Hi Viviana, >> I am doing kernel density plots, and am trying to make the lines thicker.
You need to hack the code for sm.density.compare. See the code below. This uses the same defaults as the original, but you can customize band colour, line width, and so on using arguments to the function. The easiest way to use it is to copy it into your environment space. The original code is untouched and may be accessed as sm:::sm.density.compare(). Regards, Mark. ## Hack on sm.density.compare ## Allows me to change colour of the band, to set ylim, and change lwd (was only for ## model="equal" option) sm.density.compare <- function (x, group, h, model = "none", bandcol = 'cyan', lwd = par("lwd"), usePolyg = NULL, asp=NA, xlab=opt$xlab, ylab=opt$ylab, ...) { if (!is.vector(x)) stop("sm.density.compare can handle only 1-d data") opt <- sm.options(list(...)) sm:::replace.na(opt, ngrid, 50) ## These all changed from replace.na() --> sm::: sm:::replace.na(opt, display, "line") sm:::replace.na(opt, xlab, deparse(substitute(x))) sm:::replace.na(opt, ylab, "Density") sm:::replace.na(opt, xlim, c(min(x) - diff(range(x))/4, max(x) + diff(range(x))/4)) sm:::replace.na(opt, eval.points, seq(opt$xlim[1], opt$xlim[2], length = opt$ngrid)) if (is.na(opt$band)) { if (model == "none") opt$band <- FALSE else opt$band <- TRUE } if ((model == "none") && opt$band) opt$band <- FALSE band <- opt$band ngrid <- opt$ngrid xlim <- opt$xlim nboot <- opt$nboot y <- x if (is.na(opt$test)) { if (model == "none") opt$test <- FALSE else opt$test <- TRUE } if ((model == "none") && opt$test) opt$test <- FALSE test <- opt$test if (opt$display %in% "none") band <- FALSE fact <- factor(group) fact.levels <- levels(fact) nlev <- length(fact.levels) ni <- table(fact) if (band & (nlev > 2)) { cat("Reference band available to compare two groups only.", "\n") band <- FALSE } if (length(opt$lty) < nlev) opt$lty <- 1:nlev if (length(opt$col) < nlev) opt$col <- 2:(nlev + 1) if (missing(h)) h <- h.select(x, y = NA, group = group, ...) opt$band <- band opt$test <- test estimate <- matrix(0, ncol = opt$ngrid, nrow = nlev) se <- matrix(0, ncol = opt$ngrid, nrow = nlev) for (i in 1:nlev) { sm <- sm.density(y[fact == fact.levels[i]], h = h, display = "none", eval.points = opt$eval.points) estimate[i, ] <- sm$estimate se[i, ] <- sm$se } eval.points <- sm$eval.points if (!(opt$display %in% "none" | band)) { plot(xlim, c(0, 1.1 * max(as.vector(estimate))), xlab = opt$xlab, ylab = opt$ylab, type = "n") #for (i in 1:nlev) lines(eval.points, estimate[i, ], lty = opt$lty[i], # col = opt$col[i]) for (i in 1:nlev) lines(eval.points, estimate[i, ], lty = opt$lty[i], ## lwd hacked in col = opt$col[i], lwd = lwd[i]) } est <- NULL p <- NULL if (model == "equal" & test) { if (nlev == 2) { ts <- sum((estimate[1, ] - estimate[2, ])^2) } else { sm.mean <- sm.density(y, h = h, xlim = opt$xlim, ngrid = opt$ngrid, display = "none")$estimate ts <- 0 for (i in 1:nlev) ts <- ts + ni[i] * sum((estimate[i, ] - sm.mean)^2) } p <- 0 est.star <- matrix(0, ncol = opt$ngrid, nrow = nlev) for (iboot in 1:nboot) { ind <- (1:length(y)) for (i in 1:nlev) { indi <- sample((1:length(ind)), ni[i]) est.star[i, ] <- sm.density(y[ind[indi]], h = h, ngrid = opt$ngrid, xlim = opt$xlim, display = "none")$estimate ind <- ind[-indi] } if (nlev == 2) { ts.star <- sum((est.star[1, ] - est.star[2, ])^2) } else { sm.mean <- sm.density(y, h = h, xlim = opt$xlim, ngrid = opt$ngrid, display = "none")$estimate ts.star <- 0 for (i in 1:nlev) { ts.star <- ts.star + ni[i] * sum((est.star[i, ] - sm.mean)^2) } } if (ts.star > ts) p <- p + 1 if (opt$verbose > 1) { cat(iboot) cat(" ") } } p <- p/nboot cat("\nTest of equal densities: p-value = ", round(p, 3), "\n") est <- list(p = p, h = h) } if (model == "equal" & band) { av <- (sqrt(estimate[1, ]) + sqrt(estimate[2, ]))/2 se <- sqrt(se[1, ]^2 + se[2, ]^2) upper <- (av + se)^2 lower <- pmax(av - se, 0)^2 plot(xlim, c(0, 1.1 * max(as.vector(estimate), upper)), xlab = xlab, ylab = ylab, type = "n", asp=asp, ...) ## ... and asp added; was opt$xlab and opt$ylab polygon(c(eval.points, rev(eval.points)), c(upper, rev(lower)), col = bandcol, border = 0) ## was col = "cyan" if (is.null(usePolyg)) { lines(eval.points, estimate[1, ], lty = opt$lty[1], col = opt$col[1], lwd = lwd[1]) lines(eval.points, estimate[2, ], lty = opt$lty[2], col = opt$col[2], lwd = lwd[2]) } else { polygon(eval.points, estimate[1, ], lty = opt$lty[1], col = opt$col[1], lwd = lwd[1]) polygon(eval.points, estimate[2, ], lty = opt$lty[2], col = opt$col[2], lwd = lwd[2]) } est <- list(p = p, upper = upper, lower = lower, h = h) } invisible(est) } Viviana Ruiz wrote: > > Hi, > > I am doing kernel density plots, and am trying to make the lines thicker. > I > comparing three groups, in sm.density.compare. I tried changing lwd to > make > the line sthicker right on the density compare call, but was not able to > do > it. There is not an option in sm.options to specify line thickness, as > well > as cex.ylab or cex.xlab- I tried it and it does not change the thickness > of > the lines. Does anyone know how to do this? > > Thanks! > > VRG > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > -- View this message in context: http://www.nabble.com/sm.options-tp22367057p22367994.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.