Nothing
plot.cmap <- function(x, col=2, pch=16,
main="Contact map", sub="",
xlim=NULL, ylim=NULL,
xlab = "Residue index", ylab = xlab,
axes=TRUE, ann=par("ann"),
sse=NULL, sse.type="classic", sse.min.length=5,
bot=TRUE, left=TRUE,
helix.col="gray20", sheet.col="gray80",
sse.border=FALSE, add=FALSE,
...) {
dims <- dim(x)
if(is.null(xlim))
xlim <- c(1, dims[1])
if(is.null(ylim))
ylim <- c(1, dims[2])
if(!add) {
plot.new()
}
else {
axes <- FALSE
xlab <- NA; ylab <- NA;
main <- NA; sub <- NA;
sse <- NULL;
}
plot.window(xlim=xlim, ylim=ylim, ...)
inds <- which(x==1, arr.ind=TRUE)
points(inds, pch=pch, col=col)
if(!is.null(sse)) {
## Obtain SSE vector from PDB input 'sse'
if(is.pdb(sse))
sse$sse <- pdb2sse(sse)
h <- bounds( which(sse$sse == "H") )
e <- bounds( which(sse$sse == "E") )
## Remove short h and e elements that can crowd plots
if(length(h) > 0) {
inds <- which(h[,"length"]>=sse.min.length)
h <- h[inds,,drop=FALSE]
} else { h <- NULL }
if(length(e) > 0) {
inds <- which(e[,"length"]>=sse.min.length)
e <- e[inds,,drop=FALSE]
} else { e <- NULL }
if(sse.type != "classic")
warning("Only sse.type='classic' is currently available, 'fancy' coming soon")
off <- c(0.006, 0.039)
if(left) {
## Determine bottom and top of margin region
bo <- min(xlim) - (diff(xlim)*off[1])
to <- min(xlim) - (diff(xlim)*off[2])
if(length(h) > 0)
rect(xleft=bo, xright=to,
ybottom=h[,"start"], ytop=h[,"end"],
col=helix.col, border=sse.border)
if(length(e) > 0)
rect(xleft=bo, xright=to,
ybottom=e[,"start"], ytop=e[,"end"],
col=sheet.col, border=sse.border)
}
if(bot){
to <- min(ylim) - (diff(ylim)*off[1])
bo <- min(ylim) - (diff(ylim)*off[2])
if(length(h) > 0)
rect(xleft=h[,"start"], xright=h[,"end"],
ybottom=bo, ytop=to, col=helix.col, border=sse.border)
if(length(e) > 0)
rect(xleft=e[,"start"], xright=e[,"end"],
ybottom=bo, ytop=to, col=sheet.col, border=sse.border)
}
}
if(axes) {
box()
at <- axTicks(1); at[1] = 1
axis(1, at)
axis(2, at)
}
if(ann) {
# if(is.null(xlab)) xlab=xy$xlab
# if(is.null(ylab)) ylab=xy$ylab
title(main=main, sub=sub,
xlab=xlab, ylab=ylab, ...)
}
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.