Make a density plot

Takes a list of vectors and creates a density-plot with each vector as a separate curve

Usage

create.densityplot(
  x,
  filename = NULL,
  main = NULL,
  main.just = 'center',
  main.x = 0.5,
  main.y = 0.5,
  main.cex = 3,
  xlab.label = NULL,
  ylab.label = 'Density',
  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,
  type = 'l',
  lty = 'solid',
  cex = 0.75,
  pch = 19,
  col = 'black',
  lwd = 2,
  bandwidth = 'nrd0',
  bandwidth.adjust = 1,
  xlimits = NULL,
  ylimits = NULL,
  xat = TRUE,
  yat = TRUE,
  xaxis.lab = NA,
  yaxis.lab = NA,
  xaxis.cex = 1.5,
  yaxis.cex = 1.5,
  xaxis.rot = 0,
  yaxis.rot = 0,
  xaxis.col = 'black',
  yaxis.col = 'black',
  xaxis.fontface = 'bold',
  yaxis.fontface = 'bold',
  xaxis.tck = 1,
  yaxis.tck = 1,
  xgrid.at = xat,
  ygrid.at = yat,
  key = list(text = list(lab = c(''))),
  legend = NULL,
  top.padding = 0.1,
  bottom.padding = 0.7,
  left.padding = 0.5,
  right.padding = 0.1,
  add.axes = FALSE,
  abline.h = NULL,
  abline.v = NULL,
  abline.lty = NULL,
  abline.lwd = NULL,
  abline.col = 'black',
  add.rectangle = FALSE,
  xleft.rectangle = NULL,
  ybottom.rectangle = NULL,
  xright.rectangle = NULL,
  ytop.rectangle = NULL,
  col.rectangle = 'transparent',
  alpha.rectangle = 1,
  add.text = FALSE, 
  text.labels = NULL, 
  text.x = NULL, 
  text.y = NULL, 
  text.anchor = "centre", 
  text.col = "black", 
  text.cex = 1,
        text.fontface = "bold",
  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 list of vectors, each of which will be plotted as a separate curve in the final plot

filename

Filename for tiff output, or if NULL returns the trellis object itself

main

The main title for the plot (space is reclaimed if NULL)

main.just

The justification of the main title for the plot, default is centered

main.x

The x location of the main title, deault is 0.5

main.y

The y location of the main title, default is 0.5

main.cex

Size of text for main plot title, defaults to 2

xlab.label

The label for the x-axis

ylab.label

The label for the y-axis, defaults to “Density”

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

type

Plot type

lty

Line type

cex

Character expansion for plotting symbol

pch

Plotting character

col

Point/line colour

lwd

Thickness of width of any best-fit lines

bandwidth

Smoothing bandwidth, or character string giving rule to choose bandwidth ('nrd0', 'nrd', 'ucv', 'bcv', 'sj', or 'sj-ste'). Passed to base R function density.

bandwidth.adjust

Adjustment parameter for the bandwidth (bandwidth used is bandwidth*bandwidth.adjust). Makes it easy to specify bandwidth as a proportion of the default.

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 tick labels, defaults to 1

yaxis.cex

Size of x-axis tick labels, defaults to 1

xaxis.rot

Rotation of x-axis tick labels; defaults to 0

yaxis.rot

Rotation of y-axis tick labels; defaults to 0

xaxis.col

Colour of the x-axis tick labels, defaults to “black”

yaxis.col

Colour of the y-axis tick labels, defaults to “black”

xaxis.fontface

Fontface for the x-axis scales

yaxis.fontface

Fontface for the y-axis scales

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

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

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.

top.padding

A number giving the top padding in multiples of the lattice default

bottom.padding

A number giving the bottom padding in multiples of the lattice default

left.padding

A number giving the left padding in multiples of the lattice default

right.padding

A number giving the right padding in multiples of the lattice default

add.axes

Allow axis lines to be turned on or off

abline.h

Specify the superimposed horizontal line(s)

abline.v

Specify the superimposed vertical line(s)

abline.lty

Specify the superimposed line type

abline.lwd

Specify the superimposed line width

abline.col

Specify the superimposed line colour (defaults to black)

add.rectangle

Allow a rectangle to be drawn, default is FALSE

xleft.rectangle

Specifies the left x coordinate of the rectangle to be drawn

ybottom.rectangle

Specifies the bottom y coordinate of the rectangle to be drawn

xright.rectangle

Specifies the right x coordinate of the rectangle to be drawn

ytop.rectangle

Specifies the top y coordinate of the rectangle to be drawn

col.rectangle

Specifies the colour to fill the rectangle's area

alpha.rectangle

Specifies the colour bias of the rectangle to be drawn

add.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.anchor

Part of text that should be anchored to x/y coordinates. Defaults to 'centre'. Use 'left' or 'right' to left or right-align text.

text.col

The colour of additional text

text.cex

The size of additional text

text.fontface

The fontface for additional text

height

Figure height, defaults to 6 inches

width

Figure width, defaults to 6 inches

size.units

Figure units, defaults to inches

resolution

Figure resolution in dpi, defaults to 1600

enable.warnings

Print warnings if set to TRUE, defaults to FALSE

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.

Author

Paul C. Boutros

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

xyplot, lattice or the Lattice book for an overview of the package.

Examples

set.seed(12345);

simple.data <- data.frame(
    x = rnorm(1000),
    y = rnorm(1000, mean = 3, sd = 3)
    );

create.densityplot(
    # filename = tempfile(pattern = 'Densityplot_Simple', fileext = '.tiff'),
    x = simple.data,
    main = 'Simple',
    description = 'Barplot created by BoutrosLab.plotting.general'
    );


# format data
format.data <- microarray[1:3,1:58];
format.data <- as.data.frame(t(format.data));

# Minimal Input
create.densityplot(
    # filename = tempfile(pattern = 'Densityplot_Minimal_Input', fileext = '.tiff'),
    x = format.data,
    main = 'Minimal input',
    description = 'Barplot created by BoutrosLab.plotting.general',
    resolution = 50
    );


# Line type
create.densityplot(
    # filename = tempfile(pattern = 'Densityplot_Line_Type', fileext = '.tiff'),
    x = format.data,
    main = 'Line type',
    # Line type
    lty = c('solid','dashed','dotted'),
    description = 'Barplot created by BoutrosLab.plotting.general',
    resolution = 50
    );


# Axes & Labels
create.densityplot(
    # filename = tempfile(pattern = 'Densityplot_Axes_Labels', fileext = '.tiff'),
    x = format.data,
    main = 'Axes & labels',
    lty = c('solid','dashed','dotted'),
    # Axes & Labels
    ylimits = c(-0.1, 2.5),
    ylab.cex = 1.5,
    xat = seq(0, 13, 1),
    description = 'Barplot created by BoutrosLab.plotting.general',
    resolution = 50
    );


# \donttest{
# Colour change & Legend
create.densityplot(
    # filename = tempfile(pattern = 'Densityplot_Colour_Legend', fileext = '.tiff'),
    x = format.data,
    main = 'Colour & legend',
    lty = c('solid','dashed','dotted'),
    ylimits = c(-0.1, 2.5),
    ylab.cex = 1.5,
    # Colours
    col = default.colours(3),
    # Legend
    legend = list(
        inside = list(
            fun = draw.key,
            args = list(
                key = list(
                    points = list(
                        col = default.colours(3),
                        pch = 21,
                        cex = 1.5,
                        fill = default.colours(3)
                        ),
                    text = list(
                        lab = colnames(format.data)
                        ),
                    padding.text = c(0,5,0),
                    cex = 1
                    )
                ),
            x = 0.65,
            y = 0.97,
            draw = FALSE
            )
        ),
    description = 'Barplot created by BoutrosLab.plotting.general',
    resolution = 50
    );


# Correlation key
create.densityplot(
    # filename = tempfile(pattern = 'Densityplot_Correlation_Key', fileext = '.tiff'),
    x = format.data[,1:2],
    main = 'Correlation key',
    lty = c('solid','dotted'),
    ylimits = c(-0.1, 2.5),
    ylab.cex = 1.5,
    col = default.colours(2),
    legend = list(
        inside = list(
            fun = draw.key,
            args = list(
                key = list(
                    points = list(
                        col = default.colours(2),
                        pch = 21,
                        cex = 1.5,
                        fill = default.colours(2)
                        ),
                    text = list(
                        lab = colnames(format.data)[1:2]
                        ),
                    padding.text = c(0,5,0),
                    cex = 1
                    )
                ),
            x = 0.65,
            y = 0.97,
            draw = FALSE
            ),
        # Correlation key accepts two vectors
        inside = list(
            fun = draw.key,
            args = list(
                key = get.corr.key(
                    x = as.numeric(format.data[,1]),
                    y = as.numeric(format.data[,2]),
                    label.items = c('pearson','beta1'),
                    alpha.background = 1,
                    key.cex = 1.2
                    )
                ),
            x = 0.65,
            y = 0.85,
            corner = c(0,1)
            )
        ),
    description = 'Barplot created by BoutrosLab.plotting.general',
    resolution = 200
    );


# Gridlines
create.densityplot(
    # filename = tempfile(pattern = 'Densityplot_Gridlines_1', fileext = '.tiff'),
    x = format.data,
    main = 'Gridlines',
    lty = c('solid','dashed','dotted'),
    ylimits = c(-0.1, 2.5),
    ylab.cex = 1.5,
    col = default.colours(3),
    legend = list(
        inside = list(
            fun = draw.key,
            args = list(
                key = list(
                    points = list(
                        col = default.colours(3),
                        pch = 21,
                        cex = 1.5,
                        fill = default.colours(3)
                        ),
                    text = list(
                        lab = colnames(format.data)
                        ),
                    padding.text = c(0,5,0),
                    cex = 1
                    )
                ),
            x = 0.65,
            y = 0.97,
            draw = FALSE
            )
        ),
    # Grid lines
    type = c('l','g'),
    description = 'Barplot created by BoutrosLab.plotting.general',
    resolution = 200
    );


# Gridlines
create.densityplot(
    # filename = tempfile(pattern = 'Densityplot_Gridlines_2', fileext = '.tiff'),
    x = format.data,
    main = 'Gridlines',
    lty = c('solid','dashed','dotted'),
    ylimits = c(-0.1, 2.5),
    ylab.cex = 1.5,
    col = default.colours(3),
    legend = list(
        inside = list(
            fun = draw.key,
            args = list(
                key = list(
                    points = list(
                        col = default.colours(3),
                        pch = 21,
                        cex = 1.5,
                        fill = default.colours(3)
                        ),
                    text = list(
                        lab = colnames(format.data)
                        ),
                    padding.text = c(0,5,0),
                    cex = 1
                    )
                ),
            x = 0.65,
            y = 0.97,
            draw = FALSE
            )
        ),
    # Grid lines
    type = c('l','g'),
    xgrid.at = seq(0,14,1),
    ygrid.at = seq(0,2.5,0.25),
    description = 'Barplot created by BoutrosLab.plotting.general',
    resolution = 200
    );


# Nature style
create.densityplot(
    # filename = tempfile(pattern = 'Densityplot_Nature_style', fileext = '.tiff'),
    x = format.data,
    main = 'Nature style',
    lty = c('solid','dashed','dotted'),
    ylimits = c(-0.1, 2.5),
    ylab.cex = 1.5,
    xlab.cex = 1.5,
    col = default.colours(3),
    legend = list(
        inside = list(
            fun = draw.key,
            args = list(
                key = list(
                    points = list(
                        col = default.colours(3),
                        pch = 21,
                        cex = 1.5,
                        fill = default.colours(3)
                        ),
                    text = list(
                        lab = colnames(format.data)
                        ),
                    padding.text = c(0,5,0),
                    cex = 1
                    )
                ),
            x = 0.65,
            y = 0.97,
            draw = FALSE
            )
        ),
    # Grid lines
    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.

# }