Quoting Jo?o Fadista <joao.fadista at="" agrsci.dk="">:
> Dear all,
>
> I would like to know how can I make an MA-plot where I can add
> smooth curves that represent the trends characteristic to each print
> tip.
> See the desired plot in
>
http://www.stat.unc.edu/faculty/marron/DataAnalyses/SiZer/SiZer_Exam
ples.html#Eg3:MicroArray
> <http: www.stat.unc.edu="" faculty="" marron="" dataanalyses="" sizer="" sizer_exa="" mples.html#eg3:microarray="">
>
>
> Kind regards,
> Jo?o Fadista
In Limma, the function 'plotPrintTipLoess' produces a figure with
subplots representing each print tip group, and their loess curves.
Not what you had in mind, but you may like it.
Alternatively, see ?scatter.smooth. You can use that function to add
loess curves to your MA plot. I use a version I made of it (not very
elegantly :) that allows me to choose more plotting parameters
(colours etc) than the original. You can easily modify it further to
suit your needs:
#tweak to scatter.smooth (more control over plotting parameters)
sm<-function (x, y = NULL, span = 2/3, degree = 1, family =
c("symmetric",
"gaussian"), xlab = NULL, ylab = NULL, ylim = NULL, xlim=NULL,
evaluation = 50,
pch=NULL, bg=NULL, cex=NULL, col=NULL, lwd=NULL, lty=NULL,
lcol=NULL, ...)
{
#xlabel <- if (!missing(x))
# deparse(substitute(x))
#ylabel <- if (!missing(y))
# deparse(substitute(y))
#xy <- xy.coords(x, y, xlabel, ylabel)
#x <- xy$x
#y <- xy$y
#xlab <- if (is.null(xlab))
# xy$xlab
#else xlab
#ylab <- if (is.null(ylab))
# xy$ylab
#else ylab
prediction <- loess.smooth(x, y, span, degree, family,
evaluation)
if (is.null(ylim)) ylim<-range(y, prediction$y, na.rm = TRUE)
if (is.null(xlim)) xlim<-range(x, prediction$x, na.rm = TRUE)
if (is.null(pch)) pch<-16
if (is.null(cex)) cex<-1
if (is.null(col)) col<-"black"
if (is.null(lwd)) lwd<-1
if (is.null(lty)) lty<-1
if (is.null(lcol)) lcol<-"red"
plot(x, y, xlim = xlim, ylim = ylim, ,xlab = xlab, ylab = ylab,
pch=pch, bg=bg, cex=cex, col=col)
lines(prediction,lwd=lwd,lty=lty,col=lcol,ylim = ylim, xlim =
xlim)
invisible()
}
Jose
--
Dr. Jose I. de las Heras Email: J.delasHeras at
ed.ac.uk
The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131
6513374
Institute for Cell & Molecular Biology Fax: +44 (0)131
6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK
