create.violinplot: Make a violin plot

Description

This function takes a dataframe and writes a pretty TIFF violin plot

Usage

create.violinplot(
	formula,
	data,
	filename = 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 = c(1,0),
	yaxis.tck = c(1,1),
	ylimits = NULL,
	yat = TRUE,
	col = 'black',
	lwd = 1,
	border.lwd = 1,
	bandwidth = 'nrd0',
	bandwidth.adjust = 1,
	extra.points = NULL,
	extra.points.pch = 21,
	extra.points.col = 'white',
	extra.points.border = 'black',
	extra.points.cex = 1,
	start = NULL,
	end = NULL,
	scale = FALSE,
	plot.horizontal = FALSE,
	top.padding = 0.1,
	bottom.padding = 0.7,
	left.padding = 0.5,
	right.padding = 0.3,
	key = NULL,
	legend = NULL,
	add.rectangle = FALSE,
	xleft.rectangle = NULL,
	ybottom.rectangle = NULL,
	xright.rectangle = NULL,
	ytop.rectangle = NULL,
	col.rectangle = 'transparent',
	alpha.rectangle = 1,
	height = 6,
	width = 6,
	resolution = 1600,
	size.units = 'in',
	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 violin 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

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

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 c(1,0)

yaxis.tck

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

ylimits

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

yat

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

col

Colour to use for filling the interior of the violin plots, defaults to “black”

lwd

Line width, defaults to 1

border.lwd

Width of the exterior boundary of the violin plots, defaults to 1

bandwidth

Smoothing bandwidth, or character string giving rule to choose bandwidth ('nrd0', 'nrd', 'ucv', 'bcv', 'sj', or 'sj-ste'). Passed to base R function density, via lattice::bwplot.

bandwidth.adjust

Adjustment parameter for the bandwidth (bandwidth used is bandwidth*bandwidth.adjust). Makes it easy to specify bandwidth as a proportion of the default.

extra.points

A list of numeric vectors, each one of length equal to the number of violins to be plotted. Specifies a set or sets of extra points to be plotted along the vertical spine of each violin plot. Defaults to NULL (no points to be added)

extra.points.pch

A vector of the same length as extra.points specifying the symbol to use for each set of points. Defaults to 21

extra.points.col

A vector of the same length as extra.points specifying the colour to use for each set of points. Defaults to “white”

extra.points.border

A vector of the same length as extra.points specifying the border colour to use for points >=21. Defaults to “black”

extra.points.cex

A vector of the same length as extra.points specifying the size of each set of points. Defaults to 1

start

Start of boundary cutoff, default is NULL for no boundary

end

End of boundary cutoff, default is NULL for no boundary

scale

Logical; Scales the violin plots, see ?panel.violin for more details, default is FALSE

plot.horizontal

Logical; Determines whether to draw violin plot horizontally or vertically; default is FALSE; If horizontal is FALSE, x will be coerced to a factor or shingle, and vise versa.

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

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.

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

height

Figure height, defaults to 6 inches

width

Figure width, defaults to 6 inches

resolution

Figure resolution in dpi, defaults to 1600

size.units

Figure units, defaults to inches

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)

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

Examples

Run this code

# NOT RUN {
# }
# NOT RUN {
set.seed(12345);

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

create.violinplot(
    filename = paste0(tempdir(),'/Violinplot_Simple.tiff'),
    formula = x ~ y,
    data = simple.data
    );

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

# Minimal input 
create.violinplot(
    filename = paste0(tempdir(),'/Violinplot_Minimal_Input.tiff'),
    formula = values ~ genes,
    data = violin.data,
    main = 'Minimal input',
    xaxis.rot = 90,
    description = 'Violinplot created by BoutrosLab.plotting.general'
    );

# Axes & Labels
create.violinplot(
    filename = paste0(tempdir(),'/Violinplot_Axes_Labels.tiff'),
    formula = values ~ genes,
    data = violin.data,
    main = 'Axes & labels',
    xaxis.rot = 90,
    # Adjusting axes
    xaxis.cex = 1,
    yaxis.cex = 1,
    ylimits = c(0, 13),
    yat = seq(0, 12, 2),
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.label = 'Gene',
    ylab.label = 'Change in expression',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    description = 'Violinplot created by BoutrosLab.plotting.general'
    );

# Range
create.violinplot(
    filename = paste0(tempdir(),'/Violinplot_Range.tiff'),
    formula = values ~ genes,
    data = violin.data,
    main = 'Range',
    xaxis.rot = 90,
    xaxis.cex = 1,
    yaxis.cex = 1,
    # adjusted y-axis limits
    ylimits = c(0, 11),
    yat = seq(0, 10, 2),
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.label = 'Gene',
    ylab.label = 'Change in expression',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    # Specify range
    start = 1,
    end = 10,
    description = 'Violinplot created by BoutrosLab.plotting.general'
    );

# Scaling
create.violinplot(
    filename = paste0(tempdir(),'/Violinplot_Scale.tiff'),
    formula = values ~ genes,
    data = violin.data,
    main = 'Scale',
    xaxis.rot = 90,
    xaxis.cex = 1,
    yaxis.cex = 1,
    ylimits = c(0, 13),
    yat = seq(0, 12, 2),
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.label = 'Gene',
    ylab.label = 'Change in expression',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    # Scale
    scale = TRUE,
    description = 'Violinplot created by BoutrosLab.plotting.general'
    );

# Extra points
median.points <- unlist(tapply(violin.data$values, violin.data$genes, median));
top.points <- unlist(tapply(violin.data$values, violin.data$genes, quantile, 0.90));

create.violinplot(
    filename = paste0(tempdir(),'/Violinplot_Points.tiff'),
    formula = values ~ genes,
    data = violin.data,
    main = 'Extra points',
    xaxis.rot = 90,
    xaxis.cex = 1,
    yaxis.cex = 1,
    ylimits = c(0, 13),
    yat = seq(0, 12, 2),
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.label = 'Gene',
    ylab.label = 'Change in expression',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    # Adding median and 90th percentile
    extra.points = list(median.points, top.points),
    extra.points.pch = 21,
    extra.points.col = c('white','grey'),
    extra.points.cex = 0.5,
    description = 'Violinplot created by BoutrosLab.plotting.general'
    );

# Colours
create.violinplot(
    filename = paste0(tempdir(),'/Violinplot_Colour.tiff'),
    formula = values ~ genes,
    data = violin.data,
    main = 'Colour',
    xaxis.rot = 90,
    xaxis.cex = 1,
    yaxis.cex = 1,
    ylimits = c(0, 13),
    yat = seq(0, 12, 2),
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.label = 'Gene',
    ylab.label = 'Change in expression',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    extra.points = list(median.points, top.points),
    extra.points.pch = 21,
    extra.points.col = c('white','grey'),
    extra.points.cex = 0.5,
    # Colour
    col = 'dodgerblue',
    description = 'Violinplot created by BoutrosLab.plotting.general'
    );

# Custom labels
create.violinplot(
    filename = paste0(tempdir(),'/Violinplot_Custom_Labels.tiff'),
    formula = values ~ genes,
    data = violin.data,
    main = 'Custom labels',
    xaxis.rot = 90,
    xaxis.cex = 1,
    yaxis.cex = 1,
    ylimits = c(0, 16),
    yat = c(0,1,2,4,8,16),
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.label = 'Gene',
    ylab.label = 'Change in expression',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    extra.points = list(median.points, top.points),
    extra.points.pch = 21,
    extra.points.col = c('white','grey'),
    extra.points.cex = 0.5,
    col = 'dodgerblue',
    # customizing labels
    yaxis.lab = c(
        0,
        expression(paste('2'^'0')),
        expression(paste('2'^'1')),
        expression(paste('2'^'2')),
        expression(paste('2'^'4')),
        expression(paste('2'^'5'))
        ),
    description = 'Violinplot created by BoutrosLab.plotting.general'
    );

# Orientation
create.violinplot(
    filename = paste0(tempdir(),'/Violinplot_Orientation.tiff'),
    # switch formula
    formula = genes ~ values,
    data = violin.data,
    main = 'Orientation',
    xaxis.rot = 90,
    xaxis.cex = 1,
    yaxis.cex = 1,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    ylab.label = 'Gene',
    xlab.label = 'Change in expression',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    extra.points = list(median.points, top.points),
    extra.points.pch = 21,
    extra.points.col = c('white','grey'),
    extra.points.cex = 0.5,
    col = 'dodgerblue',
    # orientation
    plot.horizontal = TRUE,
    description = 'Violinplot created by BoutrosLab.plotting.general'
    );

# background
create.violinplot(
    filename = paste0(tempdir(),'/Violinplot_Background.tiff'),
    formula = values ~ genes,
    data = violin.data,
    main = 'Background rectangle',
    xaxis.rot = 90,
    xaxis.cex = 1,
    yaxis.cex = 1,
    ylimits = c(0, 13),
    yat = seq(0, 12, 2),
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.label = 'Gene',
    ylab.label = 'Change in expression',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    extra.points = list(median.points, top.points),
    extra.points.pch = 21,
    extra.points.col = c('white','grey'),
    extra.points.cex = 0.5,
    col = 'dodgerblue',
    # background
    add.rectangle = TRUE,
    xleft.rectangle = seq(0.5, 8.5, 2),
    ybottom.rectangle = 0,
    xright.rectangle = seq(1.5, 9.5, 2),
    ytop.rectangle = 13,
    col.rectangle = 'grey',
    alpha.rectangle = 0.5,
    description = 'Violinplot created by BoutrosLab.plotting.general'
    );

# Nature style
create.violinplot(
    filename = paste0(tempdir(),'/Violinplot_Nature_style.tiff'),
    formula = values ~ genes,
    data = violin.data,
    main = 'Nature style',
    xaxis.rot = 90,
    xaxis.cex = 1,
    yaxis.cex = 1,
    ylimits = c(0, 13),
    yat = seq(0, 12, 2),
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    col = 'dodgerblue',
    add.rectangle = TRUE,
    xleft.rectangle = seq(0.5, 8.5, 2),
    ybottom.rectangle = 0,
    xright.rectangle = seq(1.5, 9.5, 2),
    ytop.rectangle = 13,
    col.rectangle = 'grey',
    alpha.rectangle = 0.5,

    # 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)),

    description = 'Violinplot created by BoutrosLab.plotting.general'
    );
# }