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# The BoutrosLab.plotting.general package is copyright (c) 2013 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 MANHATTANPLOTS ##############################################################
create.manhattanplot <- 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, xlimits = NULL,
ylimits = NULL, xat = TRUE, yat = TRUE, xaxis.lab = NA, yaxis.lab = NA, xaxis.log = FALSE, yaxis.log = FALSE,
xaxis.cex = 1.5, yaxis.cex = 1.5, xaxis.rot = 0, yaxis.rot = 0, xaxis.fontface = 'plain', yaxis.fontface = 'plain',
xaxis.col = 'black', yaxis.col = 'black', xaxis.tck = 0, yaxis.tck = c(1, 1), horizontal = FALSE, type = 'p',
cex = 2, pch = '.', col = 'black', lwd = 1, lty = 1, alpha = 1, strip.col = 'white', strip.cex = 1,
axes.lwd = 1, axes.lty = 'dashed', key = list(text = list(lab = c(''))), legend = NULL, layout = NULL,
as.table = FALSE, x.spacing = 0, y.spacing = 0, x.relation = 'same', y.relation = 'same', top.padding = 0,
bottom.padding = 0, right.padding = 0, left.padding = 0, key.top = 0, key.left.padding = 0, ylab.axis.padding = 1,
axis.key.padding = 1, abline.h = NULL, abline.col = 'black', abline.lwd = 1, abline.lty = 1, add.rectangle = FALSE,
xleft.rectangle = NULL, ybottom.rectangle = NULL, xright.rectangle = NULL, ytop.rectangle = NULL,
col.rectangle = 'transparent', alpha.rectangle = 1, add.points = FALSE, points.x = NULL, points.y = NULL,
points.pch = 19, points.col = 'black', points.cex = 1, add.text = FALSE, text.labels = NULL, text.x = NULL,
text.y = NULL, text.col = 'black', text.cex = 1, text.fontface = 'bold', height = 6, width = 10, size.units = 'in',
resolution = 1600, enable.warnings = FALSE, style = 'BoutrosLab',
description = 'Created with BoutrosLab.plotting.general', 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
);
out <- prep.axis(
at = xat,
data = unlist(data[toString(formula[[3]])]),
which.arg = 'xat'
);
if (is.list(out)) {
data[toString(formula[[3]])] <- out$x;
xat <- out$at;
xaxis.lab <- out$axis.lab;
}
out <- prep.axis(
at = yat,
data = unlist(data[toString(formula[[2]])]),
which.arg = 'yat'
);
if (is.list(out)) {
data[toString(formula[[2]])] <- out$x;
yat <- out$at;
yaxis.lab <- out$axis.lab;
}
# add preloaded defaults
if (preload.default == 'paper') {
}
else if (preload.default == 'web') {
}
# Now make the actual plot object
trellis.object <- lattice::xyplot(
formula,
data,
panel = function(subscripts, type.local = type, abline.local = abline, ...) {
# 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
);
}
# if requested, add user-defined horizontal line
if (!is.null(abline.h)) {
panel.abline(
h = abline.h,
lty = abline.lty,
lwd = abline.lwd,
col = abline.col
);
}
# create the main plot
panel.xyplot(
subscripts = subscripts,
type = setdiff(type.local, 'g'),
alpha = alpha,
horizontal = horizontal,
...
);
# 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
);
}
},
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,
limits = xlimits,
fontface = if ('Nature' == style) { 'plain' } else { xaxis.fontface },
col = xaxis.col,
at = xat,
labels = xaxis.lab,
log = xaxis.log,
relation = x.relation,
alternating = FALSE,
tck = xaxis.tck
)
),
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,
limits = ylimits,
fontface = if ('Nature' == style) { 'plain' } else { yaxis.fontface },
col = yaxis.col,
at = yat,
labels = yaxis.lab,
log = yaxis.log,
relation = y.relation,
alternating = FALSE,
tck = yaxis.tck
)
)
),
between = list(
x = x.spacing,
y = y.spacing
),
layout = layout,
as.table = as.table,
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 = key.top,
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 = key.left.padding,
key.ylab.padding = 0.5,
ylab = 1,
ylab.axis.padding = ylab.axis.padding,
axis.left = 1,
axis.panel = 0.3,
strip.left = 0.3,
panel = 1,
between = 1,
axis.right = 1,
axis.key.padding = axis.key.padding,
key.right = 1,
right.padding = right.padding
),
strip.background = list(
col = strip.col
)
),
par.strip.text = list(
cex = strip.cex
),
key = key,
legend = legend
);
if (inside.legend.auto) {
extra.parameters <- list('x' = trellis.object$panel.args[[1]]$x, 'y' = trellis.object$panel.args[[1]]$y,
'ylimits' = trellis.object$y.limits, 'xlimits' = trellis.object$x.limits);
coords <- c();
coords <- .inside.auto.legend('create.manhattanplot', 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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