| create.hexbinplot {BoutrosLab.plotting.general} | R Documentation |
Make a hexagonally binned plot
Description
Takes a data.frame and writes a hexagonally binned plot
Usage
create.hexbinplot(
formula,
data,
filename = NULL,
main = NULL,
main.just = 'center',
main.x = 0.5,
main.y = 0.5,
main.cex = 3,
aspect = 'xy',
trans = NULL,
inv = NULL,
colour.scheme = NULL,
colourkey = TRUE,
colourcut = seq(0, 1, length = 11),
mincnt = 1,
maxcnt = NULL,
xbins = 30,
legend.title = NULL,
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.cex = 1.5,
yaxis.cex = 1.5,
xaxis.rot = 0,
yaxis.rot = 0,
xaxis.col = 'black',
yaxis.col = 'black',
xaxis.tck = 1,
yaxis.tck = 1,
xaxis.fontface = 'bold',
yaxis.fontface = 'bold',
layout = NULL,
as.table = FALSE,
x.relation = 'same',
y.relation = 'same',
x.spacing = 0,
y.spacing = 0,
strip.col = 'white',
strip.cex = 1,
strip.fontface = 'bold',
add.grid = FALSE,
abline.h = NULL,
abline.v = NULL,
abline.lty = NULL,
abline.lwd = NULL,
abline.col = 'black',
abline.front = FALSE,
add.xyline = FALSE,
xyline.col = 'black',
xyline.lwd = 1,
xyline.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.text = FALSE,
text.labels = NULL,
text.x = NULL,
text.y = NULL,
text.col = 'black',
text.cex = 1,
text.fontface = 'bold',
add.axes = FALSE,
top.padding = 0.1,
bottom.padding = 0.7,
left.padding = 0.5,
right.padding = 0.1,
add.rectangle = FALSE,
xleft.rectangle = NULL,
ybottom.rectangle = NULL,
xright.rectangle = NULL,
ytop.rectangle = NULL,
col.rectangle = 'transparent',
alpha.rectangle = 1,
background.col = 'transparent',
key = NULL,
legend = NULL,
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
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 (default value) 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 the main plot title |
aspect |
This argument controls the physical aspect ratio of the panels, defaults to “xy” |
trans |
function specifying a transformation for the counts such as log, defaults to NULL |
inv |
the inverse transformation of trans, defaults to NULL |
colour.scheme |
colour scheme to be used, default NULL gives LinGray colour scale |
colourkey |
logical whether a legend should be drawn, defaults to TRUE |
colourcut |
Vector of values covering [0, 1] that determine hexagon colour class boundaries and hexagon legend size boundaries. Alternatively, an integer (<= maxcnt) specifying the number of equispaced colourcut values in [0,1]. |
mincnt |
Cells with fewer counts are ignored |
maxcnt |
Cells with more counts are ignored, defaults to auto-generation |
xbins |
Number of bins to use in x, defaults to 30 |
legend.title |
character/expression to use in place of default legend title or a named list with elements: lab, x, y; defaults to NULL |
xlab.label |
X-axis label |
ylab.label |
Y-axis label |
xlab.cex |
Size of x-axis label |
ylab.cex |
Size of y-axis label |
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 |
ylimits |
Two-element vector giving the y-axis limits |
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.cex |
Size of x-axis scales, defaults to 2 |
yaxis.cex |
Size of y-axis scales, defaults to 2 |
xaxis.rot |
Rotation of x-axis tick labels; defaults to 0 |
yaxis.rot |
Rotation of y-axis tick labels; defaults to 0 |
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 marks for x-axis, defaults to 1 |
yaxis.tck |
Specifies the length of the tick marks for y-axis, defaults to 1 |
xaxis.fontface |
Fontface for the x-axis scales |
yaxis.fontface |
Fontface for the y-axis scales |
layout |
A vector specifying the number of columns, rows (e.g., c(2,1). Default is NULL. |
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.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” |
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 |
strip.col |
Strip background colour, defaults to “white” |
strip.cex |
Strip title character expansion |
strip.fontface |
Strip title fontface, defaults to bold |
add.grid |
Allows grid lines to be turned on or off |
abline.h |
Specify the superimposed horizontal line(s) |
abline.v |
Specify the superimposed vertical line(s) |
abline.lty |
Specify the superimposed line type |
abline.lwd |
Specify the superimposed line width |
abline.col |
Specify the superimposed line colour (defaults to black) |
abline.front |
If an abline and/or a grid has been added, this controls whether they are drawn in front of the hexbins |
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) |
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.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 |
add.axes |
Allow axis lines to be turned on or off |
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 |
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 |
background.col |
Specifies the colour for the background of the plot |
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. |
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 |
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 |
Details
WARNING: this function uses highly unusual semantics, different from the rest of the BoutrosLab.plotting.general library. The underlying hexbinplot function uses an argument called maxcnt to specify the maximum number of counts per cell. The default behaviour is not sensibly encoded via a NULL or an NA, but instead by using the missing function. As a result, we need to use do.call semantics to handle this function. This can mess up anything using substitute including things that generate p-values!
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
If 'maxcnt' is passed, make sure it is not smaller than the actual maximum count (value depends on nbins). Otherwise, some data may be lost. If you aren't sure what the actual max count is, run this function without specifying the 'maxcnt' parameter using the desired number of bins.
Author(s)
Maud HW Starmans
See Also
xyplot, lattice or the Lattice book for an overview of the package.
Examples
set.seed(12345);
simple.data <- data.frame(
x = rnorm(10000),
y = rnorm(10000)
);
create.hexbinplot(
# filename = tempfile(pattern = 'Hexbinplot_Simple', fileext = '.tiff'),
formula = y ~ x,
data = simple.data,
main = 'Simple',
description = 'Hexbinplot created by BoutrosLab.plotting.general',
resolution = 50
);
create.hexbinplot(
# filename = tempfile(pattern = 'Hexbinplot_Simple_underlined_legend_title', fileext = '.tiff'),
formula = y ~ x,
data = simple.data,
legend.title = list(lab = expression(bold(underline('Counts'))), x = 1, y = 1.1),
right.padding = 4,
description = 'Hexbinplot created by BoutrosLab.plotting.general',
resolution = 50
);
# Set up data
hexbin.data <- data.frame(
x = microarray[,1],
y = microarray[,2]
);
# Minimal Input
create.hexbinplot(
# filename = tempfile(pattern = 'Hexbinplot_Minimal_Input', fileext = '.tiff'),
formula = y ~ x,
data = hexbin.data,
main = 'Minimal input',
# formatting bins
colourcut = seq(0, 1, length = 11),
# this sets the maximum value plotted -- values greater than this will not appear
maxcnt = 50,
description = 'Hexbinplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Axes & Labels
create.hexbinplot(
# filename = tempfile(pattern = 'Hexbinplot_Axes_Labels', fileext = '.tiff'),
formula = y ~ x,
data = hexbin.data,
main = 'Axes & labels',
colourcut = seq(0, 1, length = 11),
maxcnt = 50,
# Customize Axes and labels
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xlab.label = 'Sample 1',
ylab.label = 'Sample 2',
xlimits = c(0,16),
ylimits = c(0,16),
xat = seq(0,16,2),
yat = seq(0,16,2),
description = 'Hexbinplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Log Scaled Axis
log.data <- data.frame(
x = microarray[,1],
y = 10 ** microarray[,2]
);
create.hexbinplot(
formula = y ~ x,
data = log.data,
main = 'Log Scaled',
# Log base 10 scale y-axis
yat = 'auto.log',
description = 'Hexbinplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Aspect Ratio
create.hexbinplot(
# filename = tempfile(pattern = 'Hexbinplot_Aspect_Ratio', fileext = '.tiff'),
formula = y ~ x,
data = hexbin.data,
main = 'Aspect ratio',
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xlab.label = 'Sample 1',
ylab.label = 'Sample 2',
xlimits = c(0,16),
ylimits = c(0,16),
xat = seq(0,16,2),
yat = seq(0,16,2),
colourcut = seq(0, 1, length = 11),
maxcnt = 50,
# Set the aspect ratio to control plot dimensions
aspect = 2,
description = 'Hexbinplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Colour scheme
create.hexbinplot(
# filename = tempfile(pattern = 'Hexbinplot_Colour_Change', fileext = '.tiff'),
formula = y ~ x,
data = hexbin.data,
main = 'Colour change',
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xlab.label = 'Sample 1',
ylab.label = 'Sample 2',
xlimits = c(0,16),
ylimits = c(0,16),
xat = seq(0,16,2),
yat = seq(0,16,2),
aspect = 1,
colourcut = seq(0, 1, length = 11),
maxcnt = 50,
# Specify colour scheme
colour.scheme = colorRampPalette(c('dodgerblue','paleturquoise','chartreuse','yellow',
'orange','red')),
description = 'Hexbinplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Bin sizes
create.hexbinplot(
# filename = tempfile(pattern = 'Hexbinplot_Bin_Sizes', fileext = '.tiff'),
formula = y ~ x,
data = hexbin.data,
main = 'Bin sizes',
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xlab.label = 'Sample 1',
ylab.label = 'Sample 2',
xlimits = c(0,16),
ylimits = c(0,16),
xat = seq(0,16,2),
yat = seq(0,16,2),
aspect = 1,
colour.scheme = colorRampPalette(c('dodgerblue','paleturquoise','chartreuse', 'yellow',
'orange','red')),
# Specify bin sizes
colourcut = seq(0,1,length = 6),
description = 'Hexbinplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Correlation Key
create.hexbinplot(
# filename = tempfile(pattern = 'Hexbinplot_Correlation', fileext = '.tiff'),
formula = y ~ x,
data = hexbin.data,
main = 'Correlation',
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xlab.label = 'Sample 1',
ylab.label = 'Sample 2',
xlimits = c(0,16),
ylimits = c(0,16),
xat = seq(0,16,2),
yat = seq(0,16,2),
aspect = 1,
colourcut = seq(0, 1, length = 11),
maxcnt = 50,
# Correlation Key
legend = list(
inside = list(
fun = draw.key,
args = list(
key = get.corr.key(
x = hexbin.data$x,
y = hexbin.data$y,
label.items = c('beta1', 'spearman'),
alpha.background = 0
)
),
x = 0.05,
y = 0.95,
corner = c(0,1),
draw = FALSE
)
),
description = 'Hexbinplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Grid lines and diagonal
create.hexbinplot(
# filename = tempfile(pattern = 'Hexbinplot_Gridlines', fileext = '.tiff'),
formula = y ~ x,
data = hexbin.data,
main = 'Gridlines',
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xlab.label = 'Sample 1',
ylab.label = 'Sample 2',
xlimits = c(0,16),
ylimits = c(0,16),
xat = seq(0,16,2),
yat = seq(0,16,2),
aspect = 1,
colourcut = seq(0, 1, length = 11),
maxcnt = 50,
# Grid & diagonal
add.grid = TRUE,
add.xyline = TRUE,
description = 'Hexbinplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Large range
# Generate some fake data with both very low and very high values
set.seed(12345);
x <- c(rnorm(100000,0,0.1),rnorm(1000,0,0.5),rnorm(1000,0,sd=0.75));
y <- c(rnorm(100000,0,0.1),rnorm(1000,0,0.5),rnorm(1000,0,sd=0.75));
fake.data <- data.frame(
x = x,
y = y,
z = y + x*(x+1)/4
);
create.hexbinplot(
# filename = tempfile(pattern = 'Hexbinplot_Range', fileext = '.tiff'),
formula = z ~ x,
data = fake.data,
main = 'Range',
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xlab.label = 'Sample 1',
ylab.label = 'Sample 2',
aspect = 1,
# Use colourcut to divide the bins appropriately
colourcut = c(0,0.0002,0.0004,0.0008,0.0016,0.0032,0.0064,0.0128,0.0256,0.0512,0.1024,0.2048,
0.4096,0.8192,1),
# Change the colour scheme
colour.scheme = function(n){BTC(n, beg=1, end=256)},
background.col = 'grey',
description = 'Hexbinplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Outliers
# Generate data with upper bound outlier
set.seed(12345);
x <- c(rnorm(1000,0,0),rnorm(4000,0,0.5));
y <- c(rnorm(1000,0,0),rnorm(4000,0,0.5));
fake.data.outlier <- data.frame(
x = x,
y = y,
z = y + x*(x+1)/4
);
create.hexbinplot(
# filename = tempfile(pattern = 'Hexbinplot_Outlier', fileext = '.tiff'),
formula = z ~ x,
data = fake.data.outlier,
main = 'Outlier',
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xlab.label = 'Sample 1',
ylab.label = 'Sample 2',
aspect = 1,
# Use colourcut to divide the bins appropriately
colourcut = c(seq(0,0.01, length = 4),seq(0.0125,0.1,length=4), seq(0.125,1,length=4)),
xbins = 15,
mincnt = 0,
# Change the colour scheme
colour.scheme = function(n){BTC(n, beg=1, end=256)},
background.col = 'grey',
description = 'Hexbinplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Nature style
create.hexbinplot(
# filename = tempfile(pattern = 'Hexbinplot_Nature_style', fileext = '.tiff'),
formula = y ~ x,
data = hexbin.data,
main = 'Nature style',
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xlimits = c(0,16),
ylimits = c(0,16),
xat = seq(0,16,2),
yat = seq(0,16,2),
aspect = 1,
colourcut = seq(0, 1, length = 11),
maxcnt = 50,
# Grid & diagonal
add.grid = TRUE,
add.xyline = TRUE,
# 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 = 'Hexbinplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Multiplot different groups
set.seed(73);
# Randomly generate groups
simple.data$groups <- sample(1:2, 10000, replace = TRUE);
simple.data$group.labels <- as.factor(simple.data$groups);
create.hexbinplot(
formula = y ~ x | groups,
# filename = tempfile(
# pattern = 'stratified_hexbinplot_numeric_conditioning',
# fileext = '.tiff'
# ),
data = simple.data,
description = 'Hexbinplot created by BoutrosLab.plotting.general',
strip.col = 'white',
strip.cex = 0.8,
strip.fontface = 'bold',
resolution = 200
);
create.hexbinplot(
formula = y ~ x | group.labels,
# filename = tempfile(
# pattern = 'stratified_hexbinplot_factor_conditioning',
# fileext = '.tiff'
# ),
data = simple.data,
description = 'Hexbinplot created by BoutrosLab.plotting.general',
strip.col = 'white',
strip.cex = 0.8,
strip.fontface = 'bold',
resolution = 200
);