| create.barplot {BoutrosLab.plotting.general} | R Documentation |
Make a barplot
Description
Takes a data.frame and creates a barplot
Usage
create.barplot(
formula,
data,
groups = NULL,
stack = FALSE,
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,
abline.h = NULL,
abline.v = NULL,
abline.lty = 1,
abline.lwd = NULL,
abline.col = 'black',
axes.lwd = 1,
add.grid = FALSE,
xgrid.at = xat,
ygrid.at = yat,
grid.lwd = 5,
grid.col = NULL,
xaxis.lab = TRUE,
yaxis.lab = TRUE,
xaxis.col = 'black',
yaxis.col = 'black',
xaxis.fontface = 'bold',
yaxis.fontface = 'bold',
xaxis.cex = 1.5,
yaxis.cex = 1.5,
xaxis.rot = 0,
yaxis.rot = 0,
xaxis.tck = 1,
yaxis.tck = 1,
xlimits = NULL,
ylimits = NULL,
xat = TRUE,
yat = TRUE,
layout = NULL,
as.table = FALSE,
x.spacing = 0,
y.spacing = 0,
x.relation = 'same',
y.relation = 'same',
top.padding = 0.5,
bottom.padding = 1,
right.padding = 1,
left.padding = 1,
key.bottom = 0.1,
ylab.axis.padding = 0.5,
xlab.axis.padding = 0.5,
col = 'black',
border.col = 'black',
border.lwd = 1,
plot.horizontal = FALSE,
background.col = 'transparent',
origin = 0,
reference = TRUE,
box.ratio = 2,
sample.order = 'none',
group.labels = FALSE,
key = list(text = list(lab = c(''))),
legend = NULL,
add.text = FALSE,
text.labels = NULL,
text.x = NULL,
text.y = NULL,
text.col = 'black',
text.cex = 1,
text.fontface = 'bold',
strip.col = 'white',
strip.cex = 1,
y.error.up = NULL,
y.error.down = y.error.up,
y.error.bar.col = 'black',
error.whisker.width = width/(nrow(data)*4),
error.bar.lwd = 1,
error.whisker.angle = 90,
add.rectangle = FALSE,
xleft.rectangle = NULL,
ybottom.rectangle = NULL,
xright.rectangle = NULL,
ytop.rectangle = NULL,
col.rectangle = 'grey85',
alpha.rectangle = 1,
line.func = NULL,
line.from = 0,
line.to = 0,
line.col = 'transparent',
line.infront = TRUE,
text.above.bars = list(labels = NULL,
padding = NULL,
bar.locations = NULL,
rotation = 0
),
raster = NULL,
raster.vert = TRUE,
raster.just = 'center',
raster.width.dim = unit(2/37, 'npc'),
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,
disable.factor.sorting = 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 |
groups |
Optional grouping variable. Expression or variable. |
stack |
Logical, relevant when groups is non-null. If FALSE (the default), bars for different values of the grouping variable are drawn side by side, otherwise they are stacked |
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, defaults to 3 |
xlab.label |
The label for the x-axis |
ylab.label |
The label for the y-axis |
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 |
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) |
axes.lwd |
Specify line width of the axes; set to 0 to turn off axes |
add.grid |
Specify whether to draw grid or not (defaults to FALSE) |
xgrid.at |
Specify where to draw x-axis grid lines (defaults to xat) |
ygrid.at |
Specify where to draw y-axis grid lines (defaults to yat) |
grid.lwd |
Specify width of grid line (defaults to 5) |
grid.col |
Specify colour of grid line. Currently only supports one colour. Defaults to NULL, which uses the colour of the reference line. |
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.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.cex |
Size of x-axis tick labels, defaults to 1.2 |
yaxis.cex |
Size of y-axis tick labels, defaults to 1.5 |
xaxis.rot |
Rotation of x-axis tick labels; defaults to 0 |
yaxis.rot |
Rotation of y-axis tick labels; 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 |
xlimits |
Two-element vector giving the x-axis limits. Useful when plot.horizontal = TRUE |
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()'. Useful when plot.horizontal = TRUE |
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()'. |
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 0.5 |
bottom.padding |
A number specifying the distance to the bottom margin, defaults to 2 |
right.padding |
A number specifying the distance to the right margin, defaults to 1 |
left.padding |
A number specifying the distance to the left margin, defaults to 1 |
key.bottom |
A number specifying how much space should be left for the key at the bottom, defaults to 0.1 |
ylab.axis.padding |
A number specifying the distance of y-axis label to the y-axis, defaults to 0 |
,
xlab.axis.padding |
A number specifying the distance of x-axis label to the x-axis, defaults to 0.5. Named differently than ylab.axis.padding because these are lattice's internal names for these values |
col |
Filling colour of bars, defaults to black, does a grey-scale spectrum if !is.null(groups) |
border.col |
Specify border colour (defaults to black) |
border.lwd |
Specify border width (defaults to 1) |
plot.horizontal |
Plot the bars horizontally |
background.col |
Plot background colour, defaults to transparent |
origin |
The origin of the plot, generally 0 |
reference |
Should the reference line be printed at the origin |
box.ratio |
Specifies the width of each bar, defaults to 2 |
sample.order |
Should the bars be reordered, accepts values “increasing”, “decreasing” or a vector of sample names. Labels will also be reordered |
group.labels |
Should the labels be grouped to the same amount of bars per column |
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.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 |
strip.col |
Strip background colour, defaults to white |
strip.cex |
Strip title character expansion |
y.error.up |
A vector specifying the length of the error bar going up from each point. If set to NULL (the default), error bars will not be drawn |
y.error.down |
A vector specifying the length of the error bar going down from each point. By default, it is set to y.error.up |
y.error.bar.col |
A string or vector of strings specifying the colour of the error bars. Defaults to black |
error.whisker.width |
A number specifying the width of the error bars. Defaults to a rough approximation based on the size of the data |
error.bar.lwd |
The line width of the error bars. Defaults to 1 |
error.whisker.angle |
The angle of the error bar whiskers, defaults to 90. Can be changed to produce arrow-like bars |
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 |
line.func |
Function for the line that should be drawn on top of plot |
line.from |
The starting point of the line on the plot |
line.to |
The ending point of the line on the plot |
line.col |
Colour of the line on the plot |
line.infront |
Should the line appear in front of the plot or not |
text.above.bars |
Should some form of text appear above the bars; input as a list. |
raster |
The image to raster over each bar - see Raster Images in R Graphics by Paul Murrell for full details |
raster.vert |
A logical indicating whether the raster is applied vertically or horizontally |
raster.just |
A word giving the justification of the raster, can be set to “left”, “right”, “centre”, “center”, “bottom”, or “top” |
raster.width.dim |
A unit object giving the width of the raster bar |
height |
Figure height, defaults to 6 in |
width |
Figure width, defaults to 6 in |
size.units |
Figure units, defaults to inches |
resolution |
Figure resolution, defaults to 1600 |
enable.warnings |
Print warnings if set to TRUE, defaults to FALSE |
description |
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 |
disable.factor.sorting |
Disable barplot auto sorting factors alphabetically/numerically |
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
Author(s)
Mehrdad Shamsi
See Also
barchart, lattice or the Lattice book for an overview of the package.
Examples
set.seed(12345);
simple.data <- data.frame(
x = sample(1:15, 5),
y = LETTERS[1:5]
);
# Simple example
create.barplot(
# filename = tempfile(pattern = 'Barplot_Simple', fileext = '.tiff'),
formula = x ~ y,
data = simple.data,
yat = seq(0,16,2),
resolution = 30
);
# set up the data
total.counts <- apply(SNV[1:15], 2, function(x){ mutation.count <- (30 - sum(is.na(x)))});
count.nonsyn <- function(x){
mutation.count <- length(which(x == 1));
}
nonsynonymous.SNV <- apply(SNV[1:15], 2, count.nonsyn);
other.mutations <- total.counts - nonsynonymous.SNV;
# subset the first fifteen samples
barplot.data <- data.frame(
samples = rep(1:15, 2),
mutation = c(rep('nonsynonymous', 15), rep('other',15)),
type = c(rep(1, 15), rep(2,15)),
values = c(nonsynonymous.SNV, other.mutations),
sex = rep(patient$sex[1:15], 2),
stage = rep(patient$stage[1:15], 2),
msi = rep(patient$msi[1:15], 2)
);
# Minimal input
create.barplot(
# filename = tempfile(pattern = 'Barplot_Minimal_Input', fileext = '.tiff'),
formula = values ~ samples ,
data = barplot.data[barplot.data$mutation == 'nonsynonymous',],
main = 'Minimal input',
# Editing the metadata
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Axes labels & limits
create.barplot(
# filename = tempfile(pattern = 'Barplot_Custom_Axes', fileext = '.tiff'),
formula = values ~ samples,
data = barplot.data[barplot.data$mutation == 'nonsynonymous',],
main = 'Axes labels & limits',
# Setting axes labels
xlab.lab = 'Sample',
ylab.lab = 'Nonsynonymous SNVs',
# Setting y-axis limits and tick-mark locations
ylimits = c(0,30),
yat = seq(0,30,5),
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Font size and font face
create.barplot(
# filename = tempfile(pattern = 'Barplot_Font_Changes', fileext = '.tiff'),
formula = values ~ samples,
data = barplot.data[barplot.data$mutation == 'nonsynonymous',],
main = 'Font changes',
xlab.lab = 'Samples',
ylab.lab = 'Nonsynonymous SNVs',
ylimits = c(0,30),
yat = seq(0,30,5),
# Changing font sizes
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
# Changing font type
xaxis.fontface = 1,
yaxis.fontface = 1,
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Sorting data
create.barplot(
# filename = tempfile(pattern = 'Barplot_Sorted', fileext = '.tiff'),
formula = values ~ samples,
data = barplot.data[barplot.data$mutation == 'nonsynonymous',],
main = 'Sorted bars',
xlab.lab = 'Samples',
ylab.lab = 'Nonsynonymous SNVs',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
# Order bars either by 'increasing' or 'decreasing'
sample.order = 'decreasing',
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Sorting data with horizontal barplot
create.barplot(
formula = samples ~ values,
data = barplot.data[barplot.data$mutation == 'nonsynonymous',],
main = 'Sorted bars',
xlab.lab = 'Samples',
ylab.lab = 'Nonsynonymous SNVs',
xlimits = c(0,30),
xat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
# Order bars either by 'increasing' or 'decreasing'
sample.order = 'decreasing',
plot.horizontal = TRUE,
resolution = 100
)
# Log-Scaled Axis
log.data <- data.frame(
x = 10 ** sample(1:15, 5),
y = LETTERS[1:5]
);
create.barplot(
formula = x ~ y,
data = log.data,
# Log base 10 scale y-axis
yat = 'auto.log',
main = 'Log Scaled',
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Colour changes
sex.colours <- replace(as.vector(barplot.data$sex), which(barplot.data$sex == 'male'),'dodgerblue');
sex.colours <- replace(sex.colours, which(barplot.data$sex == 'female'), 'pink');
create.barplot(
# filename = tempfile(pattern = 'Barplot_Colour_Changes', fileext = '.tiff'),
formula = values ~ samples,
data = barplot.data[barplot.data$mutation == 'nonsynonymous',],
main = 'Colour changes',
xlab.lab = 'Samples',
ylab.lab = 'Nonsynonymous SNVs',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
# Colour bars based on sex
col = sex.colours,
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Legend
create.barplot(
# filename = tempfile(pattern = 'Barplot_Legend', fileext = '.tiff'),
formula = values ~ samples,
data = barplot.data[barplot.data$mutation == 'nonsynonymous',],
main = 'Legend',
xlab.lab = 'Samples',
ylab.lab = 'Nonsynonymous SNVs',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
col = sex.colours,
# Adding legend to explain bar colour-coding
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
points = list(
col = 'black',
pch = 22,
cex = 3,
fill = c('dodgerblue', 'pink')
),
text = list(
lab = c('Male','Female')
),
padding.text = 5,
cex = 1
)
),
# Positioning legend on plot
x = 0.75,
y = 0.95
)
),
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Grouped barplot
create.barplot(
# filename = tempfile(pattern = 'Barplot_Grouped', fileext = '.tiff'),
formula = values ~ samples,
data = barplot.data,
main = 'Grouped bar chart',
xlab.lab = 'Samples',
ylab.lab = 'Mutations',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
# Setting groups
groups = mutation,
col = default.colours(12, is.greyscale = FALSE)[11:12],
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
points = list(
col = 'black',
pch = 22,
cex = 2,
fill = default.colours(12, is.greyscale = FALSE)[11:12]
),
text = list(
lab = c('Nonsynonymous SNV','Other SNV')
),
padding.text = 3,
cex = 1
)
),
x = 0.55,
y = 0.95
)
),
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Grouped labels
create.barplot(
# filename = tempfile(pattern = 'Barplot_Grouped_Labels', fileext = '.tiff'),
formula = values ~ samples,
data = barplot.data,
main = 'Grouped labels',
xlab.lab = 'Samples',
ylab.lab = 'Mutations',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
# Setting groups
groups = mutation,
col = default.colours(12, is.greyscale = FALSE)[11:12],
# Grouped labels
xaxis.lab = rep(c('nonsynonymous', 'other'), 15),
xaxis.rot = 90,
group.labels = TRUE,
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Stacked barplot
create.barplot(
# filename = tempfile(pattern = 'Barplot_Stacked', fileext = '.tiff'),
formula = values ~ samples,
data = barplot.data,
main = 'Stacked bar chart',
xlab.lab = 'Samples',
ylab.lab = 'Mutations',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
groups = mutation,
col = default.colours(12, is.greyscale = FALSE)[11:12],
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
points = list(
col = 'black',
pch = 22,
cex = 2,
# reverse order to match stacked bar order
fill = rev(default.colours(12, is.greyscale = FALSE)[11:12])
),
text = list(
# reverse order to match stacked bar order
lab = rev(c('Nonsynonymous SNV','Other SNV'))
),
padding.text = 3,
cex = 1
)
),
x = 0.55,
y = 0.95
)
),
# Changing the plot from a grouped plot to a stacked plot
stack = TRUE,
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Panel organization
create.barplot(
# filename = tempfile(pattern = 'Barplot_Panel_Layout_numeric_conditioning', fileext = '.tiff'),
# Setting the panel layout
formula = values ~ samples | type,
data = barplot.data,
main = 'Panel layout',
xlab.lab = 'Samples',
ylab.lab = 'Mutations',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 200
);
create.barplot(
# Setting the panel layout
formula = values ~ samples | mutation,
data = barplot.data,
main = 'Panel layout',
xlab.lab = 'Samples',
ylab.lab = 'Mutations',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Panel organization 2
create.barplot(
# filename = tempfile(pattern = 'Barplot_Panel_Layout_2', fileext = '.tiff'),
formula = values ~ samples | mutation,
data = barplot.data,
main = 'Panel layout',
xlab.lab = 'Samples',
ylab.lab = 'Mutations',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
# Adjusting the panel layout
layout = c(1,2),
y.spacing = 1,
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Covariates
# Note: Covariates can also be created using the create.multiplot function
# set covariate colour schemes
covariate.colours.sex <- as.character(barplot.data$sex);
covariate.colours.sex[covariate.colours.sex == 'male'] <- 'dodgerblue';
covariate.colours.sex[covariate.colours.sex == 'female'] <- 'pink';
covariate.colours.stage <- as.character(barplot.data$stage);
covariate.colours.stage[covariate.colours.stage == 'I'] <- 'plum1';
covariate.colours.stage[covariate.colours.stage == 'II'] <- 'orchid1';
covariate.colours.stage[covariate.colours.stage == 'III'] <- 'orchid3';
covariate.colours.stage[covariate.colours.stage == 'IV'] <- 'orchid4';
covariate.colours.msi <- as.character(barplot.data$msi);
covariate.colours.msi[covariate.colours.msi == 'MSS'] <- 'chartreuse4';
covariate.colours.msi[covariate.colours.msi == 'MSI-High'] <- 'chartreuse2';
# create object to draw covariates
covariates.object <- list(
rect = list(
col = 'white',
fill = covariate.colours.sex,
lwd = 1.5
),
rect = list(
col = 'white',
fill = covariate.colours.stage,
lwd = 1.5
),
rect = list(
col = 'white',
fill = covariate.colours.msi,
lwd = 1.5
)
);
# see BoutrosLab.plotting.general::covariates.grob() for more information
covariate.object.grob <- covariates.grob(
covariates = covariates.object,
ord = c(1:15),
side = 'top',
size = 0.8
);
# Create legend to explain covariates
covariates.legends <- list(
legend = list(
colours = c('dodgerblue','pink'),
labels = c('male','female'),
title = 'Sex',
border = 'white'
),
legend = list(
colours = c('plum1', 'orchid1', 'orchid3', 'orchid4'),
labels = c('I','II','III','IV'),
title = 'Stage',
border = 'white'
),
legend = list(
colours = c('chartreuse4','chartreuse2'),
labels = c('MSS','MSI-High'),
title = 'MSI',
border = 'white'
)
);
# see BoutrosLab.plotting.general::legend.grob() for more information
covariate.legend.grob <- legend.grob(
legends = covariates.legends,
title.just = 'left'
);
create.barplot(
# filename = tempfile(pattern = 'Barplot_Covariates', fileext = '.tiff'),
formula = values ~ samples,
data = barplot.data[barplot.data$mutation == 'nonsynonymous',],
main = 'Covariates',
ylab.lab = 'Mutations',
ylimits = c(0,30),
yat = seq(0,30,5),
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
yaxis.fontface = 1,
# removing x-axis formatting to give space to covariates
xaxis.tck = 0,
xaxis.lab = rep('',15),
xaxis.cex = 0,
# covariates
legend = list(
bottom = list(fun = covariate.object.grob),
right = list(fun = covariate.legend.grob)
),
key = list(
x = 1,
y = -0.028,
text = list(
lab = c('Sex','Stage','MSI')
),
padding.text = 1
),
bottom.padding = 4,
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 200
);
create.barplot(
# filename = tempfile(pattern = 'Barplot_Auto_legend', fileext = '.tiff'),
formula = values ~ samples,
data = barplot.data[barplot.data$mutation == 'nonsynonymous',],
main = 'Covariates',
ylab.lab = 'Mutations',
ylimits = c(0,30),
yat = seq(0,30,5),
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
yaxis.fontface = 1,
# removing x-axis formatting to give space to covariates
xaxis.tck = 0,
xaxis.lab = rep('',15),
xaxis.cex = 0,
# covariates
legend = list(
inside = list(fun = covariate.legend.grob)
),
bottom.padding = 4,
inside.legend.auto = TRUE,
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Horizontal orientation
create.barplot(
# filename = tempfile(pattern = 'Barplot_Horizontal', fileext = '.tiff'),
# switch formula order
formula = samples ~ values,
data = barplot.data[barplot.data$mutation == 'nonsynonymous',],
main = 'Plot horizontally',
# Adjusting the panel layout
plot.horizontal = TRUE,
# covariates
legend = list(
inside = list(fun = covariate.legend.grob)
),
inside.legend.auto = TRUE,
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Change bar thickness and add text labels
create.barplot(
# filename = tempfile(pattern = 'Barplot_Text_Labels', fileext = '.tiff'),
# switch formula order
formula = samples ~ values,
data = barplot.data[barplot.data$mutation == 'nonsynonymous',],
main = 'Text labels and thin bars',
# Adjusting the panel layout
plot.horizontal = TRUE,
box.ratio = 0.6,
add.text = TRUE,
text.x = 27.75,
text.y = 1:15,
text.labels = barplot.data[barplot.data$mutation == 'nonsynonymous','values'],
text.cex = 0.8,
text.fontface = 'italic',
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Error bars
error.data <- data.frame(
genes = rownames(microarray)[1:15],
values = apply(microarray[1:15,1:58], 1, mean),
error = apply(microarray[1:15,1:58], 1, sd)
);
create.barplot(
# filename = tempfile(pattern = 'Barplot_Error_Bars', fileext = '.tiff'),
# needs sequential x-axis
formula = values ~ 1:15,
data = error.data,
y.error.up = error.data$error,
xaxis.lab = error.data$genes,
main = 'Error bars',
xlab.lab = 'Gene',
ylab.lab = 'Change in Expression',
ylimits = c(0,14),
yat = seq(0,14,2),
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.rot = 45,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 100
);
create.barplot(
# filename = tempfile(pattern = 'Barplot_Error_Bars_Horizontal', fileext = '.tiff'),
# needs sequential x-axis
formula = values ~ 1:15,
data = error.data,
y.error.up = error.data$error,
yaxis.lab = error.data$genes,
plot.horizontal = TRUE,
main = 'Error bars',
xlab.lab = 'Gene',
ylab.lab = 'Change in Expression',
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.rot = 45,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Grid lines
create.barplot(
# filename = tempfile(pattern = 'Barplot_Gridlines', fileext = '.tiff'),
formula = values ~ samples,
data = barplot.data[barplot.data$mutation == 'nonsynonymous',],
main = 'Gridlines',
xlab.lab = 'Samples',
ylab.lab = 'Nonsynonymous SNVs',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
# Grid lines
add.grid = TRUE,
xgrid.at = seq(0,15,2),
col = sex.colours,
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
points = list(
col = 'black',
pch = 22,
cex = 3,
fill = c('dodgerblue', 'pink')
),
text = list(
lab = c('Male','Female')
),
padding.text = 5,
cex = 1
)
),
# Positioning legend on plot
x = 0.75,
y = 0.95
)
),
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Grid lines 2
create.barplot(
# filename = tempfile(pattern = 'Barplot_Gridlines_GreyBG', fileext = '.tiff'),
formula = values ~ samples,
data = barplot.data[barplot.data$mutation == 'nonsynonymous',],
main = 'Gridlines & grey background',
xlab.lab = 'Samples',
ylab.lab = 'Nonsynonymous SNVs',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
# Grid lines
background.col = 'grey85',
add.grid = TRUE,
xgrid.at = seq(0,15,2),
col = sex.colours,
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
points = list(
col = 'black',
pch = 22,
cex = 3,
fill = c('dodgerblue', 'pink')
),
text = list(
lab = c('Male','Female')
),
padding.text = 5,
cex = 1
)
),
# Positioning legend on plot
x = 0.75,
y = 0.95
)
),
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Labels
create.barplot(
# filename = tempfile(pattern = 'Barplot_Labels', fileext = '.tiff'),
formula = values ~ samples,
data = barplot.data[barplot.data$mutation == 'nonsynonymous',],
main = 'Labels',
xlab.lab = 'Samples',
ylab.lab = 'Nonsynonymous SNVs',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
# Labels
text.above.bars = list(
labels = c('*','27','15','*'),
padding = 0.75,
bar.locations = c(1, 3, 12, 14),
rotation = 0
),
col = sex.colours,
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
points = list(
col = 'black',
pch = 22,
cex = 3,
fill = c('dodgerblue', 'pink')
),
text = list(
lab = c('Male','Female')
),
padding.text = 5,
cex = 1
)
),
# Positioning legend on plot
x = 0.75,
y = 0.95
)
),
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 200
);
# lines
create.barplot(
# filename = tempfile(pattern = 'Barplot_Lines', fileext = '.tiff'),
formula = values ~ samples,
data = barplot.data[barplot.data$mutation == 'nonsynonymous',],
main = 'Lines',
xlab.lab = 'Samples',
ylab.lab = 'Nonsynonymous SNVs',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
# Lines
sample.order = 'increasing',
line.func = function(x) {0.1*x**2},
line.from = 0,
line.to = 16,
line.col = 'darkgrey',
abline.h = 10,
abline.col = 'red',
col = sex.colours,
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
points = list(
col = 'black',
pch = 22,
cex = 3,
fill = c('dodgerblue', 'pink')
),
text = list(
lab = c('Male','Female')
),
padding.text = 5,
cex = 1
)
),
# Positioning legend on plot
x = 0.75,
y = 0.95
)
),
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Background rectangle
create.barplot(
# filename = tempfile(pattern = 'Barplot_Bg_Rectangle', fileext = '.tiff'),
formula = values ~ samples,
data = barplot.data[barplot.data$mutation == 'nonsynonymous',],
main = 'Background rectangle',
xlab.lab = 'Samples',
ylab.lab = 'Nonsynonymous SNVs',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
sample.order = 'increasing',
# Background rectangle
add.rectangle = TRUE,
xleft.rectangle = seq(0.5, 14.5, 2),
ybottom.rectangle = 0,
xright.rectangle = seq(1.5, 15.5, 2),
ytop.rectangle = 30,
col.rectangle = 'lightgrey',
col = sex.colours,
legend = list(
inside = list(
fun = draw.key,
args = list(
key = list(
points = list(
col = 'black',
pch = 22,
cex = 3,
fill = c('dodgerblue', 'pink')
),
text = list(
lab = c('Male','Female')
),
padding.text = 5,
cex = 1
)
),
# Positioning legend on plot
x = 0.75,
y = 0.95
)
),
description = 'Barplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Raster
create.barplot(
# filename = tempfile(pattern = 'Barplot_with_raster', fileext = '.tiff'),
formula = values ~ samples,
data = barplot.data[barplot.data$mutation == 'nonsynonymous',],
main = 'Raster fill',
xlab.lab = 'Samples',
ylab.lab = 'Nonsynonymous SNVs',
ylimits = c(0,30),
yat = seq(0,30,5),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
# filling bars with raster
raster = 1:10/10,
raster.just = 'bottom',
description = 'Description of image here',
resolution = 200
);
# Nature format
create.barplot(
# filename = tempfile(pattern = 'Barplot_Nature_style', fileext = '.tiff'),
formula = x ~ y,
data = simple.data,
yat = seq(0,16,2),
main = 'Nature style',
# 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)),
resolution = 200
);
# Left Justified Example
create.barplot(
# filename = tempfile(pattern = 'Barplot_TwoTopLabelsLeftJustified', fileext = '.tiff'),
formula = x ~ y,
data = simple.data,
yat = seq(0,16,2),
ylab.label = NULL,
# set top label details
xlab.top.label = 'Sample Label',
xlab.top.cex = 1.5,
xlab.top.x = -0.125,
xlab.top.y = 0.5,
xlab.top.just = 'left',
# set main label details
main = 'Sample Main',
main.just = 'left',
main.x = 0,
main.y = 0.6,
top.padding = 1,
resolution = 200
);