create.lollipopplot: Make a lollipopplot

In BoutrosLab.plotting.general: Functions to Create Publication-Quality Plots

Make a lollipopplot

Description

Takes a data.frame and creates a lollipopplot

Usage

create.lollipopplot(
	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);
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")
    );

BoutrosLab.plotting.general documentation built on Nov. 2, 2023, 6:01 p.m.