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# 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 DENSITYPLOTS ################################################################
create.densityplot <- function(
x, filename = NULL, main = NULL, main.just = 'center', main.x = 0.5, main.y = 0.5, main.cex = 3,
xlab.label = NULL, ylab.label = 'Density', 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, type = 'l', lty = 'solid', cex = 0.75, pch = 19, col = 'black', lwd = 2, bandwidth = 'nrd0',
bandwidth.adjust = 1, xlimits = NULL, ylimits = NULL, xat = TRUE, yat = TRUE, xaxis.lab = NA, yaxis.lab = NA,
xaxis.cex = 1.5, yaxis.cex = 1.5, xaxis.rot = 0, yaxis.rot = 0, xaxis.col = 'black', yaxis.col = 'black',
xaxis.fontface = 'bold', yaxis.fontface = 'bold', xaxis.tck = 1, yaxis.tck = 1, xgrid.at = xat,
ygrid.at = yat, key = list(text = list(lab = c(''))), legend = NULL, top.padding = 0.1, bottom.padding = 0.7,
left.padding = 0.5, right.padding = 0.1, add.axes = FALSE, abline.h = NULL, abline.v = NULL, abline.lty = NULL,
abline.lwd = NULL, abline.col = 'black', add.rectangle = FALSE, xleft.rectangle = NULL,
ybottom.rectangle = NULL, xright.rectangle = NULL, ytop.rectangle = NULL, col.rectangle = 'transparent',
alpha.rectangle = 1, add.text = FALSE, text.labels = NULL, text.x = NULL, text.y = NULL, text.anchor = 'centre', text.col = 'black',
text.cex = 1, text.fontface = 'bold', height = 6, width = 6, size.units = 'in', resolution = 1600, enable.warnings = FALSE,
description = 'Created with BoutrosLab.plotting.general', style = 'BoutrosLab', preload.default = 'custom', use.legacy.settings = FALSE,
inside.legend.auto = 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
);
text.info <- list(
labels = text.labels,
x = text.x,
y = text.y,
col = text.col,
cex = text.cex,
fontface = text.fontface,
anchor = text.anchor
);
if (!is.null(yat) && length(yat) == 1) {
if (yat == 'auto') {
out <- auto.axis(unlist(x[[1]]));
x[[1]] <- out$x;
yat <- out$at;
yaxis.lab <- out$axis.lab;
}
else if (yat == 'auto.linear') {
out <- auto.axis(unlist(x[[1]]), log.scaled = FALSE);
x[[1]] <- out$x;
yat <- out$at;
yaxis.lab <- out$axis.lab;
}
else if (yat == 'auto.log') {
out <- auto.axis(unlist(x[[1]]), log.scaled = TRUE);
x[[1]] <- out$x;
yat <- out$at;
yaxis.lab <- out$axis.lab;
}
}
if (!is.null(xat) && length(xat) == 1) {
if (xat == 'auto') {
out <- auto.axis(unlist(x[[2]]));
x[[2]] <- out$x;
xat <- out$at;
xaxis.lab <- out$axis.lab;
}
else if (xat == 'auto.linear') {
out <- auto.axis(unlist(x[[2]]), log.scaled = FALSE);
x[[2]] <- out$x;
xat <- out$at;
xaxis.lab <- out$axis.lab;
}
else if (xat == 'auto.log') {
out <- auto.axis(unlist(x[[2]]), log.scaled = TRUE);
x[[2]] <- out$x;
xat <- out$at;
xaxis.lab <- out$axis.lab;
}
}
# add preloaded defaults
if (preload.default == 'paper') {
}
else if (preload.default == 'web') {
}
# create an object to store all the data
data.to.plot <- data.frame(
x = rep(0, 512 * length(x)),
y = rep(0, 512 * length(x)),
groups = rep(NA, 512 * length(x))
);
for (i in 1:length(x)) {
this.density <- density(
x[[i]],
bw = bandwidth,
adjust = bandwidth.adjust,
na.rm = TRUE
);
start.point <- 1 + (i - 1) * 512;
end.point <- start.point + 512 - 1;
data.to.plot$x[start.point:end.point] <- this.density$x;
data.to.plot$y[start.point:end.point] <- this.density$y;
data.to.plot$groups[start.point:end.point] <- rep(names(x)[i], 512);
}
# avoid groups being plotted in alphabetical factor order.
# this seems to cause disjoint with other parameters like col
data.to.plot$groups <- factor(
data.to.plot$groups,
levels = unique(data.to.plot$groups)
);
if (length(yat) == 1 && yat == TRUE && length(ylimits) == 0) {
maximum <- max(data.to.plot$y);
# if minimum is greater than 0 make sure to display 0
lognumber <- floor(log(maximum, 10));
# depending on difference, the labels will be multiples of 5,10 or 20
if (maximum < (10 ** lognumber * 4)) { factor <- (10 ** lognumber) / 2; }
else if (maximum < (10 ** lognumber * 7)) { factor <- (10 ** lognumber); }
else { factor <- (10 ** lognumber) * 2; }
addition <- factor / 2;
# depending on minimum create a sequence of at locations with padding
at <- seq(0, factor * round(maximum / factor) + addition, factor);
maximum <- maximum + addition;
ylimits <- c(0, maximum);
yat <- at;
}
if (length(xat) == 1 && xat == TRUE && length(xlimits) == 0) {
minimum <- min(data.to.plot$x);
maximum <- max(data.to.plot$x);
# if minimum is greater than 0 make sure to display 0
minimum <- min(minimum, 0);
difference <- maximum - minimum;
lognumber <- floor(log(difference, 10));
# depending on difference, the labels will be multiples of 5,10 or 20
if (difference < (10 ** lognumber * 4)) { factor <- (10 ** lognumber) / 2; }
else if (difference < (10 ** lognumber * 7)) { factor <- (10 ** lognumber); }
else { factor <- (10 ** lognumber) * 2; }
addition <- factor / 2;
# depending on minimum create a sequence of at locations with padding
if (minimum == 0) { at <- seq(0, factor * round(maximum / factor) + addition, factor); }
else {
at <- seq(factor * round(minimum / factor), factor * round(maximum / factor) + addition, factor);
# only add padding to minium if it is not 0
minimum <- minimum - addition;
}
# add padding to max
maximum <- maximum + addition;
xlimits <- c(minimum, maximum);
xat <- at;
}
# create the plot
trellis.object <- lattice::xyplot(
y ~ x,
data.to.plot,
panel = function(groups.local = data.to.plot$groups, subscripts, type.local = type, ...) {
# add rectangle
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
);
}
panel.abline(h = abline.h, lty = abline.lty, lwd = abline.lwd, col = abline.col);
panel.abline(v = abline.v, lty = abline.lty, lwd = abline.lwd, col = abline.col);
# Add text to plot
if (add.text) {
panel.text(
x = text.info$x,
y = text.info$y,
labels = text.info$labels,
col = text.info$col,
cex = text.info$cex,
fontface = text.info$fontface,
adj = text.info$anchor
);
}
# if requested, add x=0, y=0 lines
if (add.axes) {
panel.abline(
h = 0,
v = 0,
col.line = 'black',
lty = 'dashed',
lwd = 1.5
);
}
# if grid-lines are requested, over-ride default behaviour
if ('g' %in% type) {
panel.abline(
v = BoutrosLab.plotting.general::generate.at.final(
at.input = xgrid.at,
limits = xlimits,
data.vector = data.to.plot$x
),
h = BoutrosLab.plotting.general::generate.at.final(
at.input = ygrid.at,
limits = ylimits,
data.vector = data.to.plot$y
),
col = trellis.par.get('reference.line')$col
);
panel.xyplot(
groups = groups.local,
grid = FALSE,
subscripts = subscripts,
type = setdiff(type.local, 'g'),
...
);
}
# create the main plot
panel.xyplot(
groups = groups.local,
subscripts = subscripts,
type = setdiff(type.local, 'g'),
...
);
},
type = type,
lwd = lwd,
lty = lty,
col = col,
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,
fontface = if ('Nature' == style) { 'plain' } else { 'bold' },
cex = xlab.cex,
col = xlab.col
)
),
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,
fontface = if ('Nature' == style) { 'plain' } else { 'bold' },
cex = ylab.cex,
col = ylab.col
)
),
scales = list(
x = get.defaults(
property = 'fontfamily',
use.legacy.settings = use.legacy.settings || ('Nature' == style),
add.to.list = list(
cex = xaxis.cex,
rot = xaxis.rot,
col = xaxis.col,
fontface = if ('Nature' == style) { 'plain' } else { xaxis.fontface },
limits = xlimits,
axs = 'r',
at = xat,
tck = xaxis.tck,
labels = xaxis.lab
)
),
y = BoutrosLab.plotting.general::get.defaults(
property = 'fontfamily',
use.legacy.settings = use.legacy.settings || ('Nature' == style),
add.to.list = list(
cex = yaxis.cex,
rot = yaxis.rot,
col = yaxis.col,
fontface = if ('Nature' == style) { 'plain' } else { yaxis.fontface },
limits = ylimits,
at = yat,
tck = xaxis.tck,
labels = yaxis.lab
)
)
),
key = key,
legend = legend,
par.settings = list(
axis.line = list(
lwd = 2.25,
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.key.padding = 0.1,
key.right = 0.1,
right.padding = right.padding
)
)
);
if (inside.legend.auto) {
extra.parameters <- list('data' = data.to.plot, 'ylimits' = trellis.object$y.limits, 'xlimits' = trellis.object$x.limits);
coords <- c();
coords <- .inside.auto.legend('create.densityplot', filename, trellis.object, height, width, extra.parameters);
trellis.object$legend$inside$x <- coords[1];
trellis.object$legend$inside$y <- coords[2];
}
# 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
)
);
}
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