Make a barplot

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. bar.locations is the x-axis when vertical and y-axis when horizontal. See lattice::ltext arguments for all possible values that can be passed in. (col, alpha, cex, etc, can all be passed in as a single value or vector of same length as text.above.bars$labels)

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.

Author

Mehrdad Shamsi

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
    

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
    );


# \donttest{
# 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
    );
#> Warning: Numeric values detected for conditional variable. If text labels are desired, please convert conditional variable to character.


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
    );
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)


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
    );
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)
#> Warning: Unable to calculate text width/height (using zero)


# 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
    );
#> 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.


# 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
    );

# }