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# plot.aCGHsegmented <-
# function(x, add=FALSE, y=TRUE, psi.lines=TRUE, ...){
# #se y=TRUE disegna anche le osservazioni e add e'ignorato
# if(y) add<-FALSE
# arg<-list(...)
# if(is.null(arg$col)) arg$col=1
# if(is.null(arg$lwd)) arg$lwd=1
# if(is.null(arg$lty)) arg$lty=1
# if(is.null(arg$xlab)) arg$xlab<-"Genome Location"
# if(is.null(arg$ylab)) arg$ylab<-"LogRatio"
#
# yy<-x$y
# n<-length(yy)
# if(x$n.psi<=0) {
# if(y){
# plot(yy, ylab=arg$ylab, xlab=arg$xlab, pch=20, col=grey(.7))
# abline(h=x$est.means, ...)
# } else {
# if(add) {abline(h=x$est.means, ...)} else {
# plot(yy, ylab=arg$ylab, xlab=arg$xlab, type="n")
# abline(h=x$est.means, ...) }
# }
# return(invisible(NULL))
# }
# #coll=arg$col
# psi<-x$psi
# est.means<-x$est.means
# if(y) {
# plot(yy, ylab=arg$ylab, xlab=arg$xlab, pch=20, col=grey(.7))
# points(c(1,psi,n), c(est.means,est.means[length(est.means)]),
# type="s",...)
# } else {
# if(!add) {
# plot(c(1,psi,n), c(est.means,est.means[length(est.means)]),
# type="s",ylab=arg$ylab, xlab=arg$xlab, col=arg$col, lwd=arg$lwd, lty=arg$lty)
# } else {
# points(c(1,psi,n), c(est.means,est.means[length(est.means)]),
# type="s",col=arg$col, lwd=arg$lwd, lty=arg$lty)
# }
# }
# if(psi.lines){
# segments(x0=psi,y0=par()$usr[3],x1=psi,y1=est.means[-1],lty=3 ,col=arg$col)
# points(psi,rep(par()$usr[3],length(psi)),pch=19 ,col=arg$col)
# }
# invisible(NULL)
# }
plot.aCGHsegmented <- function(x, add=FALSE, y=TRUE, psi.lines=TRUE, typeL="l", what=c("lines","criterion"),...){
#typeL if "s"..
#y: ignored if add=TRUE
#x:
what<-match.arg(what, c("lines","criterion"))
if(what=="criterion"){
if(length(x$criterion)<=0) stop("The object does not include the criterion values (set 'output' to '2' or '3' in jumpoints())")
plot(0:(length(x$criterion)-1), x$criterion, type="b", xlab="No. of change points", ylab="Criterion values", lwd=1.5, xaxt="n")
axis(1, at=0:(length(x$criterion)-1), cex.axis=.8)
points(which.min(x$criterion)-1, min(x$criterion), pch=19)
return(invisible(NULL))
}
typeL<-match.arg(typeL, c("l","s"))
arg<-list(...)
if(is.null(arg$col)) arg$col=1
if(is.null(arg$lwd)) arg$lwd=1
if(is.null(arg$lty)) arg$lty=1
if(is.null(arg$xlab)) arg$xlab<-"Genome Location"
if(is.null(arg$ylab)) arg$ylab<-"LogRatio"
yy<-x$y
xx<- if(is.null(x$x)) 1:length(yy) else x$x
n<-length(yy)
if(x$n.psi<=0) {
if(y){
plot(xx, yy, ylab=arg$ylab, xlab=arg$xlab, pch=20, col=grey(.7))
abline(h=x$est.means, ...)
} else {
if(add) {abline(h=x$est.means, ...)} else {
plot(yy, ylab=arg$ylab, xlab=arg$xlab, type="n")
abline(h=x$est.means, ...) }
}
return(invisible(NULL))
}
#coll=arg$col
psi<-x$psi
est.means<-x$est.means
m<-min(x$rangeX)
M<-max(x$rangeX)
Y<-rep(est.means,each=2)
X<-c(m,rep(psi, each=2) ,M)
id1<-seq(1,length(X), by=2)
id2<-seq(2,length(X), by=2)
if(!add){
if(y) plot(xx,yy , ylab=arg$ylab, xlab=arg$xlab, pch=20, col=grey(.7))
else plot(xx,yy , ylab=arg$ylab, xlab=arg$xlab, type="n")
}
if(typeL=="s") points(X[id1],Y[id1],X[id2],Y[id2], col=arg$col, lwd=arg$lwd, lty=arg$lty, type="s")
else segments(X[id1],Y[id1],X[id2],Y[id2], col=arg$col, lwd=arg$lwd, lty=arg$lty)
if(psi.lines){
segments(x0=psi,y0=par()$usr[3],x1=psi,y1=apply(matrix(Y[-c(1,length(Y))],ncol=2, byrow=TRUE),1,max),lty=3 ,col=arg$col)
points(psi,rep(par()$usr[3],length(psi)),pch=19 ,col=arg$col)
}
invisible(NULL)
}
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