R/create.violinplot.R

In BoutrosLab.plotting.general: Functions to Create Publication-Quality Plots

# The BoutrosLab.plotting.general package is copyright (c) 2012 Ontario Institute for Cancer Research (OICR)
# This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL
# (either version 1, or at your option, any later version) or the Artistic License 2.0.  Refer to LICENSE for the full license text.
# OICR makes no representations whatsoever as to the SOFTWARE contained herein.  It is experimental in nature and is provided WITHOUT
# WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. OICR MAKES NO REPRESENTATION
# OR WARRANTY THAT THE USE OF THIS SOFTWARE WILL NOT INFRINGE ANY PATENT OR OTHER PROPRIETARY RIGHT.
# By downloading this SOFTWARE, your Institution hereby indemnifies OICR against any loss, claim, damage or liability, of whatsoever kind or
# nature, which may arise from your Institution's respective use, handling or storage of the SOFTWARE.
# If publications result from research using this SOFTWARE, we ask that the Ontario Institute for Cancer Research be acknowledged and/or
# credit be given to OICR scientists, as scientifically appropriate.

### FUNCTION TO CREATE VIOLIN PLOTS ###############################################################
create.violinplot <- function(
	formula, data, filename = NULL, main = NULL, main.just = 'center', main.x = 0.5, main.y = 0.5,
	main.cex = 3, xlab.label = tail(sub('~', '', formula[-2]), 1), ylab.label = tail(sub('~', '', formula[-3]), 1),
	xlab.cex = 2, ylab.cex = 2, xlab.col = 'black', ylab.col = 'black', xlab.top.label = NULL,
	xlab.top.cex = 2, xlab.top.col = 'black', xlab.top.just = 'center', xlab.top.x = 0.5, xlab.top.y = 0,
	xaxis.lab = TRUE, yaxis.lab = TRUE, xaxis.cex = 1.5, yaxis.cex = 1.5, xaxis.col = 'black',
	yaxis.col = 'black', xaxis.fontface = 'bold', yaxis.fontface = 'bold', xaxis.rot = 0, yaxis.rot = 0,
	xaxis.tck = c(1, 0), yaxis.tck = c(1, 1), ylimits = NULL, yat = TRUE, col = 'black', lwd = 1,
	border.lwd = 1, bandwidth = 'nrd0', bandwidth.adjust = 1, extra.points = NULL, extra.points.pch = 21,
	extra.points.col = 'white', extra.points.border = 'black', extra.points.cex = 1, start = NULL,
	end = NULL, scale = FALSE, plot.horizontal = FALSE, top.padding = 0.1, bottom.padding = 0.7,
	left.padding = 0.5, right.padding = 0.3, key = NULL, legend = NULL, add.rectangle = FALSE,
	xleft.rectangle = NULL, ybottom.rectangle = NULL, xright.rectangle = NULL, ytop.rectangle = NULL,
	col.rectangle = 'transparent', alpha.rectangle = 1, height = 6, width = 6, resolution = 1600,
	size.units = 'in', enable.warnings = FALSE, description = 'Created with BoutrosLab.plotting.general',
	style = 'BoutrosLab', preload.default = 'custom', use.legacy.settings = FALSE, disable.factor.sorting = FALSE
    ) {

	### needed to copy in case using variable to define rectangles dimensions
        rectangle.info <- list(
        	xright = xright.rectangle,
                xleft = xleft.rectangle,
                ytop = ytop.rectangle,
                ybottom = ybottom.rectangle
                );

	# add preloaded defaults
	if (preload.default == 'paper') {
		}
	else if (preload.default == 'web') {
		}

	# Temp function to allow differential violin colour filling
	# panel.violin() author has been emailed about issue in the
	# original function preventing differential colouring.
	.panel.violin.mod <- function(x, y, box.ratio = 1, box.width = box.ratio / (1 + box.ratio),
		horizontal = TRUE, alpha = plot.polygon$alpha, border = plot.polygon$border,
		lty = plot.polygon$lty, lwd = plot.polygon$lwd, col = plot.polygon$col,
		varwidth = FALSE, bw = bandwidth, adjust = bandwidth.adjust, kernel = NULL,
		window = NULL, width = NULL, n = 50, from = NULL, to = NULL,
		cut = NULL, na.rm = TRUE, ..., identifier = 'violin') {

		if (all(is.na(x) | is.na(y))) {	return(); }

		x <- as.numeric(x);
		y <- as.numeric(y);
		plot.polygon <- trellis.par.get('plot.polygon');
		darg <- list();
		darg$bw <- bw;
		darg$adjust <- adjust;
		darg$kernel <- kernel;
		darg$window <- window;
		darg$width <- width;
		darg$n <- n;
		darg$from <- from;
		darg$to <- to;
		darg$cut <- cut;
		darg$na.rm <- na.rm;

		my.density <- function(x) {
			ans <- try(
				do.call('density', c(list(x = x), darg)),
				silent = TRUE
				);

			if (inherits(ans, 'try-error')) {
				list(x = rep(x[1], 3), y = c(0, 1, 0));
				}
			else { ans; }
			}

		numeric.list <- if (horizontal) { split(x, factor(y)); } else { split(y, factor(x)); }
		levels.fos <- as.numeric(names(numeric.list));

		# check colours are appropriate length
		if (length(col) < length(levels.fos)) { col <- rep(col, length(levels.fos)); }

		d.list <- lapply(numeric.list, my.density);
		dx.list <- lapply(d.list, '[[', 'x');
		dy.list <- lapply(d.list, '[[', 'y');
		max.d <- sapply(dy.list, max);
		if (varwidth) {	max.d[] <- max(max.d); }
		cur.limits <- current.panel.limits();
		xscale <- cur.limits$xlim;
		yscale <- cur.limits$ylim;
		height <- box.width;

		## Modified from methods::hasArg.
		hasGroupNumber <- function() {
			aname <- 'group.number';
			fnames <- names(formals(sys.function(sys.parent())));
			if (is.na(match(aname, fnames))) {
				if (is.na(match('...', fnames))) { FALSE; }
				else {
					dots.call <- eval(quote(substitute(list(...))), sys.parent());
					!is.na(match(aname, names(dots.call)));
					}
				}
			else { FALSE; }
			}

		if (hasGroupNumber()) {
			group <- list(...)$group.number;
			}
		else { group <- 0; }

		if (horizontal) {
			for (i in seq_along(levels.fos)) {
				if (is.finite(max.d[i])) {
					pushViewport(
						viewport(
							y = unit(levels.fos[i], 'native'),
							height = unit(height, 'native'),
					  		yscale = c(max.d[i] * c(-1, 1)),
							xscale = xscale
							)
						);

					grid.polygon(
						x = c(dx.list[[i]], rev(dx.list[[i]])),
						y = c(dy.list[[i]], -rev(dy.list[[i]])),
						default.units = 'native',
						name = trellis.grobname(
							identifier,
							type = 'panel',
							group = group
							),
						gp = gpar(fill = col[i], col = border, lty = lty, lwd = lwd, alpha = alpha)
						);

					popViewport();
					}
				}
			}
		else {
			for (i in seq_along(levels.fos)) {
				if (is.finite(max.d[i])) {
					pushViewport(
						viewport(
							x = unit(levels.fos[i], 'native'),
							width = unit(height, 'native'),
							xscale = c(max.d[i] * c(-1, 1)),
							yscale = yscale
							)
						);

					grid.polygon(
						y = c(dx.list[[i]], rev(dx.list[[i]])),
					  	x = c(dy.list[[i]], -rev(dy.list[[i]])),
						default.units = 'native',
						name = trellis.grobname(
							identifier,
							type = 'panel',
							group = group
							),
						gp = gpar(fill = col[i], col = border, lty = lty, lwd = lwd, alpha = alpha)
						);

					popViewport();
					}
				}
			}

		invisible();
		}

	# Now make the actual plot object
	trellis.object <- lattice::bwplot(
		formula,
		data,
		panel = function(from = start, to = end, varwidth = scale, ...) {

			# add rectangle if requested
			if (add.rectangle) {
				panel.rect(
					xleft = rectangle.info$xleft,
					ybottom = rectangle.info$ybottom,
					xright = rectangle.info$xright,
					ytop = rectangle.info$ytop,
					col = col.rectangle,
					alpha = alpha.rectangle,
					border = NA
					);
				}

			# update the plot parameters
			if (is.null(from) || is.null(to)) {
				.panel.violin.mod(varwidth = varwidth, ...);
				}
			else {
				.panel.violin.mod(from = from, to = to, varwidth = varwidth, ...);
				}

			# add extra points if requested
			if (!is.null(extra.points)) {
				for (i in 1:length(extra.points)) {

					if (is.na(extra.points.pch[i])) { extra.points.pch[i] <- extra.points.pch[1]; }
					if (is.na(extra.points.col[i])) { extra.points.col[i] <- extra.points.col[1]; }
					if (is.na(extra.points.cex[i])) { extra.points.cex[i] <- extra.points.cex[1]; }
					if (is.na(extra.points.border[i])) { extra.points.border[i] <- extra.points.border[1]; }

					for (j in 1:length(extra.points[[i]])) {
						if (!is.na(extra.points[[i]][j])) {
							panel.xyplot(
								x = j,
								y = extra.points[[i]][j],
								pch = extra.points.pch[i],
								col = if (extra.points.pch[i] %in% 0:20) { extra.points.col[i]; } else if
									(extra.points.pch[i] %in% 21:25) { extra.points.border[i]; },
								fill = if (extra.points.pch[i] %in% 0:20) { NA; } else if
									(extra.points.pch[i] %in% 21:25) { extra.points.col[i]; },
								cex = extra.points.cex[i]
								);
							}
						}
					}
				}
			},
		main = BoutrosLab.plotting.general::get.defaults(
			property = 'fontfamily',
			use.legacy.settings = use.legacy.settings || ('Nature' == style),
			add.to.list = list(
				label = main,
				fontface = if ('Nature' == style) { 'plain' } else { 'bold' },
				cex = main.cex,
				just = main.just,
				x = main.x,
				y = main.y
				)
			),
		xlab = BoutrosLab.plotting.general::get.defaults(
			property = 'fontfamily',
			use.legacy.settings = use.legacy.settings || ('Nature' == style),
			add.to.list = list(
				label = xlab.label,
				cex = xlab.cex,
				col = xlab.col,
				fontface = if ('Nature' == style) { 'plain' } else { 'bold' }
				)
			),
		xlab.top = BoutrosLab.plotting.general::get.defaults(
			property = 'fontfamily',
			use.legacy.settings = use.legacy.settings || ('Nature' == style),
			add.to.list = list(
				label = xlab.top.label,
				cex = xlab.top.cex,
				col = xlab.top.col,
				fontface = if ('Nature' == style) { 'plain' } else { 'bold' },
				just = xlab.top.just,
				x = xlab.top.x,
				y = xlab.top.y
				)
			),
		ylab = BoutrosLab.plotting.general::get.defaults(
			property = 'fontfamily',
			use.legacy.settings = use.legacy.settings || ('Nature' == style),
			add.to.list = list(
				label = ylab.label,
				cex = ylab.cex,
				col = ylab.col,
				fontface = if ('Nature' == style) { 'plain' } else { 'bold' }
				)
			),
		scales = list(
			lwd = 1,
			x = BoutrosLab.plotting.general::get.defaults(
				property = 'fontfamily',
				use.legacy.settings = use.legacy.settings || ('Nature' == style),
				add.to.list = list(
					labels = xaxis.lab,
					cex = xaxis.cex,
					rot = xaxis.rot,
					col = xaxis.col,
					tck = xaxis.tck,
					fontface = if ('Nature' == style) { 'plain' } else { xaxis.fontface }
					)
				),
			y = BoutrosLab.plotting.general::get.defaults(
				property = 'fontfamily',
				use.legacy.settings = use.legacy.settings || ('Nature' == style),
				add.to.list = list(
					labels = yaxis.lab,
					cex = yaxis.cex,
					limits = ylimits,
					at = yat,
					rot = yaxis.rot,
					col = yaxis.col,
					tck = yaxis.tck,
					fontface = if ('Nature' == style) { 'plain' } else { yaxis.fontface }
					)
				)
			),
		par.settings = list(
			axis.line = list(
				lwd = lwd,
				col = if ('Nature' == style) { 'transparent' } else { 'black' }
				),
			layout.heights = list(
				top.padding = top.padding,
				main = if (is.null(main)) { 0.3 } else { 1 },
				main.key.padding = 0.1,
				key.top = 0.1,
				key.axis.padding = 0.1,
				axis.top = 1,
				axis.bottom = 1,
				axis.xlab.padding = 1,
				xlab = 1,
				xlab.key.padding = 0.5,
				key.bottom = 0.1,
				key.sub.padding = 0.1,
				sub = 0.1,
				bottom.padding = bottom.padding
				),
			layout.widths = list(
				left.padding = left.padding,
				key.left = 0.1,
				key.ylab.padding = 0.1,
				ylab = 1,
				ylab.axis.padding = 1,
				axis.left = 1,
				axis.right = 1,
				axis.panel = 0.3,
				strip.left = 0.3,
				panel = 1,
				between = 1,
				axis.right = 1,
				axis.key.padding = 0.1,
				right.padding = right.padding
				),
			box.dot = list(
				pch = 19,
				col = '#000000',
				lty = 1
				),
			box.rectangle = list(
				lwd = 3,
				col = '#000000',
				lty = 1
				),
			box.umbrella = list(
				lwd = 2,
				col = '#000000',
				lty = 1
				),
			plot.symbol = list(
				col = '#000000',
				pch = 19,
				cex = 0.5
				),
			plot.polygon = list(
				col = col,
				lwd = border.lwd
				)
			),
		pch = '|',
		pretty = TRUE,
		horizontal = plot.horizontal,
		key = key,
		legend = legend
		);

	if (disable.factor.sorting == TRUE) {
		
		sorting.param <- '';

		if (plot.horizontal) {
			sorting.param <- 'y';
			if (is.null(trellis.object$y.scales$labels) || (is.logical(trellis.object$y.scales$labels[1]) && trellis.object$y.scales$labels[1]  == TRUE)) {
				default.labels <- unique(as.character(trellis.object$panel.args[[1]][[sorting.param]]));
				trellis.object$y.scales$labels <- default.labels;
				}
			} 
		else {
			sorting.param <- 'x';
			if (is.null(trellis.object$x.scales$labels) || (is.logical(trellis.object$x.scales$labels[1]) && trellis.object$x.scales$labels[1]  == TRUE)) {
                        	default.labels <- unique(as.character(trellis.object$panel.args[[1]][[sorting.param]]));
				trellis.object$x.scales$labels <- default.labels;
				}
			}
		
                unique.mapping <- list();
                count <- 1;
                for (x in trellis.object$panel.args[[1]][[sorting.param]]) {
                        if (is.null(unique.mapping[[as.character(x)]])) {
                                unique.mapping[as.character(x)] <- count;
                                count <- count + 1;
                                }
                        }
                temp.data <- as.character(trellis.object$panel.args[[1]][[sorting.param]]);
                for (x in 1:length(temp.data)) {
                        temp.data[x] <- as.character(unique.mapping[as.character(trellis.object$panel.args[[1]][[sorting.param]][[x]])][[1]]);
                        }
                trellis.object$panel.args[[1]][[sorting.param]] <- as.numeric(temp.data);
	
		}

	# If Nature style requested, change figure accordingly
	if ('Nature' == style) {

		# Re-add bottom and left axes
		trellis.object$axis <- function(side, line.col = 'black', ...) {
			# Only draw axes on the left and bottom
			if (side %in% c('bottom', 'left')) {
				axis.default(side = side, line.col = 'black', ...);
				lims <- current.panel.limits();
				panel.abline(h = lims$ylim[1], v = lims$xlim[1]);
				}
			}

		# Ensure sufficient resolution for graphs
		if (resolution < 1200) {
			resolution <- 1200;
			warning('Setting resolution to 1200 dpi.');
			}

		# Other required changes which are not accomplished here
		warning('Nature also requires italicized single-letter variables and en-dashes
			for ranges and negatives. See example in documentation for how to do this.');

		warning('Avoid red-green colour schemes, create TIFF files, do not outline the figure or legend.');
		}

	# Otherwise use the BL style if requested
	else if ('BoutrosLab' == style) {
		# Nothing happens
		}

	# if neither of the above is requested, give a warning
	else {
		warning("The style parameter only accepts 'Nature' or 'BoutrosLab'.");
		}

	

	# output the object
	return(
		BoutrosLab.plotting.general::write.plot(
			trellis.object = trellis.object,
			filename = filename,
			height = height,
			width = width,
			size.units = size.units,
			resolution = resolution,
			enable.warnings = enable.warnings,
			description = description
			)
		);
	}