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

Make a dotmap with coloured background

Description

Takes two data.frames and creates a dotmap with a coloured background. A dotmap is an ordered array of evenly-spaced dots whose size and colour can be user-specified to represent characteristics. For example, size gives the absolute magnitude of the correlation and colour gives the sign of the correlation. The coloured background may indicate p-values.

Usage

create.dotmap(
	x, 
	bg.data = NULL, 
	filename = NULL, 
	main = NULL, 
	main.just = "center", 
	main.x = 0.5, 
	main.y = 0.5, 
	pch = 19, 
	pch.border.col = 'black', 
	add.grid = TRUE, 
	xaxis.lab = colnames(x), 
	yaxis.lab = rownames(x), 
	xaxis.rot = 0, 
	yaxis.rot = 0, 
	main.cex = 3, 
	xlab.cex = 2, 
	ylab.cex = 2, 
	xlab.label = NULL, 
	ylab.label = NULL, 
	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.cex = 1.5, 
	yaxis.cex = 1.5, 
	xaxis.col = 'black', 
	yaxis.col = 'black', 
	xaxis.tck = 1, 
	yaxis.tck = 1, 
	axis.top = 1, 
	axis.bottom = 1, 
	axis.left = 1, 
	axis.right = 1, 
	top.padding = 0.1, 
	bottom.padding = 0.7, 
	right.padding = 0.1, 
	left.padding = 0.5, 
	key.ylab.padding = 0.1,
	key = list(text = list(lab = c(''))), 
	legend = NULL, 
	col.lwd = 1.5, 
	row.lwd = 1.5, 
	spot.size.function = 'default', 
	spot.colour.function = 'default', 
	na.spot.size = 7, 
	na.pch = 4, 
	na.spot.size.colour = 'black',
	grid.colour = NULL, 
	colour.scheme = 'white', 
	total.colours = 99, 
	at = NULL, 
	colour.centering.value = 0, 
	colourkey = FALSE, 
	colourkey.labels.at = NULL, 
	colourkey.labels = NULL, 
	colourkey.cex = 1,
	colour.alpha = 1, 
	bg.alpha = 0.5, 
	fill.colour = 'white', 
	key.top = 0.1, 
	height = 6, 
	width = 6, 
	size.units = 'in', 
	resolution = 1600, 
	enable.warnings = FALSE, 
	col.colour = 'black', 
	row.colour = 'black', 
	description = 'Created with BoutrosLab.plotting.general',
	add.rectangle = FALSE, 
	xleft.rectangle = NULL, 
	ybottom.rectangle = NULL, 
	xright.rectangle = NULL, 
	ytop.rectangle = NULL, 
	col.rectangle = 'transparent', 
	border.rectangle = NULL,
	lwd.rectangle = NULL,
	alpha.rectangle = 1,
	xaxis.fontface = 'bold', 
	yaxis.fontface = 'bold', 
	dot.colour.scheme = NULL, 
	style = 'BoutrosLab',
	preload.default = 'custom',
        use.legacy.settings = FALSE,
	remove.symmetric = FALSE,
        lwd = 2
);

Arguments

x

An unstacked data.frame to plot the dotmap

bg.data

An unstacked data.frame to plot the background, of the same size as “x”. Column names specified here may be arbitrary: they are not used in the plot.

filename

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

pch

Plotting character

pch.border.col

Colour of the dot border if using pch = 21:25

add.grid

Should a grid of black-lines separating each column/row be added?

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

xlab.label

The label for the x-axis

ylab.label

The label for the y-axis

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

main.cex

Size of text for the main title, defaults to 2

xlab.cex

Size of x-axis label, defaults to 2

ylab.cex

Size of y-axis label, defaults to 2

xaxis.lab

Vector listing x-axis tick labels, defaults to colnames(x)

yaxis.lab

Vector listing y-axis tick labels, defaults to rownames(x)

xaxis.cex

Size of x-axis tick labels, defaults to 1.2

yaxis.cex

Size of y-axis tick labels, defaults to 1.5

xaxis.rot

Rotation of x-axis tick labels; defaults to 0

yaxis.rot

Rotation of y-axis tick labels; defaults to 0

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 marks for x-axis, defaults to 1

yaxis.tck

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

axis.top

Specifies the padding on the top of the plot

axis.bottom

Specifies the padding on the bottom of the plot

axis.left

Specifies the padding on the left of the plot

axis.right

Specifies the padding on the right of the plot

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.ylab.padding

a number specifying distance between key and left label

key

A list giving the key (legend). The default suppresses drawing. If the key has a “space” component then extra space will be cleared on that side of the plot for the key

legend

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

col.lwd

Thickness of column grid lines

row.lwd

Thickness of row grid lines

spot.size.function

The function that translates values in x into dotmap spot-size. The default is 0.1 + (2 * abs(x))

spot.colour.function

The function that translates values in x into dotmap spot-colour. The default gives negative values blue, positive values red, and zero white. Parameter also accepts 'columns' and 'rows', which groups the dot colours by columns or rows (not both), respectively. For column/row grouping, there are 12 unique colours and these colours will start to repeat once there are more than 12 columns/rows.

na.spot.size

The size for plotting character for NA cells. Defaults to 7.

na.pch

The type of plotting character to represent NA cells. Defaults to 4 ('X').

na.spot.size.colour

Colour for plotting character representing NA cells. Defaults to black.

grid.colour

The colour for the grid lines. DEPRECATED

colour.scheme

Background colouring. Accepts a vector of colours. Vectors of two or three colours are gradiated to create the final palette. Defaults to “white”.

total.colours

Total number of colours to plot for the Background colours

at

A vector specifying the breakpoints along the range of bg; each interval specified by these breakpoints are assigned to a colour from the palette. Defaults to NULL, which corresponds to the range of bg being divided into total.colours equally spaced intervals. If bg has values outside of the range specified by “at”, those values are shown with colours corresponding to the extreme ends of the colour spectrum and a warning is given.

colour.centering.value

What should be the center of the background key

colourkey

Determines if the colour key should be added or not and sets up its formatting. Defaults to FALSE.

colourkey.labels.at

A vector specifying the tick-positions on the background colourkey

colourkey.labels

A vector specifying tick-labels of the background colourkey

colourkey.cex

Size of the background colourkey label text

colour.alpha

Bias to be added to background colour selection (uses x^colour.alpha in mapping)

bg.alpha

The alpha value of the background colours, defaults to 0.5 so that the background does not compete with the dot colours for attention.

fill.colour

The background fill colour (only exposed where missing values are present). Defaults to white. NOTE: If you change this colour, you may want to set bg.alpha to 1 to avoid the fill colour showing through

key.top

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

height

Figure height in size.units

width

Figure width in size.units

size.units

Units of size for the figure

resolution

Figure resolution in dpi

enable.warnings

Print warnings if set to TRUE, defaults to FALSE

col.colour

The colour for the column grid lines, defaults to “black”. Can be a vector.

row.colour

The colour for the row grid lines, defaults to “black”. Can be a vector.

description

Description of image/plot; default NULL.

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 the rectangle's area

alpha.rectangle

Specifies the colour bias of the rectangle to be drawn

border.rectangle

Specifies the colour of the rectangle border

lwd.rectangle

Specifies the thickness of the rectangle border

xaxis.fontface

Fontface for the x-axis scales

yaxis.fontface

Fontface for the y-axis scales

dot.colour.scheme

Colour Scheme for the dots

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)

remove.symmetric

boolean to set whether or not to remove the top left half of a symettrically sized matrix

lwd

line width for the axis lines

Details

It would be nice to have a library of suitable spot.size and spot.colour functions.

    Earlier ideas included: 
    (1) Changing the dot shape to triangles, so that upward or downward-pointing dots indicated direction of change. This would allow dot colour to be used to encode something else. This idea was not used because in the case of very small dots, the direction of the triangle might not be visible. 
    (2) Adding arrows above or below dots to indicate direction of change. This idea was not used because there may not always be enough space present to add such arrows. 
    (3) Adding line(s) in the background set at different angles to show data. This was found to be not intuitive to read.

A future addition may be to add the option of outlining boxes instead of adding a background. This would be applicable in cases where there is very little background space, and consequently, the background colour would not be very visible.
    

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

Examples

set.seed(12345);
simple.data <- data.frame(
    'A' = runif(n = 15, min = -1, max = 1),
    'B' = runif(n = 15, min = -1, max = 1),
    'C' = runif(n = 15, min = -1, max = 1),
    'D' = runif(n = 15, min = -1, max = 1),
    'E' = runif(n = 15, min = -1, max = 1)
    );

create.dotmap(
    filename = tempfile(pattern = 'Dotmap_Simple', fileext = '.tiff'),
    x = simple.data,
    main = 'Simple',
    description = 'Dotmap created by BoutrosLab.plotting.general',
    resolution = 100
    );

# create a function to determine the spot sizes (default function works best with values < 1)
spot.size.med <- function(x) {abs(x)/3;}

# Minimal Input
create.dotmap(
    filename = tempfile(pattern = 'Dotmap_Minimal_Input', fileext = '.tiff'),
    x = microarray[1:5,1:5],
    main = 'Minimal input',
    spot.size.function = spot.size.med,
    xaxis.rot = 90,
    description = 'Dotmap created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Axes & Labels
spot.size.small <- function(x) {abs(x)/5;}

create.dotmap(
    filename = tempfile(pattern = 'Dotmap_Axes_Labels', fileext = '.tiff'),
    x = microarray[1:15,1:15],
    main = 'Axes & labels',
    spot.size.function = spot.size.small,
    # Adjusting the font sizes and labels
    xaxis.cex = 0.8,
    yaxis.cex = 0.8,
    xaxis.lab = 1:15,
    xlab.label = 'Sample',
    ylab.label = 'Gene',
    xlab.cex = 1,
    ylab.cex = 1,
    description = 'Dotmap created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Legend
key.sizes <- seq(2,12,2);

create.dotmap(
    filename = tempfile(pattern = 'Dotmap_Legend', fileext = '.tiff'),
    x = microarray[1:15,1:15],
    main = 'Legend',
    spot.size.function = spot.size.small,
    xaxis.cex = 0.8,
    yaxis.cex = 0.8,
    xaxis.lab = 1:15,
    xlab.label = 'Sample',
    ylab.label = 'Gene',
    xlab.cex = 1,
    ylab.cex = 1,
    # Legend for dots
    key = list(
        space = 'right',
        points = list(
            cex = spot.size.small(key.sizes),
            col = default.colours(2, palette.type = 'dotmap')[2],
            pch = 19
            ),
        text = list(
            lab = as.character(key.sizes),
            cex = 1,
            adj = 1
            ),
        padding.text = 3,
        background = 'white'
        ),
    key.top = 1,
    description = 'Dotmap created by BoutrosLab.plotting.general',
    resolution = 100
    );


# Cluster by dots and add dendrogram
plot.data <- microarray[1:15,1:15];

# cluster data
clustered.data <- diana(plot.data);

# order data by cluster
plot.data <- plot.data[clustered.data$order,];

# create dendogram
dendrogram.data <- create.dendrogram(x = plot.data, clustering.method = 'diana',
	cluster.dimension = 'row');

dendrogram.grob <- latticeExtra::dendrogramGrob(
        x = dendrogram.data,
        side = 'right',
        type = 'rectangle'
        );

# create dotmap
create.dotmap(
    x = plot.data,
    filename = tempfile(pattern = 'Dotmap_clustered_dendrogram', fileext = '.tiff'),
    main = 'Clustered & dendrogram',
    spot.size.function = spot.size.small,
    # Adjusting the font sizes and labels
    xaxis.cex = 0.8,
    yaxis.cex = 0.8,
    xaxis.lab = 1:15,
    xlab.label = 'Sample',
    ylab.label = 'Gene',
    xlab.cex = 1,
    ylab.cex = 1,
    legend = list(
        right = list(fun = dendrogram.grob)
        ),
    right.padding = 4,
    description = 'Dotmap created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Add background data
key.sizes <- c(-1, 1);

CNA.colour.function <- function(x){
    colours <- rep('white', length(x));
    colours[sign(x) == 1] <- 'Red';
    colours[sign(x) == -1] <- 'Blue';
    colours[x == 0] <- 'transparent';
    return(colours);
    }

create.dotmap(
    filename = tempfile(pattern = 'Dotmap_with_Background', fileext = '.tiff'),
    # added new data for the dots
    x = CNA[1:15,1:15],
    # Moving the dot-data to be background data
    bg.data = microarray[1:15,1:15],
    colour.scheme = c('white','black'),
    main = 'Background',
    spot.size.function = 1,
    spot.colour.function = CNA.colour.function,
    xaxis.cex = 0.8,
    yaxis.cex = 0.8,
    xaxis.lab = 1:15,
    xlab.label = 'Sample',
    ylab.label = 'Gene',
    xlab.cex = 1,
    ylab.cex = 1,
    key = list(
        space = 'right',
        points = list(
            cex = 1,
            col = CNA.colour.function(key.sizes),
            pch = 19
            ),
        text = list(
            lab = c('Gain', 'Loss'),
            cex = 1,
            adj = 1
            ),
        title = 'CNA',
        padding.text = 2,
        background = 'white'
        ),
    # Adding colourkey for background data
    colourkey = TRUE,
    key.top = 1,
    description = 'Dotmap created by BoutrosLab.plotting.general',
    resolution = 200
    );

# Discrete background colours
create.dotmap(
    filename = tempfile(pattern = 'Dotmap_Discrete_Background', fileext = '.tiff'),
    x = CNA[1:15,1:15],
    bg.data = microarray[1:15,1:15],
    main = 'Discrete background',
    spot.size.function = 1,
    spot.colour.function = CNA.colour.function,
    xaxis.cex = 0.8,
    yaxis.cex = 0.8,
    xaxis.lab = 1:15,
    xlab.label = 'Sample',
    ylab.label = 'Gene',
    xlab.cex = 1,
    ylab.cex = 1,
    key = list(
        space = 'right',
        points = list(
            cex = 1,
            col = CNA.colour.function(key.sizes),
            pch = 19
            ),
        text = list(
            lab = c('Gain', 'Loss'),
            cex = 1,
            adj = 1
            ),
        title = 'CNA',
        padding.text = 2,
        background = 'white'
        ),
    colourkey = TRUE,
    key.top = 1,
    # Changing background colour scheme
    colour.scheme = c('lightyellow','gold','darkorange', 'darkorange3'),
    at = seq(0,12,3),
    colourkey.labels = seq(0,12,3),
    colourkey.labels.at = seq(0,12,3),
    bg.alpha = 0.65,
    description = 'Dotmap created by BoutrosLab.plotting.general'
    );

# Dot outlines
border.colours <- function(x){
    colours <- rep('transparent', length(x));
    colours[x > 0] <- 'black';
    colours[x == 0] <- 'transparent';
    return(colours);
    }

create.dotmap(
    filename = tempfile(pattern = 'Dotmap_Outlined_Dots', fileext = '.tiff'),
    x = CNA[1:15,1:15],
    bg.data = microarray[1:15,1:15],
    main = 'Dot outlines',
    spot.size.function = 1,
    spot.colour.function = CNA.colour.function,
    xaxis.cex = 0.8,
    yaxis.cex = 0.8,
    xaxis.lab = 1:15,
    xlab.label = 'Sample',
    ylab.label = 'Gene',
    xlab.cex = 1,
    ylab.cex = 1,
    key = list(
        space = 'right',
        points = list(
            cex = 1,
            col = 'black',
            # Remember to also change the pch in the legend
            pch = 21,
            fill = CNA.colour.function(key.sizes)
            ),
        text = list(
            lab = c('Gain', 'Loss'),
            cex = 1,
            adj = 1
            ),
        title = 'CNA',
        padding.text = 2,
        background = 'white'
        ),
    colourkey = TRUE,
    key.top = 1,
    colour.scheme = c('lightyellow','gold','darkorange', 'darkorange3'),
    at = seq(0,12,3),
    colourkey.labels = seq(0,12,3),
    colourkey.labels.at = seq(0,12,3),
    bg.alpha = 0.65,
    # Change the plotting character to one which has an outline
    pch = 21,
    pch.border.col = border.colours(CNA[1:15,1:15]),
    description = 'Dotmap created by BoutrosLab.plotting.general'
    );

# Covariates & Legend
sex.colours <- patient$sex[1:15];
sex.colours[sex.colours == 'male'] <- 'dodgerblue';
sex.colours[sex.colours == 'female'] <- 'pink';

sample.covariate <- list(
    rect = list(
        col = 'black',
        fill = sex.colours,
        lwd = 1.5
        )
    );

cov.grob <- covariates.grob(
    covariates = sample.covariate,
    ord = c(1:15),
    side = 'top'
    );

sample.cov.legend <- list(
    legend = list(
        colours = c('dodgerblue', 'pink'),
        labels = c('male','female'),
        title = 'Sex'
        )
    );

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

create.dotmap(
    filename = tempfile(pattern = 'Dotmap_Covariates', fileext = '.tiff'),
    x = CNA[1:15,1:15],
    bg.data = microarray[1:15,1:15],
    main = 'Covariates',
    spot.size.function = 1,
    spot.colour.function = CNA.colour.function,
    xaxis.cex = 0.8,
    yaxis.cex = 0.8,
    xaxis.lab = 1:15,
    xlab.label = 'Sample',
    ylab.label = 'Gene',
    xlab.cex = 1,
    ylab.cex = 1,
    key = list(
        space = 'right',
        points = list(
            cex = 1,
            col = 'black',
            pch = 21,
            fill = CNA.colour.function(key.sizes)
            ),
        text = list(
            lab = c('Gain', 'Loss'),
            cex = 1,
            adj = 1
            ),
        title = 'CNA',
        padding.text = 2,
        background = 'white'
        ),
    colourkey = TRUE,
    key.top = 1,
    colour.scheme = c('lightyellow','gold','darkorange', 'darkorange3'),
    at = seq(0,12,3),
    colourkey.labels = seq(0,12,3),
    colourkey.labels.at = seq(0,12,3),
    bg.alpha = 0.65,
    pch = 21,
    pch.border.col = border.colours(CNA[1:15,1:15]),
    # Insert covariates & legend
    legend = list(
        top = list(
            fun = cov.grob
            ),
        left = list( 
            fun = cov.legend
            )
        ),
    description = 'Dotmap created by BoutrosLab.plotting.general'
    );

# Side covariates with label
chr.cov.colours <- microarray$Chr;
chr.cov.colours[microarray$Chr == 1] <- default.colours(3, palette.type = 'chromosomes')[1];
chr.cov.colours[microarray$Chr == 2] <- default.colours(3, palette.type = 'chromosomes')[2];
chr.cov.colours[microarray$Chr == 3] <- default.colours(3, palette.type = 'chromosomes')[3];

chr.covariate <- list(
    rect = list(
        col = 'white',
        fill = chr.cov.colours,
        lwd = 1.5
        )
    );

chr.cov.grob <- covariates.grob(
    covariates = chr.covariate,
    ord = c(1:15),
    side = 'right'
    );

# create dot legend
dot.grob <- draw.key(
    list(
        space = 'right',
         points = list(
                cex = 1,
                col = 'black',
                pch = 21,
                fill = CNA.colour.function(key.sizes)
                ),
            text = list(
                lab = c('Gain', 'Loss'),
                cex = 1,
                adj = 1
                ),
            title = 'CNA',
            padding.text = 2,
            background = 'white'
        )
    );

# Setting up the layout for the joint legends
right.layout <- grid.layout(
    nrow = 1,
    ncol = 2,
    width = unit(
        x = c(0,1),
        units = rep('lines',2)
        ),
    heights = unit(
        x = c(1,1),
        units = rep('npc', 1)
        )
    );

right.grob <- frameGrob(layout = right.layout);

right.grob <- packGrob(
    frame = right.grob,
    grob = chr.cov.grob,
    row = 1,
    col = 1
    );

right.grob <- packGrob(
    frame = right.grob,
    grob = dot.grob,
    row = 1,
    col = 2
    );

temp <- create.dotmap(
    filename = tempfile(pattern = 'Dotmap_Covariates_Side', fileext = '.tiff'),
    x = CNA[1:15,1:15],
    bg.data = microarray[1:15,1:15],
    main = 'Both covariates',
    spot.size.function = 1,
    spot.colour.function = CNA.colour.function,
    xaxis.cex = 0.8,
    yaxis.cex = 0.8,
    xaxis.lab = 1:15,
    xlab.label = 'Sample',
    ylab.label = 'Gene',
    xlab.cex = 1,
    ylab.cex = 1,
    colourkey = TRUE,
    key.top = 1,
    colour.scheme = c('lightyellow','gold','darkorange', 'darkorange3'),
    at = seq(0,12,3),
    colourkey.labels = seq(0,12,3),
    colourkey.labels.at = seq(0,12,3),
    bg.alpha = 0.65,
    pch = 21,
    pch.border.col = border.colours(CNA[1:15,1:15]),
    # insert covariates & legend
    legend = list(
        right = list(
            fun = right.grob
            )
        ),
    description = 'Dotmap created by BoutrosLab.plotting.general'
    );

# add side label to covariate
print(temp, position = c(0,0,1,1), more = TRUE);

draw.key(
    key = list(
        text = list(
            lab = 'Covariate Label',
            cex = 1,
            adj = 1
            )
        ),
    # position label on the plot
    vp = viewport(x = 0.86, y = 0.155, height = 1, width = 0.5, angle = 90),
    draw = TRUE
    );

dev.off();

# Nature style
create.dotmap(
    filename = tempfile(pattern = 'Dotmap_Nature_style', fileext = '.tiff'),
    x = CNA[1:15,1:15],
    bg.data = microarray[1:15,1:15],
    main = 'Nature style',
    spot.size.function = 1,
    spot.colour.function = CNA.colour.function,
    xaxis.cex = 0.8,
    yaxis.cex = 0.8,
    xaxis.lab = 1:15,
    xlab.cex = 1,
    ylab.cex = 1,
    key = list(
        space = 'right',
        points = list(
            cex = 1,
            col = 'black',
            # Remember to also change the pch in the legend
            pch = 21,
            fill = CNA.colour.function(key.sizes)
            ),
        text = list(
            lab = c('Gain', 'Loss'),
            cex = 1,
            adj = 1
            ),
        title = 'CNA',
        padding.text = 2,
        background = 'white'
        ),
    colourkey = TRUE,
    key.top = 1,
    colour.scheme = c('lightyellow','gold','darkorange', 'darkorange3'),
    at = seq(0,12,3),
    colourkey.labels = seq(0,12,3),
    colourkey.labels.at = seq(0,12,3),
    bg.alpha = 0.65,
    # Change the plotting character to one which has an outline
    pch = 21,
    pch.border.col = border.colours(CNA[1:15,1:15]),

    # 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 = 200
    );

simple.data.sym <- data.frame(
    '1' = runif(n = 7, min = -1, max = 1),
    '2' = runif(n = 7, min = -1, max = 1),
    '3' = runif(n = 7, min = -1, max = 1),
    '4' = runif(n = 7, min = -1, max = 1),
    '5' = runif(n = 7, min = -1, max = 1),
    '6' = runif(n = 7, min = -1, max = 1),
    '7' = runif(n = 7, min = -1, max = 1)
    );

create.dotmap(
    filename = tempfile(pattern = 'Dotmap_remove_symmetric', fileext = '.tiff'),
    x = simple.data.sym,
    main = 'Simple',
    xaxis.lab = seq(1,7,1),
    description = 'Dotmap created by BoutrosLab.plotting.general',
    remove.symmetric = TRUE,
    resolution = 200
    );



[Package BoutrosLab.plotting.general version 6.0.3 Index]