Make a quantile-quantile plot of two samples

Takes two samples and creates a qq plot for comparing two distributions, possibly conditioned on other variables

Usage

create.qqplot.comparison(
  x,
  data = NULL,
  filename = NULL,
  groups = NULL,
  main = NULL,
  main.just = 'center',
  main.x = 0.5,
  main.y = 0.5,
  main.cex = 3,
  aspect = 'fill',
  prepanel = NULL,
  xlab.label = NULL,
  ylab.label = NULL,
  xlab.cex = 2,
  ylab.cex = 2,
  xlab.col = 'black',
  ylab.col = 'black',
  xlimits = NULL,
  ylimits = NULL,
  xat = TRUE,
  yat = TRUE,
  xaxis.lab = NA,
  yaxis.lab = NA,
  xaxis.cex = 1.5,
  yaxis.cex = 1.5,
  xaxis.fontface = 'bold',
  yaxis.fontface = 'bold',
  xaxis.log = FALSE,
  yaxis.log = FALSE,
  xaxis.rot = 0,
  yaxis.rot = 0,
  xaxis.col = 'black',
  yaxis.col = 'black',
  xaxis.tck = 1,
  yaxis.tck = 1,
  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,
  add.grid = FALSE,
  xgrid.at = xat,
  ygrid.at = yat,
  type = 'p',
  cex = 0.75,
  pch = 19,
  col = 'black',
  lwd = 1,
  lty = 1,
  axes.lwd = 2.25,
  key = list(text = list(lab = c(''))),
  legend = NULL,
  add.rectangle = FALSE,
  xleft.rectangle = NULL,
  ybottom.rectangle = NULL,
  xright.rectangle = NULL,
  ytop.rectangle = NULL,
  col.rectangle = 'transparent',
  alpha.rectangle = 1,
  top.padding = 3,
  bottom.padding = 0.7,
  left.padding = 0.5,
  right.padding = 0.1,
  height = 6,
  width = 6,
  size.units = 'in',
  resolution = 1600,
  enable.warnings = FALSE,
  description = 'Created with BoutrosLab.plotting.general',
  style = 'BoutrosLab',
  preload.default = 'custom',
  use.legacy.settings = FALSE,
  inside.legend.auto = FALSE
  );

Arguments

x: A formula or a list of two numeric vectors
data: An optional data source if x is a formula
filename: Filename for tiff output, or if NULL returns the trellis object itself
aspect: This argument controls the physical aspect ratio of the panels, defaults to “fill”
prepanel: A function that takes the same arguments as the “panel”
add.grid: Default manner of drawing grid lines - for custom grids, use type = c('p','g') and set the xat, yat, xgrid.at, ygrid.at parameters
groups: The grouping variable in the data-frame
main: The main plot title
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
main.cex: Size of the overall plot title, defaults to 3
xlab.cex: Size of x-axis label, defaults to 2.5
ylab.cex: Size of y-axis label, defaults to 2.5
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
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
xaxis.lab: Vector listing x-axis tick labels, defaults to automatic
yaxis.lab: Vector listing y-axis tick labels, defaults to automatic
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.cex: Size of x-axis scales, defaults to 1.5
yaxis.cex: Size of y-axis scales, defaults to 1.5
xaxis.fontface: Fontface for the x-axis scales
yaxis.fontface: Fontface for the y-axis scales
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.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.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
type: Plot type
cex: Character expansion for plotting symbol
pch: Plotting character
col: Point/line colour
lwd: Specifies line width, defaults to 1
lty: Specifies line style, defaults to 1 (solid)
axes.lwd: Thickness of width of axes lines
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 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
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.
add.rectangle: Allow a rectangle to be drawn, default is FALSE
xleft.rectangle: Specifies the left x coordinate 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
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)
inside.legend.auto: boolean specifying whether or not to use the automatic inside legend function

Value

If filename is NULL then returns the trellis object, otherwise creates a plot and returns a 0/1 success code.

Author

Ying Wu

Examples


set.seed(12345);

create.qqplot.comparison(
    # filename = tempfile(pattern = 'QQcomparison_Simple', fileext = '.tiff'),
    x = list(rnorm(100), rnorm(100)),
    resolution = 50
    );


# Minimal Input
create.qqplot.comparison(
    # filename = tempfile(pattern = 'QQcomparison_Minimal_Input', fileext = '.tiff'),
    x = list(microarray[1:500,2], microarray[1:500,2]),
    main = 'Minimal input',
    description = 'QQplot comparison created by BoutrosLab.plotting.general',
    resolution = 50
    );


# Axes & Labels
create.qqplot.comparison(
    # filename = tempfile(pattern = 'QQcomparison_Axes_Labels', fileext = '.tiff'),
    x = list(microarray[1:500,2], microarray[1:500,2]),
    main = 'Axes & labels',
    # adding axes and labels
    xlab.label = 'Sample 1',
    ylab.label = 'Sample 2',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    # adding grid for good measure
    add.grid = TRUE,
    description = 'QQplot comparison created by BoutrosLab.plotting.general',
    resolution = 100
    );


# Formula input

# 'Formula' format of data
chr.locations <- microarray$Chr[1:500];
chr.locations <- replace(chr.locations, which(chr.locations == 1), 'Chromosome 1');
chr.locations <- replace(chr.locations, which(chr.locations == 2), 'Chromosome 2');

qqplot.data <- data.frame(
    sample = c(rep('Sample 1', 500), rep('Sample 2', 500)),
    value = c(microarray[1:500,1], microarray[1:500,2]),
    chr = chr.locations
    );


create.qqplot.comparison(
    # filename = tempfile(pattern = 'QQcomparison_Formula', fileext = '.tiff'),
    # Using a different input method
    x = sample ~ value,
    data = qqplot.data,
    main = 'Formula input',
    xlab.label = 'Sample 1',
    ylab.label = 'Sample 2',
    xaxis.lab = seq(0, 15, 5),
    yaxis.lab = seq(0, 15, 5),
    xlimits = c(0, 17),
    ylimits = c(0, 17),
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    add.grid = TRUE,
    description = 'QQplot comparison created by BoutrosLab.plotting.general',
    resolution = 200
    );


# \donttest{
# Groups & Legend
create.qqplot.comparison(
 # filename = tempfile(pattern = 'QQcomparison_Groups_Legend', fileext = '.tiff'),
    x = sample ~ value,
    data = qqplot.data,
    # Using fake grouping for the sake of illustration
    groups = qqplot.data$chr,
    # Set colours to differente the gruops
    col = default.colours(3),
    # Setting different plotting characters
    pch = c(15, 16),
    main = 'Groups & legend',
    xlab.label = 'Sample 1',
    ylab.label = 'Sample 2',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    add.grid = TRUE,
    # Adding legend to explain groups
    key = list(
        text = list(
            lab = c('1','2'),
            cex = 1.5,
            col = 'black'
            ),
        points = list(
            pch = c(15, 16),
            col = default.colours(2),
            cex = 1
            ),
        x = 0.04,
        y = 0.95,
        padding.text = 2
        ),
    description = 'QQplot comparison created by BoutrosLab.plotting.general',
    resolution = 200
    );


# Multiple qq plots
create.qqplot.comparison(
    # filename = tempfile(pattern = 'QQcomparison_Multiple', fileext = '.tiff'),
    x = sample ~ value | chr,
    data = qqplot.data,
    main = 'Multiple plots',
    xlab.label = 'Sample 1',
    ylab.label = 'Sample 2',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    add.grid = TRUE,
    description = 'QQplot comparison created by BoutrosLab.plotting.general',
    resolution = 200
    );


# Nature style
create.qqplot.comparison(
    # filename = tempfile(pattern = 'QQcomparison_Nature_style', fileext = '.tiff'),
    x = sample ~ value,
    data = qqplot.data,
    main = 'Nature style',
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    add.grid = TRUE,

   # set style to Nature 
    style = 'Nature',
    
    # demonstrating how to italicize character variables
    ylab.label = expression(paste('italicized ', italic('a'))),
  
    # demonstrating how to create en-dashes
    xlab.label = expression(paste('en dashs: 1','\u2013', '10'^'\u2013', ''^3)),

    description = 'QQplot comparison created by BoutrosLab.plotting.general',
    resolution = 200
    );
#> Warning: Setting resolution to 1200 dpi.
#> Warning: Nature also requires italicized single-letter variables and en-dashes
#> 			for ranges and negatives. See example in documentation for how to do this.
#> Warning: Avoid red-green colour schemes, create TIFF files, do not outline the figure or legend.

# }

Usage

Arguments

Value

Author

See also

Examples