create.stripplot {BoutrosLab.plotting.general}R Documentation

Make a strip-plot

Description

Takes a formula and a data.frame and creates a strip-plot

Usage

create.stripplot(
	formula,
	data,
	filename = NULL,
	groups = NULL,
	jitter.data = FALSE,
	jitter.factor = 1,
	jitter.amount = 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,
	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 = 0,
	yaxis.tck = 1,
	xlimits = NULL,
	ylimits = NULL,
	xat = TRUE,
	yat = TRUE,
	lwd = 1,
	pch = 19,
	col = 'black',
	col.border = 'black',
	fill = 'transparent',
	colour.alpha = 1,
	cex = 0.75,
	top.padding = 0.1,
	bottom.padding = 0.7,
	right.padding = 0.3,
	left.padding = 0.5,
	ylab.axis.padding = 1,
	layout = NULL,
	as.table = TRUE,
	x.spacing = 0,
	y.spacing = 0,
	add.median = FALSE,
	median.values = NULL,
	add.rectangle = FALSE,
	xleft.rectangle = NULL,
	ybottom.rectangle = NULL,
	xright.rectangle = NULL,
	ytop.rectangle = NULL,
	col.rectangle = 'transparent',
	alpha.rectangle = 1,
	strip.col = 'white',
	strip.cex = 1,
	strip.fontface = 'bold',
	key = NULL,
	legend = NULL,
	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,
	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

groups

The grouping variable in the data-frame

jitter.data

Allow data to be staggered, default is FALSE

jitter.factor

Numeric value to apply to jitter, default is 1

jitter.amount

Numeric; amount of noise to add, default is NULL

main

The main title for the plot (space is reclaimed if NULL)

s

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

xlab.label

X-axis label

ylab.label

Y-axis label

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

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 scales, defaults to 2

yaxis.cex

Size of y-axis scales, 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 y-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 0

yaxis.tck

Specifies the length of the tick marks for y-axis, defaults to 1

xlimits

Two-element vector giving the x-axis limits, default is automatic

ylimits

Two-element vector giving the y-axis limits, default is automatic

xat

Vector listing where the x-axis labels should be drawn, default is automatic

yat

Vector listing where the y-axis labels should be drawn, default is automatic

lwd

Line width, defaults to 1

pch

The plotting character (defaults to filled circles)

col

Colour of the plotting character (defaults to black)

col.border

Colour of border when pch > 21. Defaults to black

fill

Fill colour of the plotting character if pch set to 21:25 (defaults to transparent)

colour.alpha

Bias to be added to colour selection (defaults to 1)

cex

The size of the plotting character

top.padding

A number specifying the distance to the top margin, defaults to 0.1

bottom.padding

A number specifying the distance to the bottom margin, defaults to 0.7

right.padding

A number specifying the distance to the right margin, defaults to 0.3

left.padding

A number specifying the distance to the left margin, defaults to 0.5

ylab.axis.padding

A number specifying the distance of ylabel to the 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 TRUE to draw from top left corner, moving right then down. Set to FALSE to draw panels from bottom left corner, moving right then up

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

add.median

TRUE/FALSE indicating whether lines should be drawn at the group medians, default is FALSE

median.values

A vector of values representing the median of each group, default is NULL

add.rectangle

Allow a rectangle to be drawn, default is FALSE

xleft.rectangle

Specifies the left x coordinate 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 to fill the rectangle's area

alpha.rectangle

Specifies the colour bias of the rectangle to be drawn

strip.col

Strip background colour, defaults to “white”

strip.cex

Strip title character expansion

strip.fontface

Strip text fontface, defaults to bold

key

A list giving the key (legend). The default suppresses drawing

legend

Add a legend to the plot. Helpful for adding multiple keys and adding keys to the margins of the plot. See xyplot.

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

Short 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)

inside.legend.auto

boolean specifying whether or not to use the automatic inside legend function

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)

Paul C. Boutros

See Also

stripplot, lattice or the Lattice book for an overview of the package.

Examples

set.seed(12345);

simple.data <- data.frame(
    x = c(rep(rnorm(50),5)),
    y = as.factor(sample(LETTERS[1:5],250,TRUE))
    );

create.stripplot(
    filename = tempfile(pattern = 'Stripplot_simple', fileext = '.tiff'),
    formula = x ~ y,
    data = simple.data,
    resolution = 50
    );

# load real datasets
stripplot.data <- data.frame(
    values = c(t(microarray[1:10, 1:58])),
    genes = rep(rownames(microarray)[1:10], each = 58),
    sex = patient$sex,
    stringsAsFactors = TRUE
    );

# Minimal Input using real data
create.stripplot(
    filename = tempfile(pattern = 'Stripplot_Minimal_Input', fileext = '.tiff'),
    formula = genes ~ values,
    data = stripplot.data,
    main = 'Minimal input',
    description = 'Stripplot created by BoutrosLab.plotting.general',
    resolution = 50
    );

# Axes & Labels
create.stripplot(
    filename = tempfile(pattern = 'Stripplot_Axes_Labels', fileext = '.tiff'),
    formula = genes ~ values,
    data = stripplot.data,
    main = 'Axes & labels',
    # formatting axes
    xlab.label = 'Change in gene expression',
    ylab.label = 'Gene',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlimits = c(0,13),
    xat = seq(0,12,2),
    description = 'Stripplot created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Colour & Legend
create.stripplot(
    filename = tempfile(pattern = 'Stripplot_Colour_Legend', fileext = '.tiff'),
    formula = genes ~ values,
    data = stripplot.data,
    main = 'Colour & legend',
    xlab.label = 'Change in gene expression',
    ylab.label = 'Gene',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlimits = c(0,13),
    xat = seq(0,12,2),
    # Colour & points adjustment
    groups = stripplot.data$sex,
    col = c('pink', 'skyblue'),
    pch = 19,
    colour.alpha = 0.5,
    cex = 1,
    # Legend
    key = list(
        space = 'right',
        text = list(
            lab = levels(stripplot.data$sex),
            cex = 1,
            col = 'black'
            ),
        points = list(
            pch = 19,
            col = c('pink','skyblue'),
            alpha = 0.5,
            cex = 1
            ),
        padding.text = 3
        ),
    description = 'Stripplot created by BoutrosLab.plotting.general',
    resolution = 100
    );


# Jitter
create.stripplot(
    filename = tempfile(pattern = 'Stripplot_Jitter', fileext = '.tiff'),
    formula = genes ~ values,
    data = stripplot.data,
    main = 'Low Jitter',
    xlab.label = 'Change in gene expression',
    ylab.label = 'Gene',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlimits = c(0,13),
    xat = seq(0,12,2),
    groups = stripplot.data$sex,
    col = c('pink', 'skyblue'),
    pch = 19,
    colour.alpha = 0.5,
    cex = 1,
    key = list(
        space = 'right',
        text = list(
            lab = levels(stripplot.data$sex),
            cex = 1,
            col = 'black'
            ),
        points = list(
            pch = 19,
            col = c('pink','skyblue'),
            alpha = 0.4,
            cex = 1
            ),
        padding.text = 3
        ),
    # Custom jitter
    jitter.data = TRUE,
    description = 'Stripplot created by BoutrosLab.plotting.general',
    resolution = 200
    );

# Jitter
create.stripplot(
    filename = tempfile(pattern = 'Stripplot_High_Jitter', fileext = '.tiff'),
    formula = genes ~ values,
    data = stripplot.data,
    main = 'High Jitter',
    xlab.label = 'Change in gene expression',
    ylab.label = 'Gene',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlimits = c(0,13),
    xat = seq(0,12,2),
    groups = stripplot.data$sex,
    col = c('pink', 'skyblue'),
    pch = 19,
    colour.alpha = 0.5,
    cex = 1,
    key = list(
        space = 'right',
        text = list(
            lab = levels(stripplot.data$sex),
            cex = 1,
            col = 'black'
            ),
        points = list(
            pch = 19,
            col = c('pink','skyblue'),
            alpha = 0.4,
            cex = 1
            ),
        padding.text = 3
        ),
    # Custom jitter
    jitter.data = TRUE,
    jitter.factor = 0.5,
    jitter.amount = 0.33,
    description = 'Stripplot created by BoutrosLab.plotting.general',
    resolution = 200
    );

# Nature style
create.stripplot(
    filename = tempfile(pattern = 'Stripplot_Nature_style', fileext = '.tiff'),
    formula = genes ~ values,
    data = stripplot.data,
    main = 'Nature style',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlimits = c(0,13),
    xat = seq(0,12,2),
    groups = stripplot.data$sex,
    col = c('pink', 'skyblue'),
    pch = 19,
    colour.alpha = 0.5,
    cex = 1,
    key = list(
        space = 'right',
        text = list(
            lab = levels(stripplot.data$sex),
            cex = 1,
            col = 'black'
            ),
        points = list(
            pch = 19,
            col = c('pink','skyblue'),
            alpha = 0.4,
            cex = 1
            ),
        padding.text = 3
        ),
    jitter.data = TRUE,
    jitter.factor = 0.5,
    jitter.amount = 0.33,

    # set style to Nature 
    style = 'Nature',
    
    # demonstrating how to italicize character variables
    ylab.label = expression(paste('italicized ', italic('a'))),
  
    # demonstrating how to create en-dashes
    xlab.label = expression(paste('en dashs: 1','\u2013', '10'^'\u2013', ''^3)),

    description = 'Stripplot created by BoutrosLab.plotting.general',
    resolution = 200
    );


[Package BoutrosLab.plotting.general version 6.0.3 Index]