
antirank <- function(x)
{
return( seq(length(x),1,by=-1 ))
}
ypi <- ypi - unlist(sapply(split(x, groups),antirank))
names(ypi) <- labels
result$ypi <- ypi
return( invisible(result) )
}
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