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# $Id: overplot.R 1947 2015-04-23 21:18:42Z warnes $
panel.overplot <- function(formula, data, subset, col, lty, ...)
{
m <- match.call()
m[[1]] <- as.name("plot")
eval(m, parent.frame() )
m[[1]] <- as.name("lowess")
tmp <- eval(m, parent.frame() )
lines( tmp, col=col, lwd=2, lty=lty )
}
overplot <- function (formula, data = parent.frame(),
same.scale=FALSE,
xlab, ylab,
xlim, ylim,
min.y, max.y,
log='',
panel='panel.overplot',
subset,
plot=TRUE,
groups,
main,
f=2/3,
... )
{
###
# check that the formula had the right form
###
if(
length(formula)!=3 ||
length(formula[[3]]) != 3 ||
formula[[3]][[1]] != as.name("|")
)
stop("Formula must be of the form y ~ x1 | x2")
if(!missing(subset))
{
flag <- eval(substitute(subset), envir=data)
data <- data[flag,]
}
###
# Get the actual formula values
###
cond <- eval(formula[[3]][[3]], envir=data, parent.frame())
x <- eval(formula[[3]][[2]], envir=data, parent.frame())
y <- eval(formula[[2]], envir=data, parent.frame())
#print(data.frame(cond,x,y))
y.all.min <- min(y, na.rm=TRUE)
y.all.max <- max(y, na.rm=TRUE)
x.all.min <- min(x, na.rm=TRUE)
x.all.max <- max(x, na.rm=TRUE)
if (length(cond) == 0) {
cond <- list(as.factor(rep(1, length(x))))
}
if (!is.factor(cond))
{
cond <- factor(cond)
}
###
# create a new call to the requested function
###
mycall <- match.call(expand.dots=FALSE)
mycall$panel <- mycall$plot <- mycall$groups <- mycall$same.scale <- NULL
mycall$min.y <- mycall$max.y <- NULL
mycall$data <- data
# remove condition from formula
mycall$formula[3] <- formula[[3]][2]
# function name
if(is.character(panel))
panel <- as.name(panel)
else
panel <- deparse(substitute(panel))
mycall[[1]] <- as.name(panel)
# ylim
if(same.scale)
{
if(missing(ylim))
mycall$ylim <- range(y[y>0],na.rm=TRUE)
}
# xlim is always the same for all graphs
if(missing(xlim))
if(log %in% c("x","xy"))
mycall$xlim <- range(x[x>0],na.rm=TRUE)
else
mycall$xlim <- range(x,na.rm=TRUE)
###
# Only plot groups with non-na entries
##
tmp <- na.omit(data.frame(x,y,cond))
leveln <- sapply( split(tmp, tmp$cond), nrow )
if(missing(groups)) groups <- names(leveln)
ngroups <- length(groups)
if(!missing(min.y) && length(min.y==1))
min.y <- rep(min.y, length=ngroups)
if(!missing(max.y) && length(max.y==1))
max.y <- rep(max.y, length=ngroups)
###
# Set up the plot regions
###
oldpar <- par()['mar']
on.exit(par(oldpar))
par(mar=par("mar") +c(0,ngroups*2.5,0,0))
###
# Ok. Now iterate over groups
##
i <- 1
for(level in groups)
{
if(i>1)
{
par(new=TRUE)
}
mycall$subset <- (cond==level)
mycall$ylab <- ''
mycall$xlab <- ''
mycall$xaxt = 'n'
mycall$yaxt = 'n'
mycall$pch = i
mycall$col = i
mycall$lty = i
tmp.y <- y[mycall$subset & cond==level]
## If nothing to plot, skip to next level
if(!any(is.finite(tmp.y))) next
min.tmp.y <- min(tmp.y, na.rm=TRUE)
max.tmp.y <- max(tmp.y, na.rm=TRUE)
if( !missing(min.y) || !missing(max.y) )
{
if(!missing(min.y) && !missing(max.y) )
{
mycall$ylim <- c(min.y[i], max.y[i])
}
else if(missing(min.y) && !missing(max.y))
{
if(same.scale)
mycall$ylim <- c(y.all.min, max.y[i])
else
mycall$ylim <- c(min.tmp.y, max.y[i])
}
else # !missing(min.y) && missing(max.y)
{
if(same.scale)
mycall$ylim <- c(min.y[i], y.all.max)
else
mycall$ylim <- c(min.y[i], max.tmp.y)
}
}
if(plot)
{
status <- try(
eval(mycall, parent.frame())
)
if('try-error' %in% class(status))
break;
}
usr <- par("usr")
axis(side=2,line=2.5*(i-1),lty=i,col=i,lwd=2)
title(ylab=level, line=2.5*(i-1))
if(i == 1)
axis(side=1)
i <- i+1
}
if(missing(xlab))
xlab <- as.character(formula[[3]][[2]])
if(missing(ylab))
ylab <- as.character(formula[[2]])
if(missing(main))
main <- paste("plot of ", xlab, "vs.", ylab, "by",
as.character(formula[[3]][[3]]))
if(i>1)
{
title(main=main,xlab=xlab)
title(ylab=ylab, line=2.5*(i-1))
}
par(oldpar)
invisible( split(data.frame(x,y),cond) )
}
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