| create.qqplot.fit {BoutrosLab.plotting.general} | R Documentation |
Make a quantile-quantile plot of a sample
Description
Takes a sample and creates a qq plot against a theoretical distribution, possibly conditioned on other variables.
Usage
create.qqplot.fit(
x,
data = NA,
filename = NULL,
groups = NULL,
confidence.bands = FALSE,
conf = 0.95,
confidence.method = 'both',
reference.line.method = 'quartiles',
distribution = qnorm,
aspect = 'fill',
prepanel = NULL,
main = NULL,
main.just = 'center',
main.x = 0.5,
main.y = 0.5,
main.cex = 3,
xlab.label = NULL,
ylab.label = NULL,
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.col = 'black',
yaxis.col = 'black',
xaxis.fontface = 'bold',
yaxis.fontface = 'bold',
xaxis.log = FALSE,
yaxis.log = FALSE,
xaxis.rot = 0,
yaxis.rot = 0,
xaxis.tck = 1,
yaxis.tck = 1,
add.grid = FALSE,
xgrid.at = xat,
ygrid.at = yat,
type = 'p',
cex = 0.75,
pch = 19,
col = 'black',
col.line = 'grey',
lwd = 2,
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 numeric vector |
data |
An optional data source if x is a formula |
filename |
Filename for tiff output, or if NULL returns the trellis object itself |
groups |
The grouping variable in the data-frame |
confidence.bands |
Add confidence bands or not, default to FALSE. Note that in this function, the confidence band can only be added to a single plot, not for multi-qq plot. |
conf |
Confidence level, default to 0.95 |
confidence.method |
Methods used to draw confidence bands: “simultaneous”, “pointwise”, “both”, defaults to “both”. |
reference.line.method |
Methods used to draw reference line and must be one of “quartiles”(default), “diagonal”, “robust”. “quartiles” will draw a line across 1/4 and 3/4 quantiles, “diagonal” will draw a 0-1 line, “robust” will draw a best fit line basing on linear model. Note: for multi-panel plot, only the default one is applicable. |
distribution |
A quantile function that takes a vector of probabilities as argument and produces the corresponding quantiles from a theoretical distribution, defaults to “qnorm”, that is normal distribution. |
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” |
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 |
main.cex |
Size of the overall plot title, defaults to 3 |
xlab.label |
x-axis title |
ylab.label |
y-axis title |
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 |
xaxis.lab |
Vector listing x-axis tick labels, defaults to automatic |
yaxis.lab |
Vector listing y-axis tick labels, defaults to automatic |
xaxis.cex |
Size of x-axis scales, defaults to 1.5 |
yaxis.cex |
Size of y-axis scales, defaults to 1.5 |
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.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 |
add.grid |
Default manner of drawing grid lines |
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 |
type |
Plot type |
cex |
Character expansion for plotting symbol |
pch |
Plotting character |
col |
Point colour |
col.line |
QQ line colour, defaults to grey |
lwd |
Specifies line width, defaults to 2 |
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. |
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 the rectangle's area |
alpha.rectangle |
Specifies the colour bias of the rectangle to be drawn |
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. |
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.
Warning
Note that the confidence band only works for a single panel qq plot, not for grouped data and multi-qq plot. Why? What's missing?
Author(s)
Ying Wu
See Also
qqmath, lattice or the Lattice book for an overview of the package.
Examples
set.seed(12345);
create.qqplot.fit(
# filename = tempfile(pattern = 'QQfit_Simple', fileext = '.tiff'),
x = rnorm(300),
# choosing to compare against a uniform distribution
distribution = qunif,
resolution = 100
);
# Minimal Input
create.qqplot.fit(
# filename = tempfile(pattern = 'QQfit_Minimal_Input', fileext = '.tiff'),
x = microarray[1:500,1],
# choosing to compare against a uniform distribution
distribution = qunif,
main = 'Minimal input',
description = 'QQplot fit created by BoutrosLab.plotting.general',
resolution = 100
);
# Axes and Labels
create.qqplot.fit(
# filename = tempfile(pattern = 'QQfit_Axes_Labels', fileext = '.tiff'),
x = microarray[1:500,1],
distribution = qunif,
main = 'Axes & labels',
# Adding axes labels
xlab.label = 'qunif',
ylab.label = 'sample values',
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
xaxis.cex = 1,
yaxis.cex = 1,
add.grid = TRUE,
description = 'QQplot fit created by BoutrosLab.plotting.general',
resolution = 100
);
# Confidence bands
create.qqplot.fit(
# filename = tempfile(pattern = 'QQfit_Confidence_Bands', fileext = '.tiff'),
x = microarray[1:500,1],
distribution = qunif,
main = 'Confidence bands',
xlab.label = 'qunif',
ylab.label = 'sample values',
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
xaxis.cex = 1,
yaxis.cex = 1,
add.grid = TRUE,
# Adding confidence bands (auto-generates legend)
confidence.bands = TRUE,
confidence.method = 'both',
description = 'QQplot fit created by BoutrosLab.plotting.general',
resolution = 100
);
# Multiple qq plot conditioned on a variable
# 'Formula' format of data
chr.locations <- microarray$Chr[1:500];
chr.locations <- replace(chr.locations, which(chr.locations == 1), 'Chromosome 1');
chr.locations <- replace(chr.locations, which(chr.locations == 2), 'Chromosome 2');
qqplot.data <- data.frame(
value = microarray[1:500,1],
chr = chr.locations
);
create.qqplot.fit(
# filename = tempfile(pattern = 'QQfit_Multiple', fileext = '.tiff'),
x = ~ value | chr,
data = qqplot.data,
distribution = qunif,
main = 'Multiple plots',
xlab.label = 'qunif',
ylab.label = 'sample values',
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
xaxis.cex = 1,
yaxis.cex = 1,
add.grid = TRUE,
confidence.bands = TRUE,
confidence.method = 'simultaneous',
description = 'QQplot fit created by BoutrosLab.plotting.general',
resolution = 100
);
# Grouped qq plot
create.qqplot.fit(
# filename = tempfile(pattern = 'QQfit_Grouped', fileext = '.tiff'),
x = ~ value,
data = qqplot.data,
# Adding groups
groups = qqplot.data$chr,
# Colouring groups
col = default.colours(2),
# Setting different plotting characters
pch = c(15, 19),
distribution = qunif,
main = 'Grouped & legend',
xlab.label = 'qunif',
ylab.label = 'sample values',
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
xaxis.cex = 1,
yaxis.cex = 1,
add.grid = TRUE,
confidence.bands = TRUE,
confidence.method = 'simultaneous',
# Adding legend for groups
key = list(
text = list(
lab = c('1','2'),
cex = 1,
col = 'black'
),
points = list(
pch = c(15, 19),
col = default.colours(2),
cex = 1
),
x = 0.04,
y = 0.95,
padding.text = 2
),
description = 'QQplot fit created by BoutrosLab.plotting.general',
resolution = 100
);
# Correlation Key
create.qqplot.fit(
# filename = tempfile(pattern = 'QQfit_Correlation_Key', fileext = '.tiff'),
x = ~ value,
data = qqplot.data,
groups = qqplot.data$chr,
col = default.colours(2),
pch = c(15, 19),
distribution = qunif,
main = 'Correlation key',
xlab.label = 'qunif',
ylab.label = 'sample values',
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
xaxis.cex = 1,
yaxis.cex = 1,
add.grid = TRUE,
confidence.bands = TRUE,
confidence.method = 'simultaneous',
# Adjusting legend to contain multiple keys
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
text = list(
lab = c('1','2'),
cex = 1,
col = 'black'
),
points = list(
pch = c(15, 19),
col = default.colours(2),
cex = 1
),
x = 0.14,
y = 0.80,
padding.text = 2
)
)
),
inside = list(
fun = draw.key,
args = list(
key = get.corr.key(
x = runif(500),
y = qqplot.data$value,
label.items = c('spearman', 'kendall','beta1'),
alpha.background = 0,
key.cex = 1
)
),
x = 0.75,
y = 0.20,
corner = c(0,1)
)
),
description = 'QQplot fit created by BoutrosLab.plotting.general',
resolution = 100
);
# Nature style
create.qqplot.fit(
# filename = tempfile(pattern = 'QQfit_Nature_style', fileext = '.tiff'),
x = microarray[1:500,1],
distribution = qunif,
main = 'Nature style',
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
xaxis.cex = 1,
yaxis.cex = 1,
add.grid = TRUE,
confidence.bands = TRUE,
confidence.method = 'both',
# 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 fit created by BoutrosLab.plotting.general',
resolution = 1200
);