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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 QQPLOT FIT #################################################################
create.qqplot.fit <- function(
x, data = NA, filename = NULL, groups = NULL, confidence.bands = FALSE, conf = 0.95,
confidence.method = 'both', reference.line.method = 'quartiles', distribution = qnorm, aspect = 'fill',
prepanel = NULL, main = NULL, main.just = 'center', main.x = 0.5, main.y = 0.5, main.cex = 3,
xlab.label = NULL, ylab.label = NULL, 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, xlimits = NULL, ylimits = NULL, xat = TRUE, yat = TRUE, xaxis.lab = NA, yaxis.lab = NA,
xaxis.cex = 1.5, yaxis.cex = 1.5, xaxis.col = 'black', yaxis.col = 'black', xaxis.fontface = 'bold',
yaxis.fontface = 'bold', xaxis.log = FALSE, yaxis.log = FALSE, xaxis.rot = 0, yaxis.rot = 0, xaxis.tck = 1,
yaxis.tck = 1, add.grid = FALSE, xgrid.at = xat, ygrid.at = yat, type = 'p', cex = 0.75, pch = 19, col = 'black',
col.line = 'grey', lwd = 2, lty = 1, axes.lwd = 2.25, key = list(text = list(lab = c(''))), legend = NULL,
add.rectangle = FALSE, xleft.rectangle = NULL, ybottom.rectangle = NULL, xright.rectangle = NULL,
ytop.rectangle = NULL, col.rectangle = 'transparent', alpha.rectangle = 1, top.padding = 3, bottom.padding = 0.7,
left.padding = 0.5, right.padding = 0.1, 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
);
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') {
}
# set main, x-axis and y-axis label defaults
# if the label is NULL, then we leave it as blank;
# if the label is NA, then we use a specific default label.
if (!is.null(main) & !is.expression(main)) {
if (is.na(main)) {
main <- 'Q-Q plot';
}
}
if (!is.null(xlab.label) & !is.expression(xlab.label)) {
if (is.na(xlab.label)) {
xlab.label <- deparse(substitute(distribution));
}
}
if (!is.null(ylab.label) & !is.expression(ylab.label)) {
if (is.na(ylab.label)) {
ylab.label <- latticeParseFormula(as.formula(x), data = data)$right.name;
}
}
# create the object to store all the data
trellis.object <- lattice::qqmath(
x = x,
data = data,
distribution = distribution,
aspect = aspect,
prepanel = prepanel.qqmathline,
panel = function(
x,
type.local = type,
groups.local = groups,
subscripts,
distribution.local = distribution,
col.local = col.line,
col = col,
lwd = lwd,
...
) {
# add rectangle if requested
if (add.rectangle) {
panel.rect(
xleft = rectangle.info$xleft,
ybottom = rectangle.info$ybottom,
xright = rectangle.info$xright,
ytop = rectangle.info$ytop,
col = col.rectangle,
alpha = alpha.rectangle,
border = NA
);
}
# if grid-lines are requested, over-ride default behaviour
if ('g' %in% type || add.grid == TRUE) {
panel.abline(
v = BoutrosLab.plotting.general::generate.at.final(
at.input = xgrid.at,
limits = xlimits,
data.vector = x
),
h = BoutrosLab.plotting.general::generate.at.final(
at.input = ygrid.at,
limits = ylimits,
data.vector = x
),
col = trellis.par.get('reference.line')$col
);
}
# draw the reference line, could be one of the following:
# quartile: across 1/4 and 3/4 quantiles
# diagonal: abline(0,1),
# robust: best fit by linear regression
if (reference.line.method == 'quartiles') {
panel.qqmathline(
x,
distribution = distribution.local,
groups = groups.local,
subscripts = subscripts,
lwd = lwd,
col = col.line,
...
);
}
if (reference.line.method == 'diagonal' & !confidence.bands) {
panel.abline(0, 1);
}
if (reference.line.method == 'robust' & !confidence.bands) {
tmp.data <- BoutrosLab.plotting.general::create.qqplot.fit.confidence.interval(
x = x,
distribution = distribution,
conf = conf,
conf.method = confidence.method,
reference.line.method = reference.line.method
);
a <- tmp.data$a;
b <- tmp.data$b;
panel.abline(a, b);
}
# if confidence bands are requested
if (confidence.bands) {
# for non-grouped data
if (is.null(groups)) {
# store the value to create the confidence bands
tmp.ci <- BoutrosLab.plotting.general::create.qqplot.fit.confidence.interval(
x = x,
distribution = distribution,
conf = conf,
conf.method = confidence.method,
reference.line.method = reference.line.method
);
if (!reference.line.method == 'quartiles') {
panel.abline(tmp.ci$a, tmp.ci$b);
}
# using the returned value to plot
if (confidence.method == 'both') {
panel.polygon(
x = c(tmp.ci$z[tmp.ci$u], rev(tmp.ci$z[tmp.ci$l])),
y = c(tmp.ci$upper.sim, rev(tmp.ci$lower.sim)),
col = '#e6e6e6',
border = '#e6e6e6',
alpha = 0.5
);
if (confidence.method == 'both') {
panel.lines(tmp.ci$z, tmp.ci$upper.pw, lty = 1, lwd = lwd, col = '#b5b5b5');
panel.lines(tmp.ci$z, tmp.ci$lower.pw, lty = 1, lwd = lwd, col = '#b5b5b5');
panel.lines(tmp.ci$z[tmp.ci$u], tmp.ci$upper.sim, lty = 1, lwd = lwd, col = '#e6e6e6');
panel.lines(tmp.ci$z[tmp.ci$l], tmp.ci$lower.sim, lty = 1, lwd = lwd, col = '#e6e6e6');
}
else {
if (confidence.method == 'simultaneous') {
panel.lines(tmp.ci$z[tmp.ci$u], tmp.ci$upper.sim, lty = 1, lwd = lwd, col = '#e6e6e6');
panel.lines(tmp.ci$z[tmp.ci$l], tmp.ci$lower.sim, lty = 1, lwd = lwd, col = '#e6e6e6');
}
if (confidence.method == 'pointwise') {
panel.lines(tmp.ci$z, tmp.ci$upper.pw, lty = 1, lwd = 2, col = '#b5b5b5');
panel.lines(tmp.ci$z, tmp.ci$lower.pw, lty = 1, lwd = 2, col = '#b5b5b5');
}
}
panel.polygon(
x = c(tmp.ci$z, rev(tmp.ci$z)),
y = c(tmp.ci$upper.pw, rev(tmp.ci$lower.pw)),
col = '#b5b5b5',
border = '#b5b5b5',
alpha = 0.5
);
draw.key(
list(
text = list(
lab = c('pointwise', 'simultaneous')
),
points = list(
pch = 15,
col = c('#b5b5b5', '#e6e6e6')
)
),
draw = TRUE,
vp = viewport(x = unit(0.82, 'npc'), y = unit(0.06, 'npc'))
);
}
else {
if (confidence.method == 'simultaneous') {
panel.polygon(
x = c(tmp.ci$z[tmp.ci$u], rev(tmp.ci$z[tmp.ci$l])),
y = c(tmp.ci$upper.sim, rev(tmp.ci$lower.sim)),
col = '#e6e6e6',
border = '#e6e6e6',
alpha = 0.5
);
}
if (confidence.method == 'pointwise') {
panel.polygon(
x = c(tmp.ci$z, rev(tmp.ci$z)),
y = c(tmp.ci$upper.pw, rev(tmp.ci$lower.pw)),
col = '#b5b5b5',
border = '#b5b5b5',
alpha = 0.5
);
}
}
}
# for grouped data
else {
grouped.data <- split(x, groups);
groups.names <- sort(unique(groups.local));
number.groups <- length(groups.names);
for (k in 1:number.groups) {
# store the value to create the confidence bands for each group
tmp.ci <- BoutrosLab.plotting.general::create.qqplot.fit.confidence.interval(
x = grouped.data[[groups.names[k]]],
distribution = distribution,
conf = conf,
conf.method = confidence.method
);
if (!reference.line.method == 'quartiles') {
panel.abline(tmp.ci$a, tmp.ci$b);
}
# using the returned value to plot
if (confidence.method == 'both') {
panel.polygon(
x = c(tmp.ci$z[tmp.ci$u], rev(tmp.ci$z[tmp.ci$l])),
y = c(tmp.ci$upper.sim, rev(tmp.ci$lower.sim)),
col = '#e6e6e6',
border = '#e6e6e6',
alpha = 0.5
);
panel.polygon(
x = c(tmp.ci$z, rev(tmp.ci$z)),
y = c(tmp.ci$upper.pw, rev(tmp.ci$lower.pw)),
col = '#b5b5b5',
border = '#b5b5b5',
alpha = 0.5
);
# draw the key to indicate the two methods only once
if (1 == k) {
draw.key(
list(
text = list(
lab = c('pointwise', 'simultaneous')
),
points = list(
pch = 15,
col = c('#b5b5b5', '#e6e6e6')
)
),
draw = TRUE,
vp = viewport(x = unit(0.82, 'npc'), y = unit(0.06, 'npc'))
);
}
}
else {
if (confidence.method == 'simultaneous') {
panel.polygon(
x = c(tmp.ci$z[tmp.ci$u], rev(tmp.ci$z[tmp.ci$l])),
y = c(tmp.ci$upper.sim, rev(tmp.ci$lower.sim)),
col = '#e6e6e6',
border = '#e6e6e6',
alpha = 0.5
);
}
if (confidence.method == 'pointwise') {
panel.polygon(
x = c(tmp.ci$z, rev(tmp.ci$z)),
y = c(tmp.ci$upper.pw, rev(tmp.ci$lower.pw)),
col = '#b5b5b5',
border = '#b5b5b5',
alpha = 0.5
);
}
}
}
}
}
# draw the main plot
panel.qqmath(
x,
distribution = distribution.local,
groups = groups.local,
subscripts = subscripts,
col = col,
...
);
},
type = type,
cex = cex,
pch = pch,
col = col,
lwd = lwd,
lty = lty,
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(
x = BoutrosLab.plotting.general::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,
limits = xlimits,
fontface = if ('Nature' == style) { 'plain' } else { xaxis.fontface },
at = xat,
labels = xaxis.lab,
log = xaxis.log,
tck = xaxis.tck,
alternating = FALSE
)
),
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,
limits = ylimits,
fontface = if ('Nature' == style) { 'plain' } else { yaxis.fontface },
at = yat,
labels = yaxis.lab,
log = yaxis.log,
tck = yaxis.tck,
alternating = FALSE
)
)
),
key = key,
legend = legend,
par.settings = list(
axis.line = list(
lwd = axes.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.key.padding = 0.1,
key.right = 0.1,
right.padding = right.padding
)
)
);
if (inside.legend.auto) {
extra.parameters <- list('x' = trellis.object$panel.args[[1]]$x,
'ylimits' = trellis.object$y.limits, 'xlimits' = trellis.object$x.limits);
coords <- c();
coords <- .inside.auto.legend('create.qqplot.fit', 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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