Make a lollipopplot

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.

Author

Paul C. Boutros

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

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")
    );