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Slight change to the vioplot function from Daniel Adler that plots median lines instead of points, and gives the option to plot either side of a violin rather than always both.
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| ### Plot with different colors, edit from kory, http://stackoverflow.com/questions/14975853/how-can-i-create-violin-plot-in-different-colours | |
| vioplot2 <- function (x, ..., range = 1.5, h = NULL, ylim = NULL, names = NULL, | |
| horizontal = FALSE, col = "magenta", border = "black", lty = 1, | |
| lwd = 1, rectCol = "black", colMed = "white", pchMed = 19, | |
| at, add = FALSE, wex = 1, drawRect = TRUE, side="both") | |
| { | |
| datas <- list(x, ...) | |
| n <- length(datas) | |
| if (missing(at)) | |
| at <- 1:n | |
| upper <- vector(mode = "numeric", length = n) | |
| lower <- vector(mode = "numeric", length = n) | |
| q1 <- vector(mode = "numeric", length = n) | |
| q2 <- vector(mode = "numeric", length = n) | |
| q3 <- vector(mode = "numeric", length = n) | |
| med <- vector(mode = "numeric", length = n) | |
| base <- vector(mode = "list", length = n) | |
| height <- vector(mode = "list", length = n) | |
| baserange <- c(Inf, -Inf) | |
| args <- list(display = "none") | |
| radj <- ifelse(side == "right", 0, 1) | |
| ladj <- ifelse(side == "left", 0, 1) | |
| if (!(is.null(h))) | |
| args <- c(args, h = h) | |
| med.dens <- rep(NA, n) | |
| for (i in 1:n) { | |
| data <- datas[[i]] | |
| data.min <- min(data) | |
| data.max <- max(data) | |
| q1[i] <- quantile(data, 0.25) | |
| q2[i] <- quantile(data, 0.5) | |
| q3[i] <- quantile(data, 0.75) | |
| med[i] <- median(data) | |
| iqd <- q3[i] - q1[i] | |
| upper[i] <- min(q3[i] + range * iqd, data.max) | |
| lower[i] <- max(q1[i] - range * iqd, data.min) | |
| est.xlim <- c(min(lower[i], data.min), max(upper[i], | |
| data.max)) | |
| smout <- do.call("sm.density", c(list(data, xlim = est.xlim), | |
| args)) | |
| med.dat <- do.call("sm.density", | |
| c(list(data, xlim=est.xlim, | |
| eval.points=med[i], display = "none"))) | |
| med.dens[i] <- med.dat$estimate | |
| hscale <- 0.4/max(smout$estimate) * wex | |
| base[[i]] <- smout$eval.points | |
| height[[i]] <- smout$estimate * hscale | |
| med.dens[i] <- med.dens[i] * hscale | |
| t <- range(base[[i]]) | |
| baserange[1] <- min(baserange[1], t[1]) | |
| baserange[2] <- max(baserange[2], t[2]) | |
| } | |
| if (!add) { | |
| xlim <- if (n == 1) | |
| at + c(-0.5, 0.5) | |
| else range(at) + min(diff(at))/2 * c(-1, 1) | |
| if (is.null(ylim)) { | |
| ylim <- baserange | |
| } | |
| } | |
| if (is.null(names)) { | |
| label <- 1:n | |
| } | |
| else { | |
| label <- names | |
| } | |
| boxwidth <- 0.05 * wex | |
| if (!add) | |
| plot.new() | |
| if (!horizontal) { | |
| if (!add) { | |
| plot.window(xlim = xlim, ylim = ylim) | |
| axis(2) | |
| axis(1, at = at, label = label) | |
| } | |
| box() | |
| for (i in 1:n) { | |
| polygon(x = c(at[i] - radj*height[[i]], rev(at[i] + ladj*height[[i]])), | |
| y = c(base[[i]], rev(base[[i]])), | |
| col = col[i %% length(col) + 1], border = border, | |
| lty = lty, lwd = lwd) | |
| if (drawRect) { | |
| lines(at[c(i, i)], c(lower[i], upper[i]), lwd = lwd, | |
| lty = lty) | |
| rect(at[i] - radj*boxwidth/2, | |
| q1[i], | |
| at[i] + ladj*boxwidth/2, | |
| q3[i], col = rectCol) | |
| # median line segment | |
| lines(x = c(at[i] - radj*med.dens[i], | |
| at[i], | |
| at[i] + ladj*med.dens[i]), | |
| y = rep(med[i],3)) | |
| } | |
| } | |
| } | |
| else { | |
| if (!add) { | |
| plot.window(xlim = ylim, ylim = xlim) | |
| axis(1) | |
| axis(2, at = at, label = label) | |
| } | |
| box() | |
| for (i in 1:n) { | |
| polygon(c(base[[i]], rev(base[[i]])), | |
| c(at[i] - radj*height[[i]], rev(at[i] + ladj*height[[i]])), | |
| col = col[i %% length(col) + 1], border = border, | |
| lty = lty, lwd = lwd) | |
| if (drawRect) { | |
| lines(c(lower[i], upper[i]), at[c(i, i)], lwd = lwd, | |
| lty = lty) | |
| rect(q1[i], at[i] - radj*boxwidth/2, q3[i], at[i] + | |
| ladj*boxwidth/2, col = rectCol) | |
| lines(y = c(at[i] - radj*med.dens[i], | |
| at[i], | |
| at[i] + ladj*med.dens[i]), | |
| x = rep(med[i],3)) | |
| } | |
| } | |
| } | |
| invisible(list(upper = upper, lower = lower, median = med, | |
| q1 = q1, q3 = q3)) | |
| } |
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