Nothing
draw.oriloc <- function(ori, main = "Title",
xlab = "Map position in Kb",
ylab = "Cumulated combined skew in Kb", las = 1, las.right = 3,
ta.mtext = "Cumul. T-A skew", ta.col = "pink", ta.lwd = 1,
cg.mtext = "Cumul. C-G skew", cg.col = "lightblue", cg.lwd = 1,
cds.mtext = "Cumul. CDS skew", cds.col = "lightgreen", cds.lwd = 1,
sk.col = "black", sk.lwd = 2,
add.grid = TRUE, ...){
#
# Get data and use Kb units for skews and map positions:
#
ta <- ori$x/1000 # Cumulated T-A skew in Kb
cg <- ori$y/1000 # Cumulated C-G skew in Kb
skew <- ori$skew/1000 # Cumulated combined skew in Kb
cdsskew <- ori$CDS.excess # Cumulated CDS orientation bias
start.kb <- ori$start.kb
end.kb <- ori$end.kb
#
# This is to deal with CDS that wrapp around the genome:
#
wrapped <- which(abs(ori$start.kb - ori$end.kb) >= 50)
if(length(wrapped)!=0){
if(wrapped == length(cdsskew)){
start.kb[wrapped] <- max(start.kb[wrapped], end.kb[wrapped])
end.kb[wrapped] <- max(start.kb[wrapped], end.kb[wrapped])
}
if(wrapped == 1){
end.kb[wrapped] <- min(start.kb[wrapped], end.kb[wrapped])
start.kb[wrapped] <- min(start.kb[wrapped], end.kb[wrapped])
}
}
#
# Use CDS midpoints as x-coordinates:
#
meancoord <- (start.kb + end.kb)/2
ymin <- min(ta, cg, skew)
ymax <- max(ta, cg, skew)
xmin <- min(meancoord)
xmax <- max(meancoord)
ticks <- pretty(cdsskew)
ticks.y <- (ymax-ymin)/(max(cdsskew) - min(cdsskew))*(ticks - min(cdsskew)) + ymin
cds.y <- (ymax-ymin)/(max(cdsskew) - min(cdsskew))*(cdsskew - min(cdsskew)) + ymin
plot(meancoord, cg, type="l", xlab = xlab,
ylab = ylab, xlim = c(xmin, xmax), ylim = c(ymin, ymax),
cex.lab = 1.35, col = cg.col, main = main, lwd = cg.lwd, las = las, ...)
axis(side = 4, at = ticks.y, labels = ticks, col = cds.col, las = las.right)
#
# Add vertical grid when required:
#
if(add.grid){
tmp <- pretty(meancoord)
abline(v = tmp, col = "grey", lty=3)
tmp <- tmp[-length(tmp)] + diff(tmp)/2
abline(v = tmp, col = "grey", lty=3)
}
lines(meancoord, ta, col = ta.col, lwd = ta.lwd)
lines(meancoord, skew, col = sk.col, lwd = sk.lwd)
lines(meancoord, cds.y, col = cds.col, lwd = cds.lwd)
mtext(ta.mtext, col = ta.col, adj = 0)
mtext(cg.mtext, col = cg.col)
mtext(cds.mtext, col = cds.col, adj=1)
}
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