create.polygonplot {BoutrosLab.plotting.general}R Documentation

Make a polygonplot

Description

Takes a data.frame and creates a polygon

Usage

create.polygonplot(
	formula,
	data,
	filename = NULL,
	groups = NULL,
	main = NULL,
	main.just = 'center',
	main.x = 0.5,
	main.y = 0.5,
	main.cex = 3,
	max,
	min,
	col = 'white',
	alpha = 0.5,
	border.col = 'black',
	xy.col = 'black',
	strip.col = 'white',
	strip.cex = 1,
	type = 'p',
	cex = 0.75,
	pch = 19,
	lwd = 1,
	lty = 1,
	axes.lwd = 1,
	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,
	xaxis.lab = TRUE,
	yaxis.lab = TRUE,
	xaxis.cex = 1.5,
	yaxis.cex = 1.5,
	xaxis.rot = 0,
	yaxis.rot = 0,
	xaxis.log = FALSE,
	yaxis.log = FALSE,
	xaxis.fontface = 'bold',
	yaxis.fontface = 'bold',
	xaxis.col = 'black',
	yaxis.col = 'black',
	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 = 2,
	right.padding = 1,
	left.padding = 2,	
	ylab.axis.padding = 0,
	add.xy.border = FALSE,
	add.median = FALSE,
	median.lty = 3,
	median.lwd = 1.5,
	use.loess.border = FALSE,
	use.loess.median = FALSE,
	median = NULL,
	median.col = 'black',
	extra.points = NULL,
	extra.points.pch = 21,
	extra.points.type = 'p',
	extra.points.col = 'black',
	extra.points.fill = 'white',
	extra.points.cex = 1,
	add.rectangle = FALSE,
	xleft.rectangle = NULL,
	ybottom.rectangle = NULL,
	xright.rectangle = NULL,
	ytop.rectangle = NULL,
	col.rectangle = 'transparent',
	alpha.rectangle = 1,
	xgrid.at = xat,
	ygrid.at = yat,
	grid.lty = 1,
	grid.col = 'grey',
	grid.lwd = 0.3,
	add.xyline = FALSE,
	xyline.col = 'black',
	xyline.lwd = 1,
	xyline.lty = 1,
	abline.h = NULL,
	abline.v = NULL,
	abline.col = 'black',
	abline.lwd = 1,
	abline.lty = 1,
	add.text = FALSE,
	text.labels = NULL,
	text.x = NULL,
	text.y = NULL,
	text.col = 'black',
	text.cex = 1,
	text.fontface = 'bold',
	key = NULL,
	legend = NULL,
	height = 6,
	width = 6,
	size.units = 'in',
	resolution = 1600,
	enable.warnings = FALSE,
	description = 'Created with BoutrosLab.plotting.general', 
	style = 'BoutrosLab',
	preload.default = 'custom',
	use.legacy.settings = FALSE,
	inside.legend.auto = FALSE
	);

Arguments

formula

The formula used to extract the boxplot components from the data-frame

data

The data-frame to plot

filename

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

groups

The grouping variable in the data-frame

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

max

Max values for polygon

min

Min values for polygon

col

Fill colour of polygon, defaults to white

alpha

Transparency of polygons when several are plotted, defaults to 0.5.

border.col

Border colour(s) of polygon(s), defaults to black

xy.col

Colour of xy coordinates, defaults to black

strip.col

Strip background colour, defaults to “white”

strip.cex

Strip title character expansion

type

Plot type

cex

Character expansion for plotting symbol

pch

Plotting character

lwd

Specifies line width, defaults to 1

lty

Specifies line style, defaults to 1 (solid)

axes.lwd

Thickness of width of axes lines

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 3

ylab.cex

Size of y-axis label, defaults to 3

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

xaxis.lab

Vector listing x-axis tick labels, defaults to automatic

yaxis.lab

Vector listing y-axis tick labels, defaults to automatic

xaxis.cex

Size of x-axis scales, defaults to 2

yaxis.cex

Size of y-axis scales, defaults to 2

xaxis.rot

Rotation of x-axis tick labels; defaults to 0

yaxis.rot

Rotation of y-axis tick labels; defaults to 0

xaxis.log

Logical indicating whether x-variable should be in logarithmic scale (and what base if numeric)

yaxis.log

Logical indicating whether y-variable should be in logarithmic scale (and what base if numeric)

xaxis.fontface

Fontface for the x-axis scales

yaxis.fontface

Fontface for the y-axis scales

xaxis.col

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

yaxis.col

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

xaxis.tck

Specifies the length of the tick marks for x-axis, defaults to 1

yaxis.tck

Specifies the length of the tick marks for y-axis, defaults to 1

xlimits

Two-element vector giving the x-axis limits

ylimits

Two-element vector giving the y-axis limits

xat

Vector listing where the x-axis labels should be drawn

yat

Vector listing where the y-axis labels should be drawn

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 2

ylab.axis.padding

A number specifying the distance of ylabel to the y-axis, defaults to 0

,

add.xy.border

Add xy border to polygon, default is FALSE

add.median

Add median line, default is FALSE

median.lty

Median line type

median.lwd

Median line width, defaults to 1.5

use.loess.border

Use loess curve for border instead of max/min values, default is FALSE

use.loess.median

Use loess curve for median values, default is FALSE

median

Median values for median line

median.col

Median line colour, default is black

extra.points

If not set to NULL (default), add a set of extra points to the plot. A list of two numeric vectors named “x” and “y” giving the co-ordinates of the points to be added

extra.points.pch

A vector specifying the types of extra points to add to the plot. Defaults to 21

extra.points.type

A vector specifying the plot type. Defaults to “p”

extra.points.col

A vector specifying the border colours of the extra points to add to the plot. Defaults to “black”

extra.points.fill

A vector specifying the fill colours of the extra points to add to the plot. Defaults to “white”

extra.points.cex

A vector specifying the sizes of the extra points to add to the plot. Defaults to 1

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

xgrid.at

A vector listing the co-ordinates at which vertical grid-lines should be drawn. Default suppresses drawing of vertical grid-lines

ygrid.at

A vector listing the co-ordinates at which horizontal grid-lines should be drawn. Default suppresses drawing of horizontal grid-lines

grid.lty

Specifies the line type to use for the grid-lines. Defaults to 1 (solid lines)

grid.col

Specifies the colour to use for the grid-lines. Defaults to “grey”

grid.lwd

Specifies the width of the grid-lines. Defaults to 0.3

add.xyline

Allow y=x line to be drawn, default is FALSE

xyline.col

y=x line colour, defaults to black

xyline.lwd

Specifies y=x line width, defaults to 1

xyline.lty

Specifies y=x line style, defaults to 1 (solid)

abline.h

Allow horizontal line to be drawn, default to NULL

abline.v

Allow vertical line to be drawn, default to NULL

abline.col

Horizontal line colour, defaults to black

abline.lwd

Specifies horizontal line width, defaults to 1

abline.lty

Specifies horizontal line style, defaults to 1 (solid)

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

key

Add a key to the plot. See xyplot.

legend

Add a legend to the plot. Helpful for adding multiple keys and adding keys to the margins of the plot. See xyplot.

height

Figure height, defaults to 6 inches

width

Figure width, defaults to 6 inches

size.units

Figure units, defaults to inches

resolution

Figure resolution in dpi, defaults to 1600

enable.warnings

Print warnings if set to TRUE, defaults to FALSE

description

Short description of image/plot; default NULL.

style

defaults to “BoutrosLab”, also accepts “Nature”, which changes parameters according to Nature formatting requirements

preload.default

ability to set multiple sets of diffrent defaults depending on publication needs

use.legacy.settings

boolean to set wheter or not to use legacy mode settings (font)

inside.legend.auto

boolean specifying whether or not to use the automatic inside legend function

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)

Denise Mak

See Also

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

Examples

set.seed(12345);

temp  <- matrix(runif(1010), ncol = 10) + sort(runif(101));

simple.data <- data.frame(
    x = 0:100,
    max = apply(temp, 1, max),
    min = apply(temp, 1, min)
    );

create.polygonplot(
    filename = tempfile(pattern = 'Polygon_Simple', fileext = '.tiff'),
    formula = NA ~ x,
    data = simple.data,
    max = simple.data$max,
    min = simple.data$min,
    main = 'Simple',
    xlimits = c(0,100),
    ylimits = c (0,2),
    col = default.colours(1),
    description = 'Polygon created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Compare two genes across increasing numbers of samples
data1 <- microarray[1,1:58];
data2 <- microarray[2,1:58];

gene1 <- as.data.frame(matrix(nrow = 58, ncol = 58));
gene2 <- as.data.frame(matrix(nrow = 58, ncol = 58));

fill.matrix <- function(x, gene, data){
    for(i in x){
        gene[i, 1:i] <- rep(NA, i);
        gene[i, i:58] <- rep(as.numeric(data[i]), 58-i+1);
        }
    return(gene);
    }; 

gene1 <- fill.matrix(1:58, gene1, data1);
gene1 <- t(matrix(unlist(gene1), ncol = 58, byrow = TRUE));

gene2 <- fill.matrix(1:58, gene2, data2);
gene2 <- t(matrix(unlist(gene2), ncol = 58, byrow = TRUE));

# Set up the data
polygon.data.gene1 <- data.frame(
    x = 1:58,
    max = apply(gene1, 2, function(x) {max(x, na.rm = TRUE)}),
    median = apply(gene1, 2, function(x) {median(x, na.rm = TRUE)}),
    min = apply(gene1, 2, function(x) {min(x, na.rm = TRUE)}),
    set = rownames(microarray[1,]),
    extra = apply(microarray[1:58], 2, function(x) {median(x)})
    );

polygon.data.two.genes <- rbind(
    polygon.data.gene1,
    data.frame(
        x = 1:58,
        max = apply(gene2, 2, function(x) {max(x, na.rm = TRUE)}),
        median = apply(gene2, 2, function(x) {median(x, na.rm = TRUE)}),
        min = apply(gene2, 2, function(x) {min(x, na.rm = TRUE)}),
        set = rownames(microarray[2,]),
        extra = apply(microarray[1:58], 2, function(x) {median(x)})
        )
    )

# Minimal Input
create.polygonplot(
    filename = tempfile(pattern = 'Polygon_Minimal_Input', fileext = '.tiff'),
    formula = NA ~ x,
    data = polygon.data.gene1,
    max = polygon.data.gene1$max,
    min = polygon.data.gene1$min,
    main = 'Minimal input',
    xlimits = c(0,58),
    ylimits = c (2,5),
    description = 'Polygon created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Axes & Labels
create.polygonplot(
    filename = tempfile(pattern = 'Polygon_Axes_Labels', fileext = '.tiff'),
    formula = NA ~ x,
    data = polygon.data.gene1,
    max = polygon.data.gene1$max,
    min = polygon.data.gene1$min,
    main = 'Axes & labels',
    xlimits = c(0,58),
    ylimits = c (0,10),
    # Axes & Labels
    xlab.label = 'Samples',
    ylab.label = 'Value',
    xaxis.cex = 1,
    yaxis.cex = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xat = seq(0, 58, 5),
    yat = seq(0, 10, 2),
    description = 'Polygon created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Colour
create.polygonplot(
    filename = tempfile(pattern = 'Polygon_Colour', fileext = '.tiff'),
    formula = NA ~ x,
    data = polygon.data.gene1,
    max = polygon.data.gene1$max,
    min = polygon.data.gene1$min,
    main = 'Colour',
    xlimits = c(0,58),
    ylimits = c (0,10),
    xlab.label = 'Samples',
    ylab.label = 'Value',
    xaxis.cex = 1,
    yaxis.cex = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xat = seq(0, 58, 5),
    yat = seq(0, 10, 2),
    # Colour
    col = default.colours(1),
    description = 'Polygon created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Add median line and points
create.polygonplot(
    filename = tempfile(pattern = 'Polygon_Median_Points', fileext = '.tiff'),
    formula = NA ~ x,
    data = polygon.data.gene1,
    max = polygon.data.gene1$max,
    min = polygon.data.gene1$min,
    # Median
    median = polygon.data.gene1$median,
    add.median = TRUE,
    main = 'Plotting character',
    xlimits = c(0,58),
    ylimits = c (0,10),
    xlab.label = 'Samples',
    ylab.label = 'Value',
    xaxis.cex = 1,
    yaxis.cex = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xat = seq(0, 58, 5),
    yat = seq(0, 10, 2),
    col = default.colours(1),
    # border points
    add.xy.border = TRUE,
    description = 'Polygon created by BoutrosLab.plotting.general',
    resolution = 100
    );


# Additional Data
create.polygonplot(
    filename = tempfile(pattern = 'Polygon_Extra_Data', fileext = '.tiff'),
    formula = NA ~ x,
    # divide data
    groups = set,
    data = polygon.data.two.genes,
    max = polygon.data.two.genes$max,
    min = polygon.data.two.genes$min,
    main = 'Two data sets',
    median = polygon.data.two.genes$median,
    add.median = TRUE,
    xlimits = c(0,58),
    ylimits = c (0,15),
    xlab.label = 'Samples',
    ylab.label = 'Value',
    xaxis.cex = 1,
    yaxis.cex = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xat = seq(0, 58, 5),
    yat = seq(0, 14, 2),
    # Increasing number of colours
    col = default.colours(2),
    description = 'Polygon created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Legend
create.polygonplot(
    filename = tempfile(pattern = 'Polygon_Legend', fileext = '.tiff'),
    formula = NA ~ x,
    groups = set,
    data = polygon.data.two.genes,
    max = polygon.data.two.genes$max,
    min = polygon.data.two.genes$min,
    main = 'Legend',
    median = polygon.data.two.genes$median,
    add.median = TRUE,
    xlimits = c(0,58),
    ylimits = c (0,15),
    xlab.label = 'Samples',
    ylab.label = 'Value',
    xaxis.cex = 1,
    yaxis.cex = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xat = seq(0, 58, 5),
    yat = seq(0, 14, 2),
    col = default.colours(2),
    # Adding legend
    key = list(
        text = list(
            lab = rownames(microarray[1:2,]),
            cex = 0.8,
            col = 'black'
            ),
        points = list(
            pch = 15,
            col = default.colours(2),
            cex = 2
            ),
        x = 0.04,
        y = 0.93,
        padding.text = 3,
        columns = 1
        ),
    description = 'Polygon created by BoutrosLab.plotting.general',
    resolution = 200
    );

# Panel Organiation
create.polygonplot(
    filename = tempfile(pattern = 'Polygon_Panel', fileext = '.tiff'),
    # divide data
    formula = NA ~ x | set,
    data = polygon.data.two.genes,
    max = polygon.data.two.genes$max,
    min = polygon.data.two.genes$min,
    main = 'Panel',
    median = polygon.data.two.genes$median,
    add.median = TRUE,
    xlimits = c(0,58),
    ylimits = c (0,15),
    xlab.label = 'Samples',
    ylab.label = 'Value',
    xaxis.cex = 1,
    yaxis.cex = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xat = seq(0, 58, 5),
    yat = seq(0, 14, 2),
    col = default.colours(1),
    description = 'Polygon created by BoutrosLab.plotting.general',
    resolution = 200
    );

# Extra Points
create.polygonplot(
    filename = tempfile(pattern = 'Polygon_Extra_Points', fileext = '.tiff'),
    formula = NA ~ x,
    groups = set,
    data = polygon.data.two.genes,
    max = polygon.data.two.genes$max,
    min = polygon.data.two.genes$min,
    main = 'Extra points',
    median = polygon.data.two.genes$median,
    add.median = TRUE,
    xlimits = c(0,58),
    ylimits = c (0,15),
    xlab.label = 'Samples',
    ylab.label = 'Value',
    xaxis.cex = 1,
    yaxis.cex = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xat = seq(0, 58, 5),
    yat = seq(0, 14, 2),
    col = default.colours(2),
    # Add to legend
    key = list(
        text = list(
            lab = c(rownames(microarray[1:2,]), 'All genes'),
            cex = 0.8,
            col = 'black'
            ),
        points = list(
            pch = c(15, 15, 3),
            col = c(default.colours(2), 'red'),
            cex = c(2, 2, 0.7)
            ),
        x = 0.04,
        y = 0.93,
        padding.text = 3,
        columns = 1
        ),
    # Extra points
    extra.points = list(
        x = polygon.data.two.genes$x,
        y = polygon.data.two.genes$extra
        ),
    extra.points.col = 'red',
    extra.points.pch = 3,
    extra.points.type = c('p', 'l'),
    extra.points.cex = 0.7,
    description = 'Polygon created by BoutrosLab.plotting.general',
    resolution = 200
    );

# Nature style
create.polygonplot(
    filename = tempfile(pattern = 'Polygon_Nature_style', fileext = '.tiff'),
    formula = NA ~ x,
    groups = set,
    data = polygon.data.two.genes,
    max = polygon.data.two.genes$max,
    min = polygon.data.two.genes$min,
    main = 'Nature style',
    median = polygon.data.two.genes$median,
    add.median = TRUE,
    xlimits = c(0,58),
    ylimits = c (0,15),
    xaxis.cex = 1,
    yaxis.cex = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xaxis.fontface = 1,
    yaxis.fontface = 1,
    xat = seq(0, 58, 5),
    yat = seq(0, 14, 2),
    col = default.colours(2),
    # Adding legend
    key = list(
        text = list(
            lab = rownames(microarray[1:2,]),
            cex = 0.8,
            col = 'black'
            ),
        points = list(
            pch = 15,
            col = default.colours(2),
            cex = 2
            ),
        x = 0.04,
        y = 0.93,
        padding.text = 3,
        columns = 1
        ),

    # set style to Nature 
    style = 'Nature',
    
    # demonstrating how to italicize character variables
    ylab.label = expression(paste('italicized ', italic('a'))),
  
    # demonstrating how to create en-dashes
    xlab.label = expression(paste('en dashs: 1','\u2013', '10'^'\u2013', ''^3)),

    description = 'Polygon created by BoutrosLab.plotting.general',
    resolution = 1200
    );


[Package BoutrosLab.plotting.general version 6.0.3 Index]