create.qqplot.comparison {BoutrosLab.plotting.general}R Documentation

Make a quantile-quantile plot of two samples

Description

Takes two samples and creates a qq plot for comparing two distributions, possibly conditioned on other variables

Usage

create.qqplot.comparison(
	x,
	data = NULL,
	filename = NULL,
	groups = NULL,
	main = NULL,
	main.just = 'center',
	main.x = 0.5,
	main.y = 0.5,
	main.cex = 3,
	aspect = 'fill',
	prepanel = NULL,
	xlab.label = NULL,
	ylab.label = NULL,
	xlab.cex = 2,
	ylab.cex = 2,
	xlab.col = 'black',
	ylab.col = 'black',
	xlimits = NULL,
	ylimits = NULL,
	xat = TRUE,
	yat = TRUE,
	xaxis.lab = NA,
	yaxis.lab = NA,
	xaxis.cex = 1.5,
	yaxis.cex = 1.5,
	xaxis.fontface = 'bold',
	yaxis.fontface = 'bold',
	xaxis.log = FALSE,
	yaxis.log = FALSE,
	xaxis.rot = 0,
	yaxis.rot = 0,
	xaxis.col = 'black',
	yaxis.col = 'black',
	xaxis.tck = 1,
	yaxis.tck = 1,
	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,
	add.grid = FALSE,
	xgrid.at = xat,
	ygrid.at = yat,
	type = 'p',
	cex = 0.75,
	pch = 19,
	col = 'black',
	lwd = 1,
	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
	);

Arguments

x

A formula or a list of two numeric vectors

data

An optional data source if x is a formula

filename

Filename for tiff output, or if NULL returns the trellis object itself

aspect

This argument controls the physical aspect ratio of the panels, defaults to “fill”

prepanel

A function that takes the same arguments as the “panel”

add.grid

Default manner of drawing grid lines - for custom grids, use type = c('p','g') and set the xat, yat, xgrid.at, ygrid.at parameters

groups

The grouping variable in the data-frame

main

The main plot title

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

xlab.label

The label for the x-axis

ylab.label

The label for the y-axis

main.cex

Size of the overall plot title, defaults to 3

xlab.cex

Size of x-axis label, defaults to 2.5

ylab.cex

Size of y-axis label, defaults to 2.5

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, defaults to automatic

ylimits

Two-element vector giving the y-axis limits, defaults to automatic

xat

Vector listing where the x-axis labels should be drawn, defaults to automatic

yat

Vector listing where the y-axis labels should be drawn, defaults to automatic

xgrid.at

Vector listing where the x-axis grid lines should be drawn, defaults to xat

ygrid.at

Vector listing where the y-axis grid lines should be drawn, defaults to yat

xaxis.lab

Vector listing x-axis tick labels, defaults to automatic

yaxis.lab

Vector listing y-axis tick labels, defaults to automatic

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.cex

Size of x-axis scales, defaults to 1.5

yaxis.cex

Size of y-axis scales, defaults to 1.5

xaxis.fontface

Fontface for the x-axis scales

yaxis.fontface

Fontface for the y-axis scales

xaxis.log

Logical indicating whether x-variable should be in logarithmic scale (and what base if numeric)

yaxis.log

Logical indicating whether y-variable should be in logarithmic scale (and what base if numeric)

xaxis.rot

Counterclockwise rotation of text in x-axis scales in degrees, defaults to 0

yaxis.rot

Counterclockwise rotation of text in y-axis scales in degrees, defaults to 0

xaxis.tck

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

yaxis.tck

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

type

Plot type

cex

Character expansion for plotting symbol

pch

Plotting character

col

Point/line colour

lwd

Specifies line width, defaults to 1

lty

Specifies line style, defaults to 1 (solid)

axes.lwd

Thickness of width of axes lines

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.

top.padding

A number giving the top padding in multiples of the lattice default

bottom.padding

A number giving the bottom padding in multiples of the lattice default

left.padding

A number giving the left padding in multiples of the lattice default

right.padding

A number giving the right padding in multiples of the lattice default

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.

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

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

Value

If filename is NULL then returns the trellis object, otherwise creates a plot and returns a 0/1 success code.

Author(s)

Ying Wu

See Also

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

Examples


set.seed(12345);

create.qqplot.comparison(
    filename = tempfile(pattern = 'QQcomparison_Simple', fileext = '.tiff'),
    x = list(rnorm(100), rnorm(100)),
    resolution = 50
    );

# Minimal Input
create.qqplot.comparison(
    filename = tempfile(pattern = 'QQcomparison_Minimal_Input', fileext = '.tiff'),
    x = list(microarray[1:500,2], microarray[1:500,2]),
    main = 'Minimal input',
    description = 'QQplot comparison created by BoutrosLab.plotting.general',
    resolution = 50
    );

# Axes & Labels
create.qqplot.comparison(
    filename = tempfile(pattern = 'QQcomparison_Axes_Labels', fileext = '.tiff'),
    x = list(microarray[1:500,2], microarray[1:500,2]),
    main = 'Axes & labels',
    # adding axes and labels
    xlab.label = 'Sample 1',
    ylab.label = 'Sample 2',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    # adding grid for good measure
    add.grid = TRUE,
    description = 'QQplot comparison created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Formula input

# 'Formula' format of data
chr.locations <- microarray$Chr[1:500];
chr.locations <- replace(chr.locations, which(chr.locations == 1), 'Chromosome 1');
chr.locations <- replace(chr.locations, which(chr.locations == 2), 'Chromosome 2');

qqplot.data <- data.frame(
    sample = c(rep('Sample 1', 500), rep('Sample 2', 500)),
    value = c(microarray[1:500,1], microarray[1:500,2]),
    chr = chr.locations
    );


create.qqplot.comparison(
    filename = tempfile(pattern = 'QQcomparison_Formula', fileext = '.tiff'),
    # Using a different input method
    x = sample ~ value,
    data = qqplot.data,
    main = 'Formula input',
    xlab.label = 'Sample 1',
    ylab.label = 'Sample 2',
    xaxis.lab = seq(0, 15, 5),
    yaxis.lab = seq(0, 15, 5),
    xlimits = c(0, 17),
    ylimits = c(0, 17),
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    add.grid = TRUE,
    description = 'QQplot comparison created by BoutrosLab.plotting.general',
    resolution = 200
    );


# Groups & Legend
create.qqplot.comparison(
 filename = tempfile(pattern = 'QQcomparison_Groups_Legend', fileext = '.tiff'),
    x = sample ~ value,
    data = qqplot.data,
    # Using fake grouping for the sake of illustration
    groups = qqplot.data$chr,
    # Set colours to differente the gruops
    col = default.colours(3),
    # Setting different plotting characters
    pch = c(15, 16),
    main = 'Groups & legend',
    xlab.label = 'Sample 1',
    ylab.label = 'Sample 2',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    add.grid = TRUE,
    # Adding legend to explain groups
    key = list(
        text = list(
            lab = c('1','2'),
            cex = 1.5,
            col = 'black'
            ),
        points = list(
            pch = c(15, 16),
            col = default.colours(2),
            cex = 1
            ),
        x = 0.04,
        y = 0.95,
        padding.text = 2
        ),
    description = 'QQplot comparison created by BoutrosLab.plotting.general',
    resolution = 200
    );

# Multiple qq plots
create.qqplot.comparison(
    filename = tempfile(pattern = 'QQcomparison_Multiple', fileext = '.tiff'),
    x = sample ~ value | chr,
    data = qqplot.data,
    main = 'Multiple plots',
    xlab.label = 'Sample 1',
    ylab.label = 'Sample 2',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    add.grid = TRUE,
    description = 'QQplot comparison created by BoutrosLab.plotting.general',
    resolution = 200
    );

# Nature style
create.qqplot.comparison(
    filename = tempfile(pattern = 'QQcomparison_Nature_style', fileext = '.tiff'),
    x = sample ~ value,
    data = qqplot.data,
    main = 'Nature style',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    add.grid = TRUE,

   # 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 = 'QQplot comparison created by BoutrosLab.plotting.general',
    resolution = 200
    );


[Package BoutrosLab.plotting.general version 6.0.3 Index]