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##
# This function draws two graphics, one of the CA of a DNA sequence, and one of
# start/stop codons positions in the three reading frames. This for the direct or
# the reverse strand.
##
#v.18.08.2011
draw.recstat <- function(rec, fac = 1, direct = TRUE, xlim = c(1, seqsize), col = c("red", "blue", "purple"))
{
if (fac < 0 | 4 < fac)
{ # test if factor is between 1 and 4
print("Factor number is not in 1:4.")
return()
}
seq <- rec[[1]] # recovery of elements of list rec
sizewin <- rec[[2]]
shift <- rec[[3]]
seqsize <- rec[[4]]
seqname <- rec[[5]]
vstopd <- rec[[8]]
vstopr <- rec[[9]]
vinitd <- rec[[10]]
vinitr <- rec[[11]]
recd <- rec[[14]]
recr <- rec[[15]]
if (xlim[1] < 1 | xlim[1] > seqsize)
{
xlim <- c(1, xlim[2])
}
if (seqsize < xlim[2] | 1 > xlim[2])
{
xlim <- c(xlim[1], seqsize)
}
par(mfrow = c(2, 1), mar = c(0, 4, 4, 2) + 0.1) # division of the window for a closer between plots
par(xaxs = "i")
seqisize <- floor((dim(recd$li)[1])/3) # number of window by reading frame, we take the integer part
if ((dim(recd$li)[1])%%3 == 1) # adaptation of number of window between each reading frame
{
seqisize1 <- seqisize + 1 # for fr1
seqisize2 <- seqisize # for fr2
}
if ((dim(recd$li)[1])%%3 == 2)
{
seqisize1 <- seqisize + 1
seqisize2 <- seqisize + 1
}
if ((dim(recd$li)[1])%%3 == 0)
{
seqisize1 <- seqisize
seqisize2 <- seqisize
}
##
##direct strand##
##
if (direct)
{
plot((sizewin/2) + (0:(seqisize1 - 1))*shift, recd$li[1:seqisize1, fac], type = "l", lty = 1,
col = col[1], xlim = xlim, ylim = c(min(recd$li[, fac]), max(recd$li[, fac])),
main = "Direct strand", xlab = "", ylab = "Factor scores", bty = 'l') # reading frame 1
lines((sizewin/2) + (0:(seqisize2 - 1))*shift + 1, recd$li[(seqisize1 + 1):(seqisize1 + seqisize2), fac],
lty = 2, col = col[2], ylab = "2") # reading frame 2
lines((sizewin/2) + (0:(seqisize - 1))*shift + 2, recd$li[(seqisize1 + seqisize2 + 1):(dim(recd$li)[1]), fac],
lty = 3, col = col[3], ylab = "3") # reading frame 3
legend("topleft", legend = c(paste("Sequence name:", seqname), paste("Sequence length:", seqsize, "bp")),
inset = c(-0.15, -0.2), bty = "n", xpd = TRUE)
vstopdindphase <- numeric()
if (length(vstopd) > 0)
{ # test if vector is not empty because problem with modulo
vstopdindphase <- sapply(1:length(vstopd), function(x)
{ # index vector of reading frame of vector vstopd
if (vstopd[x]%%3 == 1)
{
vstopdindphase <- c(vstopdindphase, 2.5)
}
else
{
if (vstopd[x]%%3 == 2)
{
vstopdindphase <- c(vstopdindphase, 1.5)
}
else
{
vstopdindphase <- c(vstopdindphase, 0.5)
}
}
})
}
vinitdindphase <- numeric()
if (length(vinitd) > 0)
{ # test if vector is not empty because problem with modulo
vinitdindphase <- sapply(1:length(vinitd), function(x)
{ # index vector of reading frame of vector vinitd
if (vinitd[x]%%3 == 1)
{
vinitdindphase <- c(vinitdindphase, 3)
}
else
{
if (vinitd[x]%%3 == 2)
{
vinitdindphase <- c(vinitdindphase, 2)
}
else
{
vinitdindphase <- c(vinitdindphase, 1)
}
}
})
}
par(mar = c(5, 4, 3, 2) + 0.1)
plot(vstopd, vstopdindphase, pch = 25, cex = 0.7, xlim = xlim, ylim = c(0.25, 3), axes = TRUE,
ann = TRUE, tcl = -0.5, bty = 'l', yaxt = 'n', xlab = "Start/Stop positions (bp)",
ylab = '', xpd = FALSE) # stop codons positions
points(vinitd, vinitdindphase, pch = 24, bg = "slategray", cex = 0.7, col = 'slategray') # start codons positions
abline(h = c(3.1, 2.4, 2.1, 1.4, 1.1, 0.4), col = c(col[1], col[1], col[2], col[2], col[3], col[3]),
lty = c(1, 1, 2, 2, 3, 3))
text(x = (xlim[1]-(xlim[2]-xlim[1])*0.75/6), pos = 4, y = c(2.75, 1.75, 0.75), labels = paste("Ph. ", c(0, 1, 2)), xpd = TRUE)
}
##
##reverse strand##
##
if (!direct)
{
plot((sizewin/2) + (0:(seqisize1 - 1))*shift, recr$li[1:seqisize1, fac], type = "l", lty = 1,
col = col[1], xlim = xlim, ylim = c(min(recr$li[, fac]), max(recr$li[, fac])),
main = "Reverse strand", xlab = "", ylab = "Factor scores", bty = 'l') # reading frame 1
lines((sizewin/2) + (0:(seqisize2-1))*shift + 1, recr$li[(seqisize1 + 1):(seqisize1 + seqisize2), fac],
lty = 2, col = col[2], ylab="2") # reading frame 2
lines((sizewin/2) + (0:(seqisize - 1))*shift + 2, recr$li[(seqisize1 + seqisize2 + 1):(dim(recr$li)[1]), fac],
lty = 3, col = col[3], ylab = "3") # reading frame 3
legend("topleft", legend = c(paste("Sequence name:", seqname), paste("Sequence length:", seqsize, "bp")),
inset = c(-0.15, -0.2), bty = "n", xpd = TRUE)
vstoprindphase <- numeric()
if (length(vstopr) > 0)
{ # test if vector is not empty because problem with modulo
vstoprindphase <- sapply(1:length(vstopr), function(x)
{ # index vector of reading frame of vector vstopr
if (vstopr[x]%%3 == 1)
{
vstoprindphase <- c(vstoprindphase, 2.5)
}
else
{
if (vstopr[x]%%3 == 2)
{
vstoprindphase <- c(vstoprindphase, 1.5)
}
else
{
vstoprindphase <- c(vstoprindphase, 0.5)
}
}
})
}
vinitrindphase <- numeric()
if (length(vinitr) > 0)
{ # test if vector is not empty because problem with modulo
vinitrindphase <- sapply(1:length(vinitr), function(x)
{ # index vector of reading frame of vector vinitr
if (vinitr[x]%%3 == 1)
{
vinitrindphase <- c(vinitrindphase, 3)
}
else
{
if (vinitr[x]%%3 == 2)
{
vinitrindphase <- c(vinitrindphase, 2)
}
else
{
vinitrindphase <- c(vinitrindphase, 1)
}
}
})
}
par(mar = c(5, 4, 3, 2) + 0.1)
plot(vstopr, vstoprindphase, pch = 25, cex = 0.7, xlim = xlim, ylim = c(0.25, 3), axes = TRUE,
ann = TRUE, tcl = -0.5, bty = 'l', yaxt = 'n', xlab = "Start/Stop positions (bp)",
ylab = '', xpd = FALSE) # stop codons positions
points(vinitr, vinitrindphase, pch = 24, bg = "slategray", cex = 0.7, col = 'slategray') # start codons positions
abline(h = c(3.1, 2.4, 2.1, 1.4, 1.1, 0.4), col = c(col[1], col[1], col[2], col[2], col[3], col[3]),
lty = c(1, 1, 2, 2, 3, 3))
text(x = (xlim[1]-(xlim[2]-xlim[1])*0.75/6), pos = 4, y = c(2.75, 1.75, 0.75), labels = paste("Ph. ", c(0, 1, 2)), xpd = TRUE)
}
}
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