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

Make a scatterplot

Description

Takes a data.frame and creates a scatterplot

Usage

create.scatterplot(
	formula,
	data,
	filename = NULL,
	groups = 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 = 'bold',
	yaxis.fontface = 'bold',
	xaxis.col = 'black',
	yaxis.col = 'black',
	xaxis.tck = c(1,1),
	yaxis.tck = c(1,1),
	add.grid = FALSE,
	xgrid.at = xat,
        ygrid.at = yat,
	grid.colour = NULL,
	horizontal = FALSE,
	type = 'p',
	cex = 0.75,
	pch = 19,
	col = 'black',
	col.border = 'black',
	lwd = 1,
	lty = 1,
	alpha = 1,
	axes.lwd = 1,
	strip.col = 'white',
	strip.cex = 1,
	strip.fontface = 'bold',
	y.error.up = NULL,
	y.error.down = y.error.up,
	x.error.right = NULL,
	x.error.left = x.error.right,
	y.error.bar.col = 'black',
	x.error.bar.col = y.error.bar.col,
	error.whisker.angle = 90,
	error.bar.lwd = 1,
	error.bar.length = 0.1,
	key = list(text = list(lab = c(''))),
	legend = NULL,
	top.padding = 0.1,
	bottom.padding = 0.7,
	right.padding = 0.1,
	left.padding = 0.5,
	key.top = 0.1,
	key.left.padding = 0,
	ylab.axis.padding = 1,
	axis.key.padding = 1,
	layout = NULL,
	as.table = FALSE,
	x.spacing = 0,
	y.spacing = 0,	
	x.relation = 'same',
	y.relation = 'same',
	add.axes = FALSE,
	axes.lty = 'dashed',
	add.xyline = FALSE,
	xyline.col = 'black',
	xyline.lwd = 1,
	xyline.lty = 1,
	abline.h = NULL,
	abline.v = NULL,
	abline.col = 'black',
	abline.lwd = 1,
	abline.lty = 1,
	add.curves = FALSE,
	curves.exprs = NULL,
	curves.from = min(data, na.rm = TRUE),
	curves.to = max(data, na.rm = TRUE),
	curves.col = 'black',
	curves.lwd = 2,
	curves.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.col.border = 'black',
	points.cex = 1,
	add.line.segments = FALSE,
	line.start = NULL,
	line.end = NULL,
	line.col = 'black',
	line.lwd = 1,
	add.text = FALSE,
	text.labels = NULL,
	text.x = NULL,
	text.y = NULL,
	text.col = 'black',
	text.cex = 1,
	text.fontface = 'bold',
	text.guess.labels = FALSE,
	text.guess.skip.labels = TRUE,
	text.guess.ignore.radius = FALSE,
	text.guess.ignore.rectangle = FALSE,
	text.guess.radius.factor = 1,
	text.guess.buffer.factor = 1,
	text.guess.label.position = NULL,
	height = 6,
	width = 6,
	size.units = 'in',
	resolution = 1600,
	enable.warnings = FALSE,
	description = 'Created with BoutrosLab.plotting.general',
	style = 'BoutrosLab',
	preload.default = 'custom',
	group.specific.colouring = TRUE,
	use.legacy.settings = FALSE,
	inside.legend.auto = FALSE,
	regions.labels = c(),
        regions.start = c(), 
	regions.stop = c(), 
	regions.color = c("red"), 
	regions.cex = 1, 
	regions.alpha = 1,
        lollipop.bar.y = NULL, 
	lollipop.bar.color = "gray",
	...
	);

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

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

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

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

xaxis.lab

Vector listing x-axis tick labels, defaults to automatic

yaxis.lab

Vector listing y-axis tick labels, defaults to automatic

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.cex

Size of x-axis scales, defaults to 2

yaxis.cex

Size of y-axis scales, defaults to 2

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.fontface

Fontface for the x-axis scales

yaxis.fontface

Fontface for the y-axis scales

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.tck

Specifies the length of the tick mark, defaults to 1 for both top and bottom axes

yaxis.tck

Specifies the length of the tick mark, defaults to 1 for both top and bottom axes

add.grid

Logical stating wheter or not the grid should be drawn on the plot

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

grid.colour

ability to set individual grid line colours

horizontal

xyplot-specific function that allows you to change if type='h' draws lines to the vertical or horizontal axis

type

Plot type

cex

Character expansion for plotting symbol

pch

Plotting character

col

Point/line colour

col.border

Colour of border when points pch >= 21. Defaults to “black”

lwd

Specifies line width, defaults to 1

lty

Specifies line style, defaults to 1 (solid)

alpha

Specifies line transparency, defaults to 1 (opaque)

axes.lwd

Thickness of width of axes lines

strip.col

Strip background colour, defaults to “white”

strip.cex

Strip title character expansion

strip.fontface

Strip title fontface, defaults to bold

y.error.up

upward error vector. Defaults to NULL. When y.error.up is NULL, vertical error bar is not drawn

y.error.down

Downward error vector. Defaults to y.error.down to show symmetric error bars

x.error.right

Rightward error vector. Defaults to NULL. When x.error.right is NULL, horizontal error bar is not drawn

x.error.left

Leftward error vector. Defaults to x.error.right to show symmetric error bars

y.error.bar.col

Colour of vertical error bar. Defaults to “black”

x.error.bar.col

Colour of horizontal error bar. Defaults to “black”

error.whisker.angle

Angle of the whisker drawn on error bar. Defaults to 90 degree

error.bar.lwd

Error bar line width. Defaults to 1

error.bar.length

Length of the error bar whiskers. Defaults to 0.1

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 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 0.1

left.padding

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

key.top

A number specifying the distance at top of key, defaults to 0.1

key.left.padding

Amount of padding to go onto any legend on the left

ylab.axis.padding

A number specifying the distance of ylabel to the y-axis, defaults to 1

axis.key.padding

A number specifying the distance from the y-axis to the key, 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”

add.axes

Allow axis lines to be turned on or off, default is FALSE

axes.lty

Specifies axis line style, defaults to “dashed”

add.xyline

Allow y=x line to be drawn, default is FALSE

xyline.col

y=x line colour, defaults to black

xyline.lwd

Specifies y=x line width, defaults to 1

xyline.lty

Specifies y=x line style, defaults to 1 (solid)

abline.h

Allow horizontal line to be drawn, default to NULL

abline.v

Allow vertical line to be drawn, default to NULL

abline.col

Horizontal line colour, defaults to black

abline.lwd

Specifies horizontal line width, defaults to 1

abline.lty

Specifies horizontal line style, defaults to 1 (solid)

add.curves

Allow curves to drawn, default is FALSE

curves.exprs

A list of functions, expressions, or calls using “x” as a variable that specify the curves to be drawn

curves.from

Specifies the x co-ordinates at which the start of each curve should be drawn, defaults to drawing the curves to the left edge of the plotting region

curves.to

Specifies the x co-ordinates at which the end of each curve should be drawn, defaults to drawing the curves to the right edge of the plotting region

curves.col

Specifies colours of curves, default is black for each curve

curves.lwd

Specifies width of curves, default is 1 for each curve

curves.lty

Specifies type of curves, default is 1 (solid) for each curve

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 to fill rectangle's area

alpha.rectangle

Specifies the colour bias of the rectangle to be drawn

add.points

Allow additional points to be drawn, default is FALSE

points.x

The x co-ordinates where additional points should be drawn

points.y

The y co-ordinates where additional points should be drawn

points.pch

The plotting character for additional points

points.col

The colour of additional points

points.col.border

Colour of the border of additional points if points.pch >= 21. Defaults to black

points.cex

The size of additional points

add.line.segments

Allow additional line segments to be drawn, default is FALSE

line.start

The y co-ordinates where additional line segments should start

line.end

The y co-ordinates where additional line segments should end

line.col

The colour of additional line segments, default is black

line.lwd

The line width of additional line segments, default is 1

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.col

The colour of additional text

text.cex

The size of additional text

text.fontface

The fontface for additional text

text.guess.labels

Allows automatic labeling by considering values in text.x and text.y as a data point to be labelled, default is FALSE

text.guess.skip.labels

Provides an option to disregard automatic labelling algorithm if no space is available around a data point, thus forcing labelling if a collision is likely, default is TRUE

text.guess.ignore.radius

Allows the automatic labeling algorithm to ignore the radius space of a data point, useful to label a cluster of data points with a single text box, default is FALSE

text.guess.ignore.rectangle

Allows the atuomatic labeling algorithm to ignore the rectangle space of multiple potential label positions, default is FALSE

text.guess.radius.factor

A numeric value to factor the radius value to alter distance from the label and the data point

text.guess.buffer.factor

A numeric value to factor the buffer value to alter the space which is used to consider if data.points are potentially going to collide

text.guess.label.position

A numeric value between 0 and 360 to specify the percise angle of a text box center and the positive x-axis. Angles move counter-clockwise beginning at the positive x axis

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

group.specific.colouring

Variable to specify if group specific multi colouring for error bars is enforced

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

regions.labels

Labels for each of the regions on the lollipop plots bars

regions.start

start x value of each of the regions

regions.stop

stop value for each of the regions

regions.color

color of each of the regions

regions.cex

size of the text of each of the regions

regions.alpha

alpha of each of the regions

lollipop.bar.y

y location of top of the lollipop plot bar – defaults to right above the bottom y axis

lollipop.bar.color

color of the lollipop plot bar

...

Additional arguments to be passed to xyplot

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

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

Examples

set.seed(12345);

simple.data <- data.frame(
    x = rnorm(800),
    y = rnorm(800)
    );
create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Simple', fileext = '.tiff'),
    formula = y ~ x,
    data = simple.data,
    resolution = 50
    );

scatter.data <- data.frame(
    sample.one = microarray[1:800,1],
    sample.two = microarray[1:800,2],
    chr = microarray$Chr[1:800]
    );

# Minimal Input
create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Minimal_Input', fileext = '.tiff'),
    formula = sample.two ~ sample.one,
    data = scatter.data,
    main = 'Minimal Input',
    description = 'Scatter plot created by BoutrosLab.plotting.general',
    resolution = 50
    );

# Axes & Labels
create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Axes_Labels', fileext = '.tiff'),
    formula = sample.two ~ sample.one,
    data = scatter.data,
    main = 'Axes & Labels',
    # Axes and labels
    xlab.label = colnames(microarray[1]),
    ylab.label = colnames(microarray[2]),
    xat = seq(0, 16, 2),
    yat = seq(0, 16, 2),
    xlimits = c(0, 15),
    ylimits = c(0, 15),
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    description = 'Scatter plot created by BoutrosLab.plotting.general',
    resolution = 50
    );

# Plotting space
create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Plotting_Space', fileext = '.tiff'),
    formula = sample.two ~ sample.one,
    data = scatter.data,
    main = 'Plotting Space',
    xlab.label = colnames(microarray[1]),
    ylab.label = colnames(microarray[2]),
    # change axes accordingly 
    xat = 2 ** (0:4),
    yat = seq(0, 16, 2),
    # change axes range accordingly
    xlimits = c(2 ** 0,16),
    ylimits = c(0, 15),
    # format labels
    xaxis.lab = c(
        expression('2'^'0'),
        expression('2'^'1'),
        expression('2'^'2'),
        expression('2'^'3'),
        expression('2'^'4')
        ),
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    # Transform the x-axis into log-2 space
    xaxis.log = 2,
    description = 'Scatter plot created by BoutrosLab.plotting.general',
    resolution = 50
    );

# Colour & Plotting Character
create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Colour_Pch', fileext = '.tiff'),
    formula = sample.two ~ sample.one,
    data = scatter.data,
    main = 'Colour & Pch',
    xlab.label = colnames(microarray[1]),
    ylab.label = colnames(microarray[2]),
    xat = seq(0, 16, 2),
    yat = seq(0, 16, 2),
    xlimits = c(0, 15),
    ylimits = c(0, 15),
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    # setting the colour
    col = default.colours(2)[2],
    # setting the plotting character type & size
    pch = 21,
    cex = 1.5,
    description = 'Scatter plot created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Colour depth
# create colour scheme to illustrate adding a colourkey
chr.palette <- colour.gradient(default.colours(2)[2], 800);

create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Colour_Depth', fileext = '.tiff'),
    formula = sample.two ~ sample.one,
    data = scatter.data,
    main = 'Colour Depth',
    xlab.label = colnames(microarray[1]),
    ylab.label = colnames(microarray[2]),
    xat = seq(0, 16, 2),
    yat = seq(0, 16, 2),
    xlimits = c(0, 15),
    ylimits = c(0, 15),
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    # setting the colour
    col = chr.palette,
    # setting the plotting character type & size
    pch = 19,
    cex = 1,
    # adding key for colours
    key.top = 1.5,
    legend = list(
        bottom = list(
            fun = draw.colorkey,
            args = list(
                key = list(
                    col = chr.palette,
                    at = 1:800,
                    tick.number = 3,
                    space = 'bottom',
                    size = 1,
                    width = 1.25,
                    height = 1,
                    labels = list(
                        labels = 1:3,
                        cex = 1,
                        at = c(1, which(scatter.data$chr == 2)[1], which(scatter.data$chr == 3)[1])
                        )
                    )
                )
            )
        ),
    description = 'Scatter plot created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Groups & Legend
create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Groups_Legend', fileext = '.tiff'),
    formula = sample.two ~ sample.one,
    data = scatter.data,
    main = 'Groups & Legend',
    # using arbitrary groups for the sake of illustration
    groups = scatter.data$chr,
    xlab.label = colnames(microarray[1]),
    ylab.label = colnames(microarray[2]),
    xat = seq(0, 16, 2),
    yat = seq(0, 16, 2),
    xlimits = c(0, 15),
    ylimits = c(0, 15),
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    col = default.colours(3),
    # Adding legend for groups
    key = list(
        text = list(
            lab = c('1','2','3'),
            cex = 1,
            col = 'black'
            ),
        points = list(
            pch = 19,
            col = default.colours(3),
            cex = 1
            ),
        x = 0.04,
        y = 0.95,
        padding.text = 2
        ),
    description = 'Scatter plot created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Correlation Key
create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Correlation_Key', fileext = '.tiff'),
    formula = sample.two ~ sample.one,
    data = scatter.data,
    main = 'Correlation Key',
    xlab.label = colnames(microarray[1]),
    ylab.label = colnames(microarray[2]),
    xat = seq(0, 16, 2),
    yat = seq(0, 16, 2),
    xlimits = c(0, 15),
    ylimits = c(0, 15),
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    col = 'black',
    pch = 21,
    # Adding correlation key
    legend = list(
        inside = list(
            fun = draw.key,
            args = list(
                key = get.corr.key(
                    x = scatter.data$sample.one,
                    y = scatter.data$sample.two,
                    label.items = c('spearman','spearman.p','kendall','beta1'),
                    alpha.background = 0,
                    key.cex = 1
                    )
                ),
            x = 0.04,
            y = 0.95,
            corner = c(0,1)
            )
        ),
    description = 'Scatter plot created by BoutrosLab.plotting.general',
    resolution = 100
    );


# Panel Organization
create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Panel_numeric_conditional', fileext = '.tiff'),
    formula = sample.two ~ sample.one | chr,
    data = scatter.data,
    main = 'Panel',
    xlab.label = colnames(microarray[1]),
    ylab.label = colnames(microarray[2]),
    xat = seq(0, 16, 2),
    yat = seq(0, 16, 2),
    xlimits = c(0, 15),
    ylimits = c(0, 15),
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    pch = 21,
    col = 'black',
    fill = 'transparent',
    # set up panel layout
    layout = c(1,3),
    yrelation = 'free',
    description = 'Scatter plot created by BoutrosLab.plotting.general',
    resolution = 100
    );

scatter.data$chromosome <- as.character(scatter.data$chr);

create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Panel_character_conditional', fileext = '.tiff'),
    formula = sample.two ~ sample.one | chromosome,
    data = scatter.data,
    main = 'Panel',
    xlab.label = colnames(microarray[1]),
    ylab.label = colnames(microarray[2]),
    xat = seq(0, 16, 2),
    yat = seq(0, 16, 2),
    xlimits = c(0, 15),
    ylimits = c(0, 15),
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    pch = 21,
    col = 'black',
    fill = 'transparent',
    # set up panel layout
    layout = c(1,3),
    yrelation = 'free',
    description = 'Scatter plot created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Covariates
cov.colours <- as.character(microarray$Chr[1:800]);
cov.colours[cov.colours == '1'] <- default.colours(3, palette.type = 'chromosomes')[1];
cov.colours[cov.colours == '2'] <- default.colours(3, palette.type = 'chromosomes')[2];
cov.colours[cov.colours == '3'] <- default.colours(3, palette.type = 'chromosomes')[3];

cov <- list(
    rect = list(
        col = 'transparent',
        fill = cov.colours
        )
    );

cov.grob <- covariates.grob(
    covariates = cov,
    ord = c(1:length(cov.colours)),
    side = 'top',
    size = 1
    );

cov.legend <- list(
    legend = list(
        colours = default.colours(3, palette.type = 'chromosomes'),
        labels = c('1', '2', '3'),
        title = 'Chromosome',
        border = 'transparent'
        )
    );

cov.legend.grob <- legend.grob(
    legends = cov.legend
    );

create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Covariates', fileext = '.tiff'),
    formula = sample.two ~ sample.one,
    data = scatter.data,
    main = 'Covariates',
    xlab.label = colnames(microarray[1]),
    ylab.label = colnames(microarray[2]),
    xat = seq(0, 16, 2),
    yat = seq(0, 16, 2),
    xlimits = c(0, 15),
    ylimits = c(0, 15),
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    pch = 21,
    col = 'black',
    fill = 'transparent',
    # Adding covariate & legend
    legend = list(
        bottom = list(fun = cov.grob),
        right = list(fun = cov.legend.grob)
        ),
    # Ensuring sufficient spacing for covariate
    key.top = 3,
    description = 'Scatter plot created by BoutrosLab.plotting.general',
    resolution = 200
    );

# Error bars
error.data <- data.frame(
    chr = (microarray$Start)[1:20],
    values = apply(microarray[1:20,1:58], 1, mean),
    error = apply(microarray[1:20,1:58], 1, sd)
    );

create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Error_Bars', fileext = '.tiff'),
    formula = values ~ chr,
    data = error.data,
    main = 'Error Bars',
    xlab.label = 'Base pair location on chromosome one',
    ylab.label = 'Gene expression change',
    # xat = seq(0, 16, 2),
    yat = seq(0, 14, 2),
    # xlimits = c(0, 15),
    ylimits = c(0, 13),
    # Format xaxes
    xaxis.lab = c(
        scientific.notation(0, 1),
        scientific.notation(1000000, 1),
        scientific.notation(2000000, 1),
        scientific.notation(3000000, 1),
        scientific.notation(4000000, 1),
        scientific.notation(5000000, 1),
        scientific.notation(6000000, 1),
        scientific.notation(7000000, 1)
        ),
    xaxis.rot = 90,
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    pch = 19,
    col = 'black',
    fill = 'transparent',
    # Specifying error bars
    error.bar.lwd = 1,
    error.whisker.angle = 120,
    y.error.up = error.data$error,
    y.error.bar.col = 'black',
    description = 'Scatter plot created by BoutrosLab.plotting.general',
    resolution = 200
    );

create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Error_Bars_MultiColor', fileext = '.tiff'),
    formula = values ~ chr,
    data = error.data,
    main = 'Error Bars',
    xlab.label = 'Base pair location on chromosome one',
    ylab.label = 'Gene expression change',
    # xat = seq(0, 16, 2),
    yat = seq(0, 14, 2),
    # xlimits = c(0, 15),
    ylimits = c(0, 13),
    # Format xaxes
    xaxis.lab = c(
        scientific.notation(0, 1),
        scientific.notation(1000000, 1),
        scientific.notation(2000000, 1),
        scientific.notation(3000000, 1),
        scientific.notation(4000000, 1),
        scientific.notation(5000000, 1),
        scientific.notation(6000000, 1),
        scientific.notation(7000000, 1)
        ),
    xaxis.rot = 90,
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    pch = 19,
    col = 'black',
    fill = 'transparent',
    # Specifying error bars
    error.bar.lwd = 1,
    error.whisker.angle = 120,
    y.error.up = error.data$error,
    y.error.bar.col = c('black','red','blue'),
    description = 'Scatter plot created by BoutrosLab.plotting.general',
    group.specific.colouring = FALSE,
    resolution = 200
    );


# Gridlines
create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Gridlines', fileext = '.tiff'),
    formula = sample.two ~ sample.one,
    data = scatter.data,
    main = 'Gridlines',
    xlab.label = colnames(microarray[1]),
    ylab.label = colnames(microarray[2]),
    xat = seq(0, 16, 2),
    yat = seq(0, 16, 2),
    xlimits = c(0, 15),
    ylimits = c(0, 15),
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    pch = 21,
    col = 'black',
    fill = 'transparent',
    # Adding gridlines
    type = c('p','g'),
    description = 'Scatter plot created by BoutrosLab.plotting.general',
    resolution = 200
    );

# lines & background rectangle
create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Lines_BG', fileext = '.tiff'),
    formula = sample.two ~ sample.one,
    data = scatter.data,
    main = 'Lines & BG rectangle',
    xlab.label = colnames(microarray[1]),
    ylab.label = colnames(microarray[2]),
    xat = seq(0, 16, 2),
    yat = seq(0, 16, 2),
    xlimits = c(0, 15),
    ylimits = c(0, 15),
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    pch = 21,
    col = 'black',
    fill = 'transparent',
    type = c('p','g'),
    # add xy line
    add.xyline = TRUE,
    xyline.lty = 3,
    xyline.col = 'red',
    xyline.lwd = 3,
    # add background rectangle
    add.rectangle = TRUE,
    xleft.rectangle = which(scatter.data$chr == 2)[1]/800*15,
    xright.rectangle = which(scatter.data$chr == 3)[1]/800*15,
    ybottom.rectangle = 0,
    ytop.rectangle = 15,
    col.rectangle = 'grey',
    alpha.rectangle = 0.5,
    description = 'Scatter plot created by BoutrosLab.plotting.general',
    resolution = 200
    );

# attach lines to points
create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Lines', fileext = '.tiff'),
    formula = sample.two ~ sample.one | chr,
    data = scatter.data,
    main = 'Lines',
    xlab.label = colnames(microarray[1]),
    ylab.label = colnames(microarray[2]),
    xat = seq(0, 16, 2),
    yat = seq(0, 16, 2),
    xlimits = c(0, 15),
    ylimits = c(0, 15),
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    pch = 21,
    col = 'black',
    fill = 'transparent',
    # attach lines
    type = c('h','p'),
    layout = c(1,3),
    description = 'Scatter plot created by BoutrosLab.plotting.general',
    resolution = 200
    );

# ROC curve
set.seed(123456);

class.values <- runif(50, 0, 1);
observed.values <- sample(c(0,1), size = 50, replace = TRUE);
cutoffs <- seq(1,0,-0.01);
tprs <- c();
fprs <- c();

for (c in cutoffs) {
        roc.classification <- rep(0, length(class.values));
        roc.classification[class.values >= c] <- 1;
        roc.results <- table(
                factor(roc.classification, levels = c(0,1)),
                factor(observed.values, levels = c(0,1)),
                dnn = c('pred', 'obs')
                );
        tprs <- c(tprs, roc.results[2,2] / (roc.results[2,2] + roc.results[1,2]));
        fprs <- c(fprs, roc.results[2,1] / (roc.results[2,1] + roc.results[1,1]));
        }

roc.data <- data.frame(cutoff = cutoffs, TPR = tprs, FPR = fprs);
points.x <- roc.data[match(c(0.25, 0.5, 0.75), roc.data$cutoff), 'FPR'];
points.y <- roc.data[match(c(0.25, 0.5, 0.75), roc.data$cutoff), 'TPR'];

create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_ROC', fileext = '.tiff'),
    formula = TPR ~ FPR,
    data = roc.data,
    main = 'ROC',
    xlab.label = 'False positive rate',
    ylab.label = 'True positive rate',
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    type = 's',
    lwd = 3,
    add.xyline = TRUE,
    xyline.col = 'grey',
    add.points = TRUE,
    points.x = points.x,
    points.y = points.y,
    points.col = c('blue', 'darkgreen', 'red'),
    add.text = TRUE,
    text.labels = paste('cutoff = ', c(0.25, 0.5, 0.75), sep = ''),
    #text.x = points.x - 0.14,
    #text.y = points.y + 0.03,
    text.x = points.x,
    text.y = points.y,
    text.guess.labels = TRUE,
    text.guess.label.position = 155,
    text.guess.radius.factor = 2.5,
    description = 'Scatter plot created by BoutrosLab.plotting.general',
    resolution = 200
    );

# Volcano Plots
fold.change <- apply(microarray[,1:29], 1, mean) - apply(microarray[,30:58], 1, mean);

fake.microarray <- microarray[,1:58] - log(mean(apply(microarray[,1:58],1, mean)));
fake.microarray[,30:58] <-  fake.microarray[,30:58] + mean(fold.change);
fake.microarray[fake.microarray < 0] <- 0;

p.values <- apply(fake.microarray[,1:58], 1, function(x) {t.test(x=x[1:29],y=x[30:58])$p.value} );
fold.change <- apply(fake.microarray[, 1:29], 1, mean) - apply(fake.microarray[, 30:58], 1,mean);
p.values.adjusted <- p.adjust(p.values, 'fdr');

dot.colours <- vector(length=length(p.values));
dot.colours[p.values.adjusted < .05 & fold.change < 0] <- 'green';
dot.colours[p.values.adjusted < .05 & fold.change > 0] <- 'red';
dot.colours[p.values.adjusted > .05] <- 'black';


volcano.data <- data.frame(
    p.values = -log10(p.values.adjusted),
    fold.change = fold.change
    );

create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Volcano_Plot', fileext = '.tiff'),
    formula = p.values ~ fold.change,
    data = volcano.data,
    col = dot.colours,
    alpha = .5,
    yat = c(0,2,4,6,8),
    ylimits = c(-0.1,8.1),
    yaxis.lab = expression(10^0,10^-2,10^-4,10^-6,10^-8),
    yaxis.cex = 1.5,
    xaxis.cex = 1.5,
    xlab.label = 'foldChange',
    ylab.label = 'pValues',
    xlab.cex = 1.75,
    ylab.cex = 1.75,
    resolution = 200
    );

# Automatic Labeling
interesting.fold.change <- (fold.change < -.9 | fold.change > .9);
interesting.p.value <- (-log10(p.values.adjusted) < 8 & -log10(p.values.adjusted) > 2);
interesting.points <- interesting.fold.change & interesting.p.value;

text.x <- fold.change[interesting.points];
text.y <- (-log10(p.values.adjusted))[interesting.points];
text.labels <- rownames(microarray)[interesting.points];

create.scatterplot(
    filename = tempfile(pattern = 'Scatterplot_Volcano_Plot_With_Labels', fileext = '.tiff'),
    formula = p.values ~ fold.change,
    data = volcano.data,
    alpha = .5,
    yat = c(0,2,4,6,8),
    ylimits = c(-0.1,8.1),
    xlimits = c(-1.5,1.5),
    yaxis.lab = expression(10^0,10^-2,10^-4,10^-6,10^-8),
    yaxis.cex = 1.5,
    xaxis.cex = 1.5,
    xlab.label = 'foldChange',
    ylab.label = 'pValues',
    xlab.cex = 1.75,
    ylab.cex = 1.75,
    add.text = TRUE,
    text.x = text.x,
    text.y = text.y,
    text.labels = text.labels,
    text.guess.labels = TRUE,
    resolution = 200
    );

# With line segments
line.data <- data.frame(
    group = c('A','B','C'),
    x = sample(1:10,3),
    y = sample(1:10,3),
    z = sample(1:10,3)
    );

create.scatterplot(
    (x+y+z) ~ group,
    line.data,
    filename = tempfile(pattern = 'Scatterplot_with_LineSegments', fileext = '.tiff'),
    cex = 0,
    add.line.segments = TRUE,
    line.start = list(
	rep(0,nrow(line.data)), 
	line.data$x,
	c(line.data$x + line.data$y)
	),
    line.end = list(
	line.data$x, 
	c(line.data$x + line.data$y),
	c(line.data$x + line.data$y + line.data$z)
	),
    line.col = list('red','blue','green'),
    line.lwd = list(3,3,3),
    resolution = 200
    );

lollipop.data <- data.frame(
    y = seq(1,100,1),
    x = rnorm(100)
    );

create.lollipopplot(
    filename = tempfile(pattern = 'Lollipop_Simple', fileext = '.tiff'),
    formula = x ~ y,
    data = lollipop.data,
    main = 'Lollipop plot',
    xaxis.cex = 1,
    xlimits = c(-1,102),
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    pch = 21,
    col = 'black',
    fill = 'transparent',
    description = 'Scatter plot created by BoutrosLab.plotting.general',
    regions.start = c(1,26,48),
    regions.stop = c(15,35,72),
    regions.labels = c("test 1", "test2", "test 3"),
    regions.color = c("#66b3ff", "#5cd65c", "#ff3333"),
    resolution = 200
    );


[Package BoutrosLab.plotting.general version 6.0.3 Index]