create.boxplot: Make a boxplot
In BoutrosLab.plotting.general: Functions to Create Publication-Quality Plots
View source: R/create.boxplot.R
create.boxplot R Documentation
Make a boxplot
Description
Takes a data.frame and creates a boxplot
Usage
create.boxplot(
formula,
data,
filename = NULL,
main = NULL,
main.just = 'center',
main.x = 0.5,
main.y = 0.5,
main.cex = 3,
add.stripplot = FALSE,
jitter.factor = 1,
jitter.amount = NULL,
points.pch = 19,
points.col = 'darkgrey',
points.cex = 0.5,
points.alpha = 1,
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,
box.ratio = 1,
col = 'transparent',
alpha = 1,
border.col = 'black',
symbol.cex = 0.8,
lwd = 1,
outliers = TRUE,
sample.order = 'none',
order.by = 'median',
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 = 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 = 1,
layout = NULL,
as.table = FALSE,
x.spacing = 0,
y.spacing = 0,
x.relation = 'same',
y.relation = 'same',
top.padding = 0.5,
bottom.padding = 2,
right.padding = 1,
left.padding = 2,
ylab.axis.padding = 0,
add.text = FALSE,
text.labels = NULL,
text.x = NULL,
text.y = NULL,
text.anchor = 'centre',
text.col = 'black',
text.cex = 1,
text.fontface = 'bold',
key = NULL,
legend = NULL,
strip.col = 'white',
strip.cex = 1,
strip.fontface = 'bold',
line.func = NULL,
line.from = 0,
line.to = 0,
line.col = 'transparent',
line.infront = TRUE,
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,
disable.factor.sorting = FALSE
);
Arguments
formula
The formula used to extract the x & y components from the data-frame. Transforming data within formula is not compatible with automatic scaling with 'xat' or 'yat'.
data
The data-frame to plot
filename
Filename for tiff output, or if NULL returns the trellis object itself
main
The main title for the plot (space is reclaimed if NULL)
main.just
The justification of the main title for the plot, default is centered
main.x
The x location of the main title, deault is 0.5
main.y
The y location of the main title, default is 0.5
main.cex
Size of text for main plot title, defaults to 3
add.stripplot
logical whether to plot all points, defaults to FALSE
jitter.factor
Numeric value to apply to jitter, default is 1
jitter.amount
Numeric; amount of noise to add, default is NULL
points.pch
pch value to use for stripplot
points.col
colour(s) to use for stripplot (either a single colour
or a vector)
points.cex
cex value to use for stripplot
points.alpha
alpha value to use for stripplot
abline.h
Specify the horizontal superimpose line
abline.v
Specify the vertical superimpose line
abline.lty
Specify the superimpose line type
abline.lwd
Specify the superimpose line width
abline.col
Specify the superimpose line colour (defaults to black)
add.rectangle
Allow a rectangle to be drawn, default is FALSE
xleft.rectangle
Specifies the left x ooordinate of the rectangle to be drawn
ybottom.rectangle
Specifies the bottom y coordinate of the rectangle to be drawn
xright.rectangle
Specifies the right x coordinate of the rectangle to be drawn
ytop.rectangle
Specifies the top y coordinate of the rectangle to be drawn
col.rectangle
Specifies the colour of the rectangle to be drawn
alpha.rectangle
Specifies the colour bias of the rectangle to be drawn
box.ratio
ability to change the box width, defaults to 1
col
The colour to fill the interior of the boxplot, defaults to white
alpha
The alpha of the interior boxplot colour specified in 'col'. Defaults to 1 (opaque)
border.col
Colour of the boxplot, defaults to black
symbol.cex
Size of the boxplot outlier-symbol
lwd
Line width, defaults to 1
outliers
logical whether to plot outliers, defaults to TRUE
sample.order
String specifying how samples should be ordered. Either none, increasing, or decreasing.
order.by
A string specifying what the sample order should be ordered by, either max, min, median or mean
xlab.label
The label for the x-axis
ylab.label
The label for the y-axis
xlab.cex
Size of x-axis label, defaults to 3
ylab.cex
Size of y-axis label, defaults to 3
xlab.col
Colour of the x-axis label, defaults to “black”
ylab.col
Colour of the y-axis label, defaults to “black”
xlab.top.label
The label for the top x-axis
xlab.top.cex
Size of top x-axis label
xlab.top.col
Colour of the top x-axis label
xlab.top.just
Justification of the top x-axis label, defaults to centered
xlab.top.x
The x location of the top x-axis label
xlab.top.y
The y location of the top y-axis label
xlimits
Two-element vector giving the x-axis limits
ylimits
Two-element vector giving the y-axis limits
xat
Accepts a vector listing where x-axis ticks should be drawn or if automatic scaling is desired, one of three strings: “auto”, “auto.linear” or “auto.log”. Automatic scaling fixes x-axis tick locations, labels, and data values dependent on given data. “auto” will determine whether linear or logarithmic scaling fits the given data best, “auto.linear” or “auto.log” will force data to be scaled linearly or logarithmically respectively. Defaults to lattice automatic (TRUE). For more details see 'auto.axis()'.
yat
Accepts a vector listing where y-axis ticks should be drawn or if automatic scaling is desired, one of three strings: “auto”, “auto.linear” or “auto.log”. Automatic scaling fixes y-axis tick locations, labels, and data values dependent on given data. “auto” will determine whether linear or logarithmic scaling fits the given data best, “auto.linear” or “auto.log” will force data to be scaled linearly or logarithmically respectively. Defaults to lattice automatic (TRUE). For more details see 'auto.axis()'.
xaxis.lab
Vector listing x-axis tick labels, defaults to automatic (TRUE). Using automatic scaling with xat will overwrite user input. Set to NULL to remove x-axis labels.
yaxis.lab
Vector listing y-axis tick labels, defaults to automatic (TRUE). Using automatic scaling with yat will overwrite user input. Set to NULL to remove y-axis labels.
xaxis.cex
Size of x-axis tick labels, defaults to 2
yaxis.cex
Size of y-axis tick labels, defaults to 2
xaxis.col
Colour of the x-axis tick labels, defaults to “black”
yaxis.col
Colour of the y-axis tick labels, defaults to “black”
xaxis.fontface
Fontface for the x-axis scales
yaxis.fontface
Fontface for the y-axis scales
xaxis.rot
Rotation of x-axis tick labels; defaults to 0
yaxis.rot
Rotation of y-axis tick labels; defaults to 0
xaxis.tck
Specifies the length of the tick marks for x-axis, defaults to 1 (bottom) and 0 (top)
yaxis.tck
Specifies the length of the tick marks for y-axis, defaults to 1
layout
A vector specifying the number of columns, rows (e.g., c(2,1). Default is NULL; see lattice::xyplot for more details
.
as.table
Specifies panel drawing order, default is FALSE which draws panels from bottom left corner, moving right then up. Set to TRUE to draw from top left corner, moving right then down
x.spacing
A number specifying the distance between panels along the x-axis, defaults to 0
y.spacing
A number specifying the distance between panels along the y-axis, defaults to 0
x.relation
Allows x-axis scales to vary if set to “free”, defaults to “same”
y.relation
Allows y-axis scales to vary if set to “free”, defaults to “same”
top.padding
A number specifying the distance to the top margin, defaults to 0.5
bottom.padding
A number specifying the distance to the bottom margin, defaults to 2
right.padding
A number specifying the distance to the right margin, defaults to 1
left.padding
A number specifying the distance to the left margin, defaults to 2
ylab.axis.padding
A number specifying the distance of y-axis label to the y-axis, defaults to 0
,
add.text
Allow additional text to be drawn, default is FALSE
text.labels
Labels for additional text. If the formula contains group, the length of this argument should match with the number of groups.
text.x
The x co-ordinates where additional text should be placed
text.y
The y co-ordinates where additional text should be placed
text.anchor
Part of text that should be anchored to x/y coordinates. Defaults to 'centre'. Use 'left' or 'right' to left or right-align text.
text.col
The colour of additional text
text.cex
The size of additional text
text.fontface
The fontface for additional text
key
Add a key to the plot. See xyplot.
legend
Add a legend to the plot. Helpful for adding multiple keys and adding keys to the margins of the plot. See xyplot.
strip.col
Strip background colour, defaults to “white”
strip.cex
Strip title character expansion
strip.fontface
Strip title fontface, defaults to bold
line.func
Function for the line that should be drawn on top of plot
line.from
The starting point of the line on the plot
line.to
The ending point of the line on the plot
line.col
Colour of the line on the plot
line.infront
Should the line appear in front of the plot or not
height
Figure height, defaults to 6 inches
width
Figure width, defaults to 6 inches
size.units
Figure units, defaults to inches
resolution
Figure resolution in dpi, defaults to 1600
enable.warnings
Print warnings if set to TRUE, defaults to FALSE
description
Description of image/plot; default NULL.
style
defaults to “BoutrosLab”, also accepts “Nature”, which changes parameters according to Nature formatting requirements
preload.default
ability to set multiple sets of diffrent defaults depending on publication needs
use.legacy.settings
boolean to set wheter or not to use legacy mode settings (font)
disable.factor.sorting
Disable barplot auto sorting factors alphabetically/numerically
Value
If filename is NULL then returns the trellis object, otherwise creates a plot and returns a 0/1 success code.
Warning
If this function is called without capturing the return value, or specifying a filename, it may crash while trying to draw the histogram. In particular, if a script that uses such a call of create histogram is called by reading the script in from the command line, it will fail badly, with an error message about unavailable fonts:
Error in grid.Call.graphics("L_text", as.graphicsAnnot(x$label), x$x, )
Invalid font type
Calls: print ... drawDetails.text -> grid.Call.graphics -> .Call.graphics
Author(s)
Maud H.W. Starmans
See Also
bwplot, lattice or the Lattice book for an overview of the package.
Examples
set.seed(12345);
simple.data <- data.frame(
x = rnorm(1000),
y = rep('A',1000)
);
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Simple', fileext = '.tiff'),
formula = y ~ x,
data = simple.data,
main = 'Simple',
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 50
);
# add stripplot behind boxplot
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_with_Stripplot', fileext = '.tiff'),
formula = y ~ x,
data = simple.data,
main = 'With Stripplot',
add.stripplot = TRUE,
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 50
);
# Multi-coloured stripplot
strip.data <- data.frame(
score = c(rnorm(30, 15, 3), rnorm(50, 20, 4)),
sex = sample(c('male', 'female'), 80, replace = TRUE),
gene = sample(c('a', 'b'), 80, replace = TRUE)
);
create.boxplot(
filename = NULL,
formula = score ~ sex | gene,
data = strip.data,
main = 'Multi-Coloured Stripplot',
add.stripplot = TRUE,
points.col = c('pink', 'dodgerblue'),
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 100
);
# format data
reformatted.data <- data.frame(
x = as.vector(t(microarray[1:10,1:58])),
y = as.factor(rep(rownames(microarray[1:10,1:58]),each = 58)),
z = sample(1:10, 580, replace = TRUE)
);
# Minimal Input
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Minimal_Input', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'Minimal input',
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 50
);
# Minimal Input
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Disable_Factor_Sorting_Input', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'No Factor Sorting',
disable.factor.sorting = TRUE,
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 50
);
# Axes and labels
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Axes_Labels', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'Axes & labels',
# Adjusting axes size
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
# Adding y-axis label
ylab.label = 'Gene',
# setting axes limits
xlimits = c(0,13),
xat = seq(0,12,2),
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Sorting
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Sorted', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'Sorting',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
ylab.label = 'Gene',
xlimits = c(0,13),
xat = seq(0,12,2),
# Reordered by median
sample.order = 'increasing',
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Colour change
sex.colour <- as.character(patient$sex);
sex.colour[sex.colour == 'male'] <- 'dodgerblue';
sex.colour[sex.colour == 'female'] <- 'pink';
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Colour_Change', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'Colour change',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
ylab.label = 'Gene',
xlimits = c(0,13),
xat = seq(0,12,2),
# Colour change
col = sex.colour,
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Remove y-axis labels
create.boxplot(
formula = y ~ x,
data = reformatted.data,
main = 'Remove y-axis labels',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
ylab.label = 'Gene',
xlimits = c(0,13),
xat = seq(0,12,2),
yaxis.lab = NULL, # Remove labels with NULL
# Colour change
col = sex.colour,
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Log Scaled Axis
log.data <- data.frame(
x = 10 ** rnorm(1000, 5, 2),
y = rep('A',1000)
);
create.boxplot(
formula = x ~ y,
data = log.data,
# Log base 10 scale y axis
yat = 'auto.log',
main = 'Log Scale',
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Legend
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Legend', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'Legend',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
ylab.label = 'Gene',
xlimits = c(0,13),
xat = seq(0,12,2),
col = sex.colour,
# legend
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
points = list(
col = 'black',
pch = 22,
cex = 1.5,
fill = c('dodgerblue','pink')
),
text = list(
lab = c('male','female')
),
cex = 1
)
),
x = 0.03,
y = 0.97,
corner = c(0,1),
draw = FALSE
)
),
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Orientation
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Orientation', fileext = '.tiff'),
# switch the order
formula = x ~ y,
data = reformatted.data,
main = 'Orientation',
xaxis.cex = 1,
yaxis.cex = 1,
# adjust the axes
ylimits = c(0,13),
yat = seq(0,12,2),
# rotate the labels
xaxis.rot = 90,
xlab.label = 'Gene',
xlab.cex = 1.5,
col = sex.colour,
# legend
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
points = list(
col = 'black',
pch = 22,
cex = 1.5,
fill = c('dodgerblue','pink')
),
text = list(
lab = c('male','female')
),
cex = 1
)
),
x = 0.23,
y = 0.97,
corner = c(0,1),
draw = FALSE
)
),
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Background rectangle
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_BG_Rect', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'Bg rectangle',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
ylab.label = 'Gene',
xlimits = c(0,13),
xat = seq(0,12,2),
# draw rectangle
add.rectangle = TRUE,
xleft.rectangle = 0,
xright.rectangle = 13,
ybottom.rectangle = seq(0.5, 8.5, 2),
ytop.rectangle = seq(1.5, 9.5, 2),
col.rectangle = 'grey',
alpha.rectangle = 0.5,
col = sex.colour,
# legend
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
points = list(
col = 'black',
pch = 22,
cex = 1.5,
fill = c('dodgerblue','pink')
),
text = list(
lab = c('male','female')
),
cex = 1
)
),
x = 0.03,
y = 0.97,
corner = c(0,1),
draw = FALSE
)
),
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Line
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Line', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'Line',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
ylab.label = 'Gene',
xlimits = c(0,13),
xat = seq(0,12,2),
# draw line
line.func = function(x){c(0.5, 10.5)},
line.from = 11,
line.to = 11,
line.col = 'grey',
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Panel Organization
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Panels_numeric_conditioning', fileext = '.tiff'),
formula = ~ x | z,
data = reformatted.data,
main = 'Panels',
xaxis.cex = 1,
yaxis.cex = 1,
xlimits = c(0,13),
xat = seq(0,12,2),
# Setting up the layout
layout = c(2,5),
x.relation = 'free',
x.spacing = 1,
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 200
);
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Panels_factor_conditioning', fileext = '.tiff'),
formula = ~ x | y,
data = reformatted.data,
main = 'Panels',
xaxis.cex = 1,
yaxis.cex = 1,
xlimits = c(0,13),
xat = seq(0,12,2),
# Setting up the layout
layout = c(2,5),
x.relation = 'free',
x.spacing = 1,
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Nature format
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Nature_style', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'Nature style',
xaxis.cex = 1,
yaxis.cex = 1,
# set style to Nature
style = 'Nature',
# demonstrating how to italicize character variables
ylab.lab = expression(paste('italicized ', italic('a'))),
# demonstrating how to create en-dashes
xlab.lab = expression(paste('en dashs: 1','\u2013', '10'^'\u2013', ''^3)),
resolution = 1200
);
# Sorting by mean and multiple filenames
create.boxplot(
filename = c(
tempfile(pattern = 'Boxplot_Sorted1', fileext = '.tiff'),
tempfile(pattern = 'Boxplot_Sorted2', fileext = '.tiff')
),
formula = y ~ x,
data = reformatted.data,
main = 'Sorting',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
ylab.label = 'Gene',
xlimits = c(0,13),
xat = seq(0,12,2),
# Reordered by median
sample.order = 'increasing',
order.by = 'mean',
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Adding text to plot
# Generate normally distributed variables with two different means
set.seed(779);
groupA <- rnorm(n = 100, mean = 10, sd = 2);
groupB <- rnorm(n = 134, mean = 10.5, sd = 2);
# Create data frame for plotting
to.plot <- data.frame(
y = rep(
c('1', '2'),
times = c(100, 134)
),
x = c(groupA, groupB)
);
# Get difference between means
diff.mean <- round(mean(groupB) - mean(groupA), 2);
# Plot and display difference
create.boxplot(
formula = x ~ y,
# filename = tempfile(pattern = 'boxplot_with_text', fileext = '.tiff'),
data = to.plot,
add.stripplot = TRUE,
add.text = TRUE,
text.labels = bquote(mu[B] - mu[A] == .(diff.mean)),
text.x = 2.1,
text.y = 15.3,
text.col = 'black',
text.cex = 1.5,
text.fontface = 'bold',
ylimits = c(
min(to.plot$x) - abs(min(to.plot$x) * 0.1),
max(to.plot$x) + abs(max(to.plot$x) * 0.1)
),
resolution = 200
);
BoutrosLab.plotting.general documentation built on Nov. 2, 2023, 6:01 p.m.
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View source: R/create.boxplot.R
| create.boxplot | R Documentation |
Make a boxplot
Description
Takes a data.frame and creates a boxplot
Usage
create.boxplot(
formula,
data,
filename = NULL,
main = NULL,
main.just = 'center',
main.x = 0.5,
main.y = 0.5,
main.cex = 3,
add.stripplot = FALSE,
jitter.factor = 1,
jitter.amount = NULL,
points.pch = 19,
points.col = 'darkgrey',
points.cex = 0.5,
points.alpha = 1,
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,
box.ratio = 1,
col = 'transparent',
alpha = 1,
border.col = 'black',
symbol.cex = 0.8,
lwd = 1,
outliers = TRUE,
sample.order = 'none',
order.by = 'median',
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 = 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 = 1,
layout = NULL,
as.table = FALSE,
x.spacing = 0,
y.spacing = 0,
x.relation = 'same',
y.relation = 'same',
top.padding = 0.5,
bottom.padding = 2,
right.padding = 1,
left.padding = 2,
ylab.axis.padding = 0,
add.text = FALSE,
text.labels = NULL,
text.x = NULL,
text.y = NULL,
text.anchor = 'centre',
text.col = 'black',
text.cex = 1,
text.fontface = 'bold',
key = NULL,
legend = NULL,
strip.col = 'white',
strip.cex = 1,
strip.fontface = 'bold',
line.func = NULL,
line.from = 0,
line.to = 0,
line.col = 'transparent',
line.infront = TRUE,
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,
disable.factor.sorting = FALSE
);
Arguments
formula |
The formula used to extract the x & y components from the data-frame. Transforming data within formula is not compatible with automatic scaling with 'xat' or 'yat'. |
data |
The data-frame to plot |
filename |
Filename for tiff output, or if NULL returns the trellis object itself |
main |
The main title for the plot (space is reclaimed if NULL) |
main.just |
The justification of the main title for the plot, default is centered |
main.x |
The x location of the main title, deault is 0.5 |
main.y |
The y location of the main title, default is 0.5 |
main.cex |
Size of text for main plot title, defaults to 3 |
add.stripplot |
logical whether to plot all points, defaults to FALSE |
jitter.factor |
Numeric value to apply to jitter, default is 1 |
jitter.amount |
Numeric; amount of noise to add, default is NULL |
points.pch |
pch value to use for stripplot |
points.col |
colour(s) to use for stripplot (either a single colour or a vector) |
points.cex |
cex value to use for stripplot |
points.alpha |
alpha value to use for stripplot |
abline.h |
Specify the horizontal superimpose line |
abline.v |
Specify the vertical superimpose line |
abline.lty |
Specify the superimpose line type |
abline.lwd |
Specify the superimpose line width |
abline.col |
Specify the superimpose line colour (defaults to black) |
add.rectangle |
Allow a rectangle to be drawn, default is FALSE |
xleft.rectangle |
Specifies the left x ooordinate of the rectangle to be drawn |
ybottom.rectangle |
Specifies the bottom y coordinate of the rectangle to be drawn |
xright.rectangle |
Specifies the right x coordinate of the rectangle to be drawn |
ytop.rectangle |
Specifies the top y coordinate of the rectangle to be drawn |
col.rectangle |
Specifies the colour of the rectangle to be drawn |
alpha.rectangle |
Specifies the colour bias of the rectangle to be drawn |
box.ratio |
ability to change the box width, defaults to 1 |
col |
The colour to fill the interior of the boxplot, defaults to white |
alpha |
The alpha of the interior boxplot colour specified in 'col'. Defaults to 1 (opaque) |
border.col |
Colour of the boxplot, defaults to black |
symbol.cex |
Size of the boxplot outlier-symbol |
lwd |
Line width, defaults to 1 |
outliers |
logical whether to plot outliers, defaults to TRUE |
sample.order |
String specifying how samples should be ordered. Either none, increasing, or decreasing. |
order.by |
A string specifying what the sample order should be ordered by, either max, min, median or mean |
xlab.label |
The label for the x-axis |
ylab.label |
The label for the y-axis |
xlab.cex |
Size of x-axis label, defaults to 3 |
ylab.cex |
Size of y-axis label, defaults to 3 |
xlab.col |
Colour of the x-axis label, defaults to “black” |
ylab.col |
Colour of the y-axis label, defaults to “black” |
xlab.top.label |
The label for the top x-axis |
xlab.top.cex |
Size of top x-axis label |
xlab.top.col |
Colour of the top x-axis label |
xlab.top.just |
Justification of the top x-axis label, defaults to centered |
xlab.top.x |
The x location of the top x-axis label |
xlab.top.y |
The y location of the top y-axis label |
xlimits |
Two-element vector giving the x-axis limits |
ylimits |
Two-element vector giving the y-axis limits |
xat |
Accepts a vector listing where x-axis ticks should be drawn or if automatic scaling is desired, one of three strings: “auto”, “auto.linear” or “auto.log”. Automatic scaling fixes x-axis tick locations, labels, and data values dependent on given data. “auto” will determine whether linear or logarithmic scaling fits the given data best, “auto.linear” or “auto.log” will force data to be scaled linearly or logarithmically respectively. Defaults to lattice automatic (TRUE). For more details see 'auto.axis()'. |
yat |
Accepts a vector listing where y-axis ticks should be drawn or if automatic scaling is desired, one of three strings: “auto”, “auto.linear” or “auto.log”. Automatic scaling fixes y-axis tick locations, labels, and data values dependent on given data. “auto” will determine whether linear or logarithmic scaling fits the given data best, “auto.linear” or “auto.log” will force data to be scaled linearly or logarithmically respectively. Defaults to lattice automatic (TRUE). For more details see 'auto.axis()'. |
xaxis.lab |
Vector listing x-axis tick labels, defaults to automatic (TRUE). Using automatic scaling with xat will overwrite user input. Set to NULL to remove x-axis labels. |
yaxis.lab |
Vector listing y-axis tick labels, defaults to automatic (TRUE). Using automatic scaling with yat will overwrite user input. Set to NULL to remove y-axis labels. |
xaxis.cex |
Size of x-axis tick labels, defaults to 2 |
yaxis.cex |
Size of y-axis tick labels, defaults to 2 |
xaxis.col |
Colour of the x-axis tick labels, defaults to “black” |
yaxis.col |
Colour of the y-axis tick labels, defaults to “black” |
xaxis.fontface |
Fontface for the x-axis scales |
yaxis.fontface |
Fontface for the y-axis scales |
xaxis.rot |
Rotation of x-axis tick labels; defaults to 0 |
yaxis.rot |
Rotation of y-axis tick labels; defaults to 0 |
xaxis.tck |
Specifies the length of the tick marks for x-axis, defaults to 1 (bottom) and 0 (top) |
yaxis.tck |
Specifies the length of the tick marks for y-axis, defaults to 1 |
layout |
A vector specifying the number of columns, rows (e.g., c(2,1). Default is NULL; see lattice::xyplot for more details |
.
as.table |
Specifies panel drawing order, default is FALSE which draws panels from bottom left corner, moving right then up. Set to TRUE to draw from top left corner, moving right then down |
x.spacing |
A number specifying the distance between panels along the x-axis, defaults to 0 |
y.spacing |
A number specifying the distance between panels along the y-axis, defaults to 0 |
x.relation |
Allows x-axis scales to vary if set to “free”, defaults to “same” |
y.relation |
Allows y-axis scales to vary if set to “free”, defaults to “same” |
top.padding |
A number specifying the distance to the top margin, defaults to 0.5 |
bottom.padding |
A number specifying the distance to the bottom margin, defaults to 2 |
right.padding |
A number specifying the distance to the right margin, defaults to 1 |
left.padding |
A number specifying the distance to the left margin, defaults to 2 |
ylab.axis.padding |
A number specifying the distance of y-axis label to the y-axis, defaults to 0 |
,
add.text |
Allow additional text to be drawn, default is FALSE |
text.labels |
Labels for additional text. If the formula contains group, the length of this argument should match with the number of groups. |
text.x |
The x co-ordinates where additional text should be placed |
text.y |
The y co-ordinates where additional text should be placed |
text.anchor |
Part of text that should be anchored to x/y coordinates. Defaults to 'centre'. Use 'left' or 'right' to left or right-align text. |
text.col |
The colour of additional text |
text.cex |
The size of additional text |
text.fontface |
The fontface for additional text |
key |
Add a key to the plot. See xyplot. |
legend |
Add a legend to the plot. Helpful for adding multiple keys and adding keys to the margins of the plot. See xyplot. |
strip.col |
Strip background colour, defaults to “white” |
strip.cex |
Strip title character expansion |
strip.fontface |
Strip title fontface, defaults to bold |
line.func |
Function for the line that should be drawn on top of plot |
line.from |
The starting point of the line on the plot |
line.to |
The ending point of the line on the plot |
line.col |
Colour of the line on the plot |
line.infront |
Should the line appear in front of the plot or not |
height |
Figure height, defaults to 6 inches |
width |
Figure width, defaults to 6 inches |
size.units |
Figure units, defaults to inches |
resolution |
Figure resolution in dpi, defaults to 1600 |
enable.warnings |
Print warnings if set to TRUE, defaults to FALSE |
description |
Description of image/plot; default NULL. |
style |
defaults to “BoutrosLab”, also accepts “Nature”, which changes parameters according to Nature formatting requirements |
preload.default |
ability to set multiple sets of diffrent defaults depending on publication needs |
use.legacy.settings |
boolean to set wheter or not to use legacy mode settings (font) |
disable.factor.sorting |
Disable barplot auto sorting factors alphabetically/numerically |
Value
If filename is NULL then returns the trellis object, otherwise creates a plot and returns a 0/1 success code.
Warning
If this function is called without capturing the return value, or specifying a filename, it may crash while trying to draw the histogram. In particular, if a script that uses such a call of create histogram is called by reading the script in from the command line, it will fail badly, with an error message about unavailable fonts:
Error in grid.Call.graphics("L_text", as.graphicsAnnot(x$label), x$x, )
Invalid font type
Calls: print ... drawDetails.text -> grid.Call.graphics -> .Call.graphics
Author(s)
Maud H.W. Starmans
See Also
bwplot, lattice or the Lattice book for an overview of the package.
Examples
set.seed(12345);
simple.data <- data.frame(
x = rnorm(1000),
y = rep('A',1000)
);
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Simple', fileext = '.tiff'),
formula = y ~ x,
data = simple.data,
main = 'Simple',
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 50
);
# add stripplot behind boxplot
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_with_Stripplot', fileext = '.tiff'),
formula = y ~ x,
data = simple.data,
main = 'With Stripplot',
add.stripplot = TRUE,
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 50
);
# Multi-coloured stripplot
strip.data <- data.frame(
score = c(rnorm(30, 15, 3), rnorm(50, 20, 4)),
sex = sample(c('male', 'female'), 80, replace = TRUE),
gene = sample(c('a', 'b'), 80, replace = TRUE)
);
create.boxplot(
filename = NULL,
formula = score ~ sex | gene,
data = strip.data,
main = 'Multi-Coloured Stripplot',
add.stripplot = TRUE,
points.col = c('pink', 'dodgerblue'),
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 100
);
# format data
reformatted.data <- data.frame(
x = as.vector(t(microarray[1:10,1:58])),
y = as.factor(rep(rownames(microarray[1:10,1:58]),each = 58)),
z = sample(1:10, 580, replace = TRUE)
);
# Minimal Input
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Minimal_Input', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'Minimal input',
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 50
);
# Minimal Input
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Disable_Factor_Sorting_Input', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'No Factor Sorting',
disable.factor.sorting = TRUE,
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 50
);
# Axes and labels
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Axes_Labels', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'Axes & labels',
# Adjusting axes size
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
# Adding y-axis label
ylab.label = 'Gene',
# setting axes limits
xlimits = c(0,13),
xat = seq(0,12,2),
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Sorting
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Sorted', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'Sorting',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
ylab.label = 'Gene',
xlimits = c(0,13),
xat = seq(0,12,2),
# Reordered by median
sample.order = 'increasing',
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Colour change
sex.colour <- as.character(patient$sex);
sex.colour[sex.colour == 'male'] <- 'dodgerblue';
sex.colour[sex.colour == 'female'] <- 'pink';
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Colour_Change', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'Colour change',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
ylab.label = 'Gene',
xlimits = c(0,13),
xat = seq(0,12,2),
# Colour change
col = sex.colour,
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Remove y-axis labels
create.boxplot(
formula = y ~ x,
data = reformatted.data,
main = 'Remove y-axis labels',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
ylab.label = 'Gene',
xlimits = c(0,13),
xat = seq(0,12,2),
yaxis.lab = NULL, # Remove labels with NULL
# Colour change
col = sex.colour,
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Log Scaled Axis
log.data <- data.frame(
x = 10 ** rnorm(1000, 5, 2),
y = rep('A',1000)
);
create.boxplot(
formula = x ~ y,
data = log.data,
# Log base 10 scale y axis
yat = 'auto.log',
main = 'Log Scale',
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Legend
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Legend', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'Legend',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
ylab.label = 'Gene',
xlimits = c(0,13),
xat = seq(0,12,2),
col = sex.colour,
# legend
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
points = list(
col = 'black',
pch = 22,
cex = 1.5,
fill = c('dodgerblue','pink')
),
text = list(
lab = c('male','female')
),
cex = 1
)
),
x = 0.03,
y = 0.97,
corner = c(0,1),
draw = FALSE
)
),
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Orientation
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Orientation', fileext = '.tiff'),
# switch the order
formula = x ~ y,
data = reformatted.data,
main = 'Orientation',
xaxis.cex = 1,
yaxis.cex = 1,
# adjust the axes
ylimits = c(0,13),
yat = seq(0,12,2),
# rotate the labels
xaxis.rot = 90,
xlab.label = 'Gene',
xlab.cex = 1.5,
col = sex.colour,
# legend
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
points = list(
col = 'black',
pch = 22,
cex = 1.5,
fill = c('dodgerblue','pink')
),
text = list(
lab = c('male','female')
),
cex = 1
)
),
x = 0.23,
y = 0.97,
corner = c(0,1),
draw = FALSE
)
),
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Background rectangle
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_BG_Rect', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'Bg rectangle',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
ylab.label = 'Gene',
xlimits = c(0,13),
xat = seq(0,12,2),
# draw rectangle
add.rectangle = TRUE,
xleft.rectangle = 0,
xright.rectangle = 13,
ybottom.rectangle = seq(0.5, 8.5, 2),
ytop.rectangle = seq(1.5, 9.5, 2),
col.rectangle = 'grey',
alpha.rectangle = 0.5,
col = sex.colour,
# legend
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
points = list(
col = 'black',
pch = 22,
cex = 1.5,
fill = c('dodgerblue','pink')
),
text = list(
lab = c('male','female')
),
cex = 1
)
),
x = 0.03,
y = 0.97,
corner = c(0,1),
draw = FALSE
)
),
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Line
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Line', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'Line',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
ylab.label = 'Gene',
xlimits = c(0,13),
xat = seq(0,12,2),
# draw line
line.func = function(x){c(0.5, 10.5)},
line.from = 11,
line.to = 11,
line.col = 'grey',
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Panel Organization
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Panels_numeric_conditioning', fileext = '.tiff'),
formula = ~ x | z,
data = reformatted.data,
main = 'Panels',
xaxis.cex = 1,
yaxis.cex = 1,
xlimits = c(0,13),
xat = seq(0,12,2),
# Setting up the layout
layout = c(2,5),
x.relation = 'free',
x.spacing = 1,
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 200
);
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Panels_factor_conditioning', fileext = '.tiff'),
formula = ~ x | y,
data = reformatted.data,
main = 'Panels',
xaxis.cex = 1,
yaxis.cex = 1,
xlimits = c(0,13),
xat = seq(0,12,2),
# Setting up the layout
layout = c(2,5),
x.relation = 'free',
x.spacing = 1,
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Nature format
create.boxplot(
# filename = tempfile(pattern = 'Boxplot_Nature_style', fileext = '.tiff'),
formula = y ~ x,
data = reformatted.data,
main = 'Nature style',
xaxis.cex = 1,
yaxis.cex = 1,
# set style to Nature
style = 'Nature',
# demonstrating how to italicize character variables
ylab.lab = expression(paste('italicized ', italic('a'))),
# demonstrating how to create en-dashes
xlab.lab = expression(paste('en dashs: 1','\u2013', '10'^'\u2013', ''^3)),
resolution = 1200
);
# Sorting by mean and multiple filenames
create.boxplot(
filename = c(
tempfile(pattern = 'Boxplot_Sorted1', fileext = '.tiff'),
tempfile(pattern = 'Boxplot_Sorted2', fileext = '.tiff')
),
formula = y ~ x,
data = reformatted.data,
main = 'Sorting',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
ylab.label = 'Gene',
xlimits = c(0,13),
xat = seq(0,12,2),
# Reordered by median
sample.order = 'increasing',
order.by = 'mean',
description = 'Boxplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Adding text to plot
# Generate normally distributed variables with two different means
set.seed(779);
groupA <- rnorm(n = 100, mean = 10, sd = 2);
groupB <- rnorm(n = 134, mean = 10.5, sd = 2);
# Create data frame for plotting
to.plot <- data.frame(
y = rep(
c('1', '2'),
times = c(100, 134)
),
x = c(groupA, groupB)
);
# Get difference between means
diff.mean <- round(mean(groupB) - mean(groupA), 2);
# Plot and display difference
create.boxplot(
formula = x ~ y,
# filename = tempfile(pattern = 'boxplot_with_text', fileext = '.tiff'),
data = to.plot,
add.stripplot = TRUE,
add.text = TRUE,
text.labels = bquote(mu[B] - mu[A] == .(diff.mean)),
text.x = 2.1,
text.y = 15.3,
text.col = 'black',
text.cex = 1.5,
text.fontface = 'bold',
ylimits = c(
min(to.plot$x) - abs(min(to.plot$x) * 0.1),
max(to.plot$x) + abs(max(to.plot$x) * 0.1)
),
resolution = 200
);
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