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## plot method for objects seqrf produced by seqrf.
## author: Gilbert Ritschard
plot.seqrf <- function(x, space=0, border=NA, which.plot="medoids", ylab=NA,
main=NULL, frame.plot=FALSE, info="all", skipar = FALSE, ...){
dotargs <- list(...)
if (!skipar){
def.par <- par(no.readonly = TRUE) # save default, for resetting...
on.exit(par(def.par))
}
plot.types <- c("both","medoids","diss.to.med")
if (! which.plot %in% plot.types)
stop(" which.plot must be one of ", paste(plot.types, collapse=", "))
info.types <- c("all","stat","subtitle","none")
if (is.null(ylab)) ylab <- NA
xaxt <- "s"
if (!is.null(dotargs[["xaxis"]]))
if(!dotargs[["xaxis"]]) xaxt <- "n"
xaxis <- xaxt == "s"
yaxt <- "n"
if (!is.null(dotargs[["yaxis"]]) & which.plot=="diss.to.med")
if(dotargs[["yaxis"]]) yaxt <- "s"
yaxis <- yaxt == "s"
sep.ylab <- (isFALSE(dotargs[["yaxis"]]) && (is.null(ylab) || !is.na(ylab)))
cex.lab <- par("cex.lab")
if ("cex.lab" %in% names(list(...))) cex.lab <- list(...)[["cex.lab"]]
if(!skipar & which.plot=="both"){
##opar <- par(mfrow=c(1,2), oma=c(3,(!is.na(ylab)*5),(!is.null(main))*3,0), mar=c(1, 1, 2, 0))
if (info %in% c("all","stat"))
par(oma=c(3,0,(!is.null(main))*3,.5))
else
par(oma=c(0,0,(!is.null(main))*3,.5))
layout(matrix(c(1,2),ncol=2), widths=c(.6,.4))
}
if (info %in% c("all","subtitle")){
titmed <- "Group medoids"
titbxp <- "Distances to medoids"
if (!is.null(main)) {
if (which.plot=="medoids")
titmed <- paste(main,titmed, sep=": ")
else if (which.plot=="diss.to.med")
titbxp <- paste(main, titbxp, sep=": ")
}
}
else if (!is.null(main) & which.plot == "both")
titmed <- titbxp <- NULL
else
titmed <- titbxp <- main
if (!skipar){
if (!is.na(ylab))
par(mar=c(xaxis * 2.5, 4 , (info %in% c("all","subtitle")) * 2, .5))
else if (!is.null(main) & info %in% c("none","stat"))
par(mar=c(xaxis * 2.5, 2 + yaxis , 2, .5))
else
par(mar=c(xaxis * 2.5, 2 + yaxis , (info %in% c("all","subtitle")) * 2, .5))
}
if (sep.ylab) {
sylab <- ylab
ylab <- NA
}
if (which.plot %in% c("medoids","both")){
plot(x[["seqtoplot"]], idxs = 0, space=space, border=border, ylab=ylab, main=titmed, ...)
if (sep.ylab)
title(ylab=sylab, line=1, cex.lab=cex.lab)
}
#if (!is.null(main) & which.plot == "diss.to.med")
# titbxp <- paste(main,titbxp, sep=": ")
if (which.plot %in% c("diss.to.med","both")){
heights <- x[["rf"]][["heights"]]
at <- x[["rf"]][["at"]]
pars = list(boxwex = 0.8, staplewex = 0.5, outwex = 0.5, frame.plot=frame.plot)
if (which.plot == "both" & !skipar){
if (!is.null(main) & info %in% c("none","stat"))
par(mar=c(xaxis * 2.5, 0, 2, .5))
else
par(mar=c(xaxis * 2.5, 0, (info %in% c("all","subtitle")) * 2, .5))
}
wtd.boxplot.tmr(x[["rf"]][["dist.list"]], x[["rf"]][["weights.list"]], horizontal=TRUE, width=heights,
main=titbxp, pars=pars, yaxt=yaxt, xaxt=xaxt, frame.plot=frame.plot,
ylim=range(unlist(x[["rf"]][["dist.list"]])), at=at, ylab=ylab, cex.lab=cex.lab)
if (which.plot=="diss.to.med" & sep.ylab)
title(ylab=sylab, line=1, cex.lab=cex.lab)
}
if (which.plot=="both") {
if(!is.null(main)) title(main=main, outer=TRUE)
if(info %in% c("all","stat"))title(sub=sprintf("Representation quality: R2=%0.2f and F=%0.2f",
x[["rf"]][["R2"]], x[["rf"]][["Fstat"]]), outer=TRUE, line=2)
}
}
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