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

Make a segplot

Description

Takes a data.frame and creates a segplot

Usage

create.segplot(
	formula,
	data,
	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,
	xaxis.lab = TRUE,
	yaxis.lab = TRUE,
	xaxis.cex = 1.5,
	yaxis.cex = 1.5,
	xaxis.col = 'black',
	yaxis.col = 'black',
	xaxis.fontface = 'bold',
	yaxis.fontface = 'bold',
	xaxis.rot = 0,
	yaxis.rot = 0,
	xaxis.tck = 1,
	yaxis.tck = 1,
	xlimits = NULL,
	ylimits = NULL,
	xat = TRUE,
	yat = TRUE,
	abline.h = NULL,
	abline.v = NULL,
	abline.lty = 1,
	abline.lwd = 1,
	abline.col = 'black',
	segments.col = 'black',
	segments.lwd = 1,
	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,
	level = NULL,
	col.regions = NULL,
	centers = NULL,
	plot.horizontal = TRUE,
	draw.bands = FALSE,
	pch = 16,
	symbol.col = 'black',
	symbol.cex = 1,
	add.rectangle = FALSE,
	xleft.rectangle = NULL,
	ybottom.rectangle = NULL,
	xright.rectangle = NULL,
	ytop.rectangle = NULL,
	col.rectangle = 'transparent',
	alpha.rectangle = 1,
	axes.lwd = 1,
	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,
	disable.factor.sorting = FALSE
	)

Arguments

formula

The formula used to extract the x & y components from the data-frame

data

The data-frame to 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 3

xlab.label

x-axis label

ylab.label

y-axis label

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

xaxis.lab

Vector listing x-axis tick labels, defaults to automatic

yaxis.lab

Vector listing y-axis tick labels, defaults to automatic

xaxis.cex

Size of x-axis scales, defaults to 1.5

yaxis.cex

Size of y-axis scales, defaults to 1.5

xaxis.col

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

yaxis.col

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

xaxis.fontface

Fontface for the x-axis scales, defaults to “plain”

yaxis.fontface

Fontface for the y-axis scales, defaults to “plain”

xaxis.rot

Counterclockwise rotation of text in x-axis scales in degrees, defaults to 0

yaxis.rot

Counterclockwise rotation of text in y-axis scales in degrees, defaults to 0

xaxis.tck

Specifies the length of the tick mark, defaults to 1 for both top and bottom axes

yaxis.tck

Specifies the length of the tick mark, defaults to 1 for both top and bottom axes

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

abline.h

Allow horizontal line to be drawn, default to NULL

abline.v

Allow vertical line to be drawn, default to NULL

abline.lty

Specifies horizontal line style, defaults to 1 (solid)

abline.lwd

Specifies horizontal line width, defaults to 1

abline.col

Horizontal line colour, defaults to black

segments.col

Colour of segments, defaults to “black”

segments.lwd

Line width of segments, defaults to 1

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 0.1

bottom.padding

A number specifying the distance to the bottom margin, defaults to 0.7

right.padding

A number specifying the distance to the right margin, defaults to 0.1

left.padding

A number specifying the distance to the left margin, defaults to 0.5

ylab.axis.padding

A number specifying the distance of ylabel to the y-axis, defaults to 1

,

level

Optional covariate that determines colour coding of the segments, if specified overwrites segments.col, can contain actual colors or values to determine colors, then col.regions should be defined

col.regions

Vector of colors, define if level is numeric

centers

Optional vector for centers of segments, defaults to NULL

plot.horizontal

Logical whether segments should be drawn horizontally (default) or vertically

draw.bands

Logical to specify whether to draw lines (default) or rectangles

pch

Plotting character for centers

symbol.col

Colour of plotting character for centers, defaults to “black”

symbol.cex

Size of plotting character for centers, 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 to be drawn

axes.lwd

Specifies axes line width, defaults to 1

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.

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

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)

Paul C. Boutros

See Also

levelplot, segplot or the Lattice book for an overview of the package.

Examples

set.seed(12345);

simple.data <- data.frame(
    min = runif(10,5,15),
    max = runif(10,15,25),
    labels = as.factor(LETTERS[1:10])
    );

create.segplot(
    filename = tempfile(pattern = 'Segplot_simple', fileext = '.tiff'),
    formula = labels ~ min + max,
    data = simple.data,
    resolution = 50
    );

# load some data
length.of.gene <- apply(microarray[1:10,60:61], 1, diff);
bin.length <- length.of.gene;
bin.length[which(bin.length < 20000)] <- 'A';
bin.length[which(bin.length < 40000)] <- 'B';
bin.length[which(bin.length < 60000)] <- 'C';

segplot.data <- data.frame(
    min = apply(microarray[1:10,1:58], 1, min),
    max = apply(microarray[1:10,1:58], 1, max),
    median = apply(microarray[1:10,1:58], 1, median),
    gene = rownames(microarray)[1:10],
    # approximating length of gene 
    length = as.factor(bin.length)
    );

# Minimal Input using real data
create.segplot(
    filename = tempfile(pattern = 'Segplot_Minimal_Input', fileext = '.tiff'),
    formula = gene ~ min + max,
    data = segplot.data,
    main = 'Minimal input',
    description = 'Segplot created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Axes & Labels
create.segplot(
    filename = tempfile(pattern = 'Segplot_Axes_Labels', fileext = '.tiff'),
    formula = gene ~ min + max,
    data = segplot.data,
    main = 'Axes & labels',
    # Formatting axes
    xlab.label = 'Change in gene expression',
    ylab.label = 'Gene',
    xaxis.cex = 1,
    yaxis.cex = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xlimits = c(0,13),
    xat = seq(0, 12, 2),
    description = 'Segplot created by BoutrosLab.plotting.general',
    resolution = 100
    );


# Bands
create.segplot(
    filename = tempfile(pattern = 'Segplot_Bands', fileext = '.tiff'),
    formula = gene ~ min + max,
    data = segplot.data,
    main = 'Bands',
    xlab.label = 'Change in gene expression',
    ylab.label = 'Gene',
    xaxis.cex = 1,
    yaxis.cex = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xlimits = c(0,13),
    xat = seq(0, 12, 2),
    # drawing rectangles instead of lines
    draw.bands = TRUE,
    description = 'Segplot created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Colours
create.segplot(
    filename = tempfile(pattern = 'Segplot_Colours', fileext = '.tiff'),
    formula = reorder(gene, median) ~ min + max,
    data = segplot.data,
    main = 'Colours',
    xlab.label = 'Change in gene expression',
    ylab.label = 'Gene',
    xaxis.cex = 1,
    yaxis.cex = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xlimits = c(0,13),
    xat = seq(0, 12, 2),
    draw.bands = FALSE,
    # Changing the colours based on a covariate ('level' parameter)
    level = segplot.data$length,
    col.regions = default.colours(3),
    description = 'Segplot created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Median
create.segplot(
    filename = tempfile(pattern = 'Segplot_Median', fileext = '.tiff'),
    formula = gene ~ min + max,
    data = segplot.data,
    main = 'Medians',
    xlab.label = 'Change in gene expression',
    ylab.label = 'Gene',
    xaxis.cex = 1,
    yaxis.cex = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xlimits = c(0,13),
    draw.bands = FALSE,
    xat = seq(0, 12, 2),
    level = segplot.data$length,
    col.regions = default.colours(3),
    # Adding center values
    centers = segplot.data$median,
    description = 'Segplot created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Reorder by center value
create.segplot(
    filename = tempfile(pattern = 'Segplot_Reorder', fileext = '.tiff'),
    formula = reorder(gene, median) ~ min + max,
    data = segplot.data,
    main = 'Reordered',
    xlab.label = 'Change in gene expression',
    ylab.label = 'Gene',
    xaxis.cex = 1,
    yaxis.cex = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xlimits = c(0,13),
    xat = seq(0, 12, 2),
    draw.bands = FALSE,
    centers = segplot.data$median,
    level = segplot.data$length,
    col.regions = default.colours(3),
    description = 'Segplot created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Legend
create.segplot(
    filename = tempfile(pattern = 'Segplot_Legend', fileext = '.tiff'),
    formula = reorder(gene, median) ~ min + max,
    data = segplot.data,
    main = 'Legend',
    xlab.label = 'Change in gene expression',
    ylab.label = 'Gene',
    xaxis.cex = 1,
    yaxis.cex = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xlimits = c(0,13),
    xat = seq(0, 12, 2),
    draw.bands = FALSE,
    centers = segplot.data$median,
    level = segplot.data$length,
    col.regions = default.colours(3),
    # Adding legend to explain colours
    legend = list(
        inside = list(
            fun = draw.key,
            args = list(
                key = list(
                    points = list(
                        col = default.colours(3),
                        pch = 19,
                        cex = 1
                        ),
                    text = list(
                        lab = c('1-20000 bp', '20001-40000 bp','40001-60000 bp')
                        ),
                    padding.text = 1,
                    cex = 1
                    )
                ),
            x = 0.60,
            y = 0.15,
            corner = c(0,1)
            )
        ),
    description = 'Segplot created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Background
create.segplot(
    filename = tempfile(pattern = 'Segplot_Background', fileext = '.tiff'),
    formula = reorder(gene, median) ~ min + max,
    data = segplot.data,
    main = 'Background rectangle',
    xlab.label = 'Change in gene expression',
    ylab.label = 'Gene',
    xaxis.cex = 1,
    yaxis.cex = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xlimits = c(0,13),
    xat = seq(0, 12, 2),
    draw.bands = FALSE,
    centers = segplot.data$median,
    level = segplot.data$length,
    col.regions = default.colours(3),
    # Adding legend to explain colours
    legend = list(
        inside = list(
            fun = draw.key,
            args = list(
                key = list(
                    points = list(
                        col = default.colours(3),
                        pch = 19,
                        cex = 1
                        ),
                    text = list(
                        lab = c('1-20000 bp', '20001-40000 bp','40001-60000 bp')
                        ),
                    padding.text = 1,
                    cex = 1
                    )
                ),
            x = 0.50,
            y = 0.15,
            corner = c(0,1)
            )
        ),
    # adding background shading
    add.rectangle = TRUE,
    xleft.rectangle = 0,
    ybottom.rectangle = seq(0.5, 8.5, 2),
    xright.rectangle = 13,
    ytop.rectangle = seq(1.5, 9.5, 2),
    col.rectangle = 'grey',
    alpha.rectangle = 0.5,
    description = 'Segplot created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Nature style
create.segplot(
    filename = tempfile(pattern = 'Segplot_Nature_style', fileext = '.tiff'),
    formula = reorder(gene, median) ~ min + max,
    data = segplot.data,
    main = 'Nature style',
    xaxis.cex = 1,
    yaxis.cex = 1,
    xlab.cex = 1.5,
    ylab.cex = 1.5,
    xlimits = c(0,13),
    xat = seq(0, 12, 2),
    draw.bands = FALSE,
    centers = segplot.data$median,
    level = segplot.data$length,
    col.regions = default.colours(3),
    legend = list(
        inside = list(
            fun = draw.key,
            args = list(
                key = list(
                    points = list(
                        col = default.colours(3),
                        pch = 19,
                        cex = 1
                        ),
                    text = list(
                        lab = c('1-20000 bp', '20001-40000 bp','40001-60000 bp')
                        ),
                    padding.text = 1,
                    cex = 1
                    )
                ),
            x = 0.50,
            y = 0.15,
            corner = c(0,1)
            )
        ),
    add.rectangle = TRUE,
    xleft.rectangle = 0,
    ybottom.rectangle = seq(0.5, 8.5, 2),
    xright.rectangle = 13,
    ytop.rectangle = seq(1.5, 9.5, 2),
    col.rectangle = 'grey',
    alpha.rectangle = 0.5,

    # 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 = 'Segplot created by BoutrosLab.plotting.general',
    resolution = 100
    );

# example of bands and lines
create.segplot(
    filename = tempfile(pattern = 'Segplot_BandsAndLines', fileext = '.tiff'),
    formula = labels ~ min + max,
    data = simple.data,
    draw.bands = c(1,3,5,7,9),
    resolution = 200
    );


[Package BoutrosLab.plotting.general version 6.0.3 Index]