create.boxplot {BoutrosLab.plotting.general}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',
	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

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 to use for stripplot

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

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

Vector listing where the x-axis labels should be drawn

yat

Vector listing where the y-axis labels should be drawn

xaxis.lab

Vector listing x-axis tick labels, defaults to automatic

yaxis.lab

Vector listing y-axis tick labels, defaults to automatic

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

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
    );

# 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
    );

# 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
    );


[Package BoutrosLab.plotting.general version 6.0.3 Index]