Make a Manhattan plot

Takes a data.frame and creates a Manhattan plot

Usage

create.manhattanplot(
  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,
  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 = 'plain',
  yaxis.fontface = 'plain',
  xaxis.col = 'black',
  yaxis.col = 'black',
  xaxis.tck = 0,
  yaxis.tck = c(1,1),
  horizontal = FALSE,
  type = 'p',
  cex = 2,
  pch = '.',
  col = 'black',
  lwd = 1,
  lty = 1,
  alpha = 1,
  strip.col = 'white',
  strip.cex = 1,
  axes.lwd = 1,
  axes.lty = 'dashed',
  key = list(text = list(lab = c(''))),
  legend = NULL,
  layout = NULL,
  as.table = FALSE,
  x.spacing = 0,
  y.spacing = 0,
  x.relation = 'same',
  y.relation = 'same',
  top.padding = 0,
  bottom.padding = 0,
  right.padding = 0,
  left.padding = 0,
  key.top = 0,
  key.left.padding = 0,
  ylab.axis.padding = 1,
  axis.key.padding = 1,
  abline.h = NULL,
  abline.col = 'black',
  abline.lwd = 1,
  abline.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.cex = 1,
  add.text = FALSE,
  text.labels = NULL,
  text.x = NULL,
  text.y = NULL,
  text.col = 'black',
  text.cex = 1,
  text.fontface = 'bold',
  height = 6,
  width = 10,
  size.units = 'in',
  resolution = 1600,
  enable.warnings = FALSE,
  style = 'BoutrosLab',
  description = 'Created with BoutrosLab.plotting.general',
  preload.default = 'custom',
        use.legacy.settings = FALSE,
        inside.legend.auto = FALSE,
  ...
  );

Arguments

formula: The formula used to extract the x & y components from the data-frame. Transforming data within formula is not compatible with automatic scaling with `xat` or `yat`.
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
xlab.label: x-axis label
ylab.label: y-axis label
xlab.cex: Size of x-axis label, defaults to 2
ylab.cex: Size of y-axis label, defaults to 2
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: Accepts a vector listing where x-axis ticks should be drawn or if automatic scaling is desired, one of three strings: “auto”, “auto.linear” or “auto.log”. Automatic scaling fixes x-axis tick locations, labels, and data values dependent given data. “auto” will determine whether linear or logarithmic scaling fits the given data best, “auto.linear” or “auto.log” will force data to be scaled linearly or logarithmically respectively. Defaults to lattice automatic (TRUE). For more details see `auto.axis()`.
yat: Accepts a vector listing where y-axis ticks should be drawn or if automatic scaling is desired, one of three strings: “auto”, “auto.linear” or “auto.log”. Automatic scaling fixes y-axis tick locations, labels, and data values dependent given data. “auto” will determine whether linear or logarithmic scaling fits the given data best, “auto.linear” or “auto.log” will force data to be scaled linearly or logarithmically respectively. Defaults to lattice automatic (TRUE). For more details see `auto.axis()`.
xaxis.lab: Vector listing x-axis tick labels, defaults to automatic (TRUE). Using automatic scaling with xat will overwrite user input. Set to NULL to remove x-axis labels.
yaxis.lab: Vector listing y-axis tick labels, defaults to automatic (TRUE). Using automatic scaling with yat will overwrite user input. Set to NULL to remove y-axis labels.
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 1
yaxis.cex: Size of y-axis scales, defaults to 1
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
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
lwd: Specifies line width, defaults to 1
lty: Specifies line style, defaults to 1 (solid)
alpha: Specifies line transparency, defaults to 1 (opaque)
strip.col: Strip background colour, defaults to “white”
strip.cex: Strip title character expansion
axes.lwd: Thickness of width of axis lines
axes.lty: Specifies axis line style, defaults to “dashed”
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.
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”
top.padding: A number specifying the distance to the top margin, defaults to 0
bottom.padding: A number specifying the distance to the bottom margin, defaults to 0
right.padding: A number specifying the distance to the right margin, defaults to 0
left.padding: A number specifying the distance to the left margin, defaults to 0
key.top: A number specifying the distance at top of key, defaults to 0
key.left.padding: Amount of padding to go onto any legend on the left
ylab.axis.padding: A number specifying the distance of label 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
abline.h: Allow horizontal 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.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
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.cex: The size of additional points
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
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
style: defaults to “BoutrosLab”, also accepts “Nature”, which changes parameters according to Nature formatting requirements
description: Short description of image/plot; default NULL
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
...: 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

Christine P'ng, Cindy Q. Yao

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);
simple.data <- data.frame(
    x = runif(20000, 0, 1),
    y = 1:20000
    );

create.manhattanplot(
    # filename = tempfile(pattern = 'Manhattan_Simple', fileext = '.tiff'),
    formula = -log10(x) ~ y,
    data = simple.data,
    main = 'Simple',
    description = 'Manhattan plot created using BoutrosLab.plotting.general',
    resolution = 50
    );


# set up chromosome covariate colours to use for chr covariate, below
chr.colours <- force.colour.scheme(microarray$Chr, scheme = 'chromosome');

# make chr covariate and chr labels 
chr.n.genes       <- vector();
chr.tck           <- vector();
chr.pos.genes     <- vector();
chr.break         <- vector();
chr.break[1]      <- 0;
# get a list of chromosomes to loop
chr <- unique(microarray$Chr);

# loop over each chromosome
for ( i in 1:length(chr) ) {

    # get the number of genes that belong to one chromosome
    n <- sum(microarray$Chr == chr[i]);

    # calculate where the labels go
    chr.n.genes[i]   <- n;
    chr.break[i+1] <- n + chr.break[i];
    chr.pos.genes[i] <- floor(chr.n.genes[i]/2);
    chr.tck[i]       <- chr.pos.genes[i] + which(microarray$Chr == chr[i])[1];
    }

# add an indicator function for the data-frame
microarray$ind <- 1:nrow(microarray);

# Minimal input
create.manhattanplot(
    # filename = tempfile(pattern = 'Manhattan_Minimal_Input', fileext = '.tiff'),
    formula = -log10(pval) ~ ind,
    data = microarray,
    main = 'Minimal input',
    description = 'Manhattan plot created using BoutrosLab.plotting.general',
    resolution = 100
    );


# Custom Axes
create.manhattanplot(
    # filename = tempfile(pattern = 'Manhattan_Custom_Axes', fileext = '.tiff'),
    formula = -log10(pval) ~ ind,
    data = microarray,
    main = 'Custom axes',
    xlab.label = expression('Chromosomes'),
    ylab.label = expression('P'['adjusted']),
    xat = chr.tck,
    xaxis.lab = c(1:22, 'X', 'Y'),
    xaxis.tck = 0,
    xaxis.cex = 1,
    yaxis.cex = 1,
    yat = seq(0,5,1),
    yaxis.lab = c(
        1,
        expression(10^-1),
        expression(10^-2),
        expression(10^-3),
        expression(10^-4)
        ),
    description = 'Manhattan plot created using BoutrosLab.plotting.general',
    resolution = 100
    );


# Log-Scaled Axis
log.data <- data.frame(
    x = 10 ** runif(20000, 1, 5),
    y = 1:20000
    );

create.manhattanplot(
    formula = x ~ y,
    data = log.data,
    main = 'Log Scaled',
    # Log base 10 scale x-axis
    xat = 'auto.log',
    description = 'Manhattan plot created using BoutrosLab.plotting.general',
    resolution = 50
    );


# Colour scheme
create.manhattanplot(
    # filename = tempfile(pattern = 'Manhattan_Colour_Scheme', fileext = '.tiff'),
    formula = -log10(pval) ~ ind,
    data = microarray,
    main = 'Colour scheme',
    xlab.label = expression('Chromosomes'),
    ylab.label = expression('P'['adjusted']),
    xat = chr.tck,
    xaxis.lab = c(1:22, 'X', 'Y'),
    xaxis.tck = 0,
    xaxis.cex = 1,
    yaxis.cex = 1,
    yat = seq(0,5,1),
    yaxis.lab = c(
        1,
        expression(10^-1),
        expression(10^-2),
        expression(10^-3),
        expression(10^-4)
        ),
    col = chr.colours,
    description = 'Manhattan plot created using BoutrosLab.plotting.general',
    resolution = 200
    );


# Plotting Character
create.manhattanplot(
    # filename = tempfile(pattern = 'Manhattan_Plotting_Character', fileext = '.tiff'),
    formula = -log10(pval) ~ ind,
    data = microarray,
    main = 'Plotting character',
    xlab.label = expression('Chromosomes'),
    ylab.label = expression('P'['adjusted']),
    xat = chr.tck,
    xaxis.lab = c(1:22, 'X', 'Y'),
    xaxis.tck = 0,
    xaxis.cex = 1,
    yaxis.cex = 1,
    yat = seq(0,5,1),
    yaxis.lab = c(
        1,
        expression(10^-1),
        expression(10^-2),
        expression(10^-3),
        expression(10^-4)
        ),
    col = chr.colours,
    # Change plotting character and size of plotting character
    pch = 18,
    cex = 0.75,
    description = 'Manhattan plot created using BoutrosLab.plotting.general',
    resolution = 200
    );


# \donttest{
# Line
create.manhattanplot(
    # filename = tempfile(pattern = 'Manhattan_Added_Line', fileext = '.tiff'),
    formula = -log10(pval) ~ ind,
    data = microarray,
    main = 'Line',
    xlab.label = expression('Chromosomes'),
    ylab.label = expression('P'['adjusted']),
    xat = chr.tck,
    xaxis.lab = c(1:22, 'X', 'Y'),
    xaxis.tck = 0,
    xaxis.cex = 1,
    yaxis.cex = 1,
    yat = seq(0,5,1),
    yaxis.lab = c(
        1,
        expression(10^-1),
        expression(10^-2),
        expression(10^-3),
        expression(10^-4)
        ),
    col = chr.colours,
    pch = 18,
    cex = 0.75,
    # draw horizontal line
    abline.h = 2,
    abline.lty = 2,
    abline.lwd = 1,
    abline.col = 'black',
    description = 'Manhattan plot created using BoutrosLab.plotting.general',
    resolution = 200
    );


# Background shading
create.manhattanplot(
    # filename = tempfile(pattern = 'Manhattan_BG', fileext = '.tiff'),
    formula = -log10(pval) ~ ind,
    data = microarray,
    main = 'Bg rectangles',
    xlab.label = expression('Chromosomes'),
    ylab.label = expression('P'['adjusted']),
    xat = chr.tck,
    xaxis.lab = c(1:22, 'X', 'Y'),
    xaxis.tck = 0,
    xaxis.cex = 1,
    yaxis.cex = 1,
    yat = seq(0,5,1),
    yaxis.lab = c(
        1,
        expression(10^-1),
        expression(10^-2),
        expression(10^-3),
        expression(10^-4)
        ),
    col = chr.colours,
    pch = 18,
    cex = 0.75,
    abline.h = 2,
    abline.lty = 2,
    abline.lwd = 1,
    abline.col = 'black',
    # Adding rectangles
    add.rectangle = TRUE,
    xleft.rectangle = chr.break[seq(1, length(chr.break) - 1, 2)],
    ybottom.rectangle = 0,
    xright.rectangle = chr.break[seq(2, length(chr.break) - 1, 2)],
    ytop.rectangle = 4.5,
    col.rectangle = 'grey',
    alpha.rectangle = 0.5,
    description = 'Manhattan plot created using BoutrosLab.plotting.general',
    resolution = 200
    );
#> Warning: longer object length is not a multiple of shorter object length
#> Warning: longer object length is not a multiple of shorter object length


# Nature style
create.manhattanplot(
    # filename = tempfile(pattern = 'Manhattan_Nature_style', fileext = '.tiff'),
    formula = -log10(pval) ~ ind,
    data = microarray,
    main = 'Nature style',
    xat = chr.tck,
    xaxis.lab = c(1:22, 'X', 'Y'),
    xaxis.tck = 0,
    xaxis.cex = 1,
    yaxis.cex = 1,
    yat = seq(0,5,1),
    yaxis.lab = c(
        1,
        expression(10^-1),
        expression(10^-2),
        expression(10^-3),
        expression(10^-4)
        ),
    col = chr.colours,
    pch = 18,
    cex = 0.75,
    abline.h = 2,
    abline.lty = 2,
    abline.lwd = 1,
    abline.col = 'black',
    # Adding rectangles
    add.rectangle = TRUE,
    xleft.rectangle = chr.break[seq(1, length(chr.break) - 1, 2)],
    ybottom.rectangle = 0,
    xright.rectangle = chr.break[seq(2, length(chr.break) - 1, 2)],
    ytop.rectangle = 4.5,
    col.rectangle = 'grey',
    alpha.rectangle = 0.5,

    # 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 = 'Manhattan plot created using BoutrosLab.plotting.general',
    resolution = 1200
    );
#> 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.
#> Warning: longer object length is not a multiple of shorter object length
#> Warning: longer object length is not a multiple of shorter object length

# }