R: Make a histogram

create.histogram {BoutrosLab.plotting.general}

R Documentation

Make a histogram

Description

Takes a vector and creates a histogram

Usage

create.histogram(
	x,
	data,
	filename = NULL,
	main = NULL,
	main.just = 'center',
	main.x = 0.5,
	main.y = 0.5,
	main.cex = 3,
	xlab.label = NULL,
	ylab.label = NULL,
	xlab.cex = 2,
	ylab.cex = 2,
	xlab.col = 'black',
	ylab.col = 'black',
	xaxis.lab = TRUE,
	yaxis.lab = TRUE,
	xaxis.cex = 1.5,
	yaxis.cex = 1.5,
	xlimits = NULL,
	ylimits = NULL,
	xat = TRUE,
	yat = TRUE,
	xaxis.rot = 0,
	yaxis.rot = 0,
	xaxis.col = 'black',
	yaxis.col = 'black',
	xaxis.tck = 1,
	yaxis.tck = 1,
	xaxis.fontface = 'bold',
	yaxis.fontface = 'bold',
	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 = 'percent',
	breaks = NULL,
	col = 'white',
	border.col = 'black',
	lwd = 2,
	lty = 1,
	layout = NULL,
	x.spacing = 0,
	y.spacing = 0,
	x.relation = 'same',
	y.relation = 'same',
	strip.col = 'white',
	strip.cex = 1,
	top.padding = 0.1,
	bottom.padding = 0.7,
	right.padding = 0.1,
	left.padding = 0.5,
	ylab.axis.padding = 0,
	abline.h = NULL,
	abline.v = NULL,
	abline.col = 'black',
	abline.lwd = 1,
	abline.lty = 1,
	key = NULL,
	legend = NULL,
	add.text = FALSE,
	text.labels = NULL,
	text.x = NULL,
	text.y = NULL,
	text.col = 'black',
	text.cex = 1,
	text.fontface = 'bold',	
	add.rectangle = FALSE,
	xleft.rectangle = NULL,
	ybottom.rectangle = NULL,
	xright.rectangle = NULL,
	ytop.rectangle = NULL,
	col.rectangle = 'transparent',
	alpha.rectangle = 1,
	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 formula or a numeric vector (not frequencies!)
`data`	An optional data source if x is a formula
`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`	x-axis title
`ylab.label`	y-axis title
`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”
`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 y-axis tick labels, 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 ticks should be drawn
`yat`	Vector listing where the y-axis ticks should be drawn
`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.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
`xaxis.fontface`	Fontface for the x-axis scales
`yaxis.fontface`	Fontface for the y-axis scales
`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`	Should the plot be of the “percent” (default), “density” or “count”
`breaks`	A vector listing the break-points of the histogram, or an integer specifying the desired number of breaks.
`col`	Fill colour for the histograms
`border.col`	Specify border colour (defaults to black)
`lwd`	Specifies line width
`lty`	Specifies line style
`layout`	A vector specifying the number of columns, rows (e.g., c(2,1). Default is NULL; see lattice::xyplot for more details

`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”
`strip.col`	Strip background colour, defaults to “white”
`strip.cex`	Strip title character expansion
`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 0.5
`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 0

`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 and vertical line colour, defaults to black
`abline.lwd`	Specifies horizontal/vertical line width, defaults to 1
`abline.lty`	Specifies horizontal/vertical line style, defaults to 1 (solid)
`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.
`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
`add.rectangle`	Allow a rectangle to be drawn, default is FALSE
`xleft.rectangle`	Specifies the left x ooordinate 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
`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)

Paul C. Boutros

Examples

set.seed(12345);

create.histogram(
    # filename = tempfile(pattern = 'Histogram_Simple', fileext = '.tiff'),
    x = rnorm(5000),
    main = 'Simple',
    description = 'Histogram created by BoutrosLab.plotting.general',
    resolution = 50
    );

create.histogram(
    # filename = tempfile(pattern = 'Histogram_Simple_Count', fileext = '.tiff'),
    x = rnorm(5000),
    main = 'Simple Count',
    description = 'Histogram created by BoutrosLab.plotting.general',
    type = 'count',
    resolution = 50
    );

# Minimal Input
create.histogram(
    # filename = tempfile(pattern = 'Histogram_Minimal_Input', fileext = '.tiff'),
    x = microarray[,1],
    main = 'Minimal input',
    description = 'Histogram created by BoutrosLab.plotting.general',
    resolution = 50
    );

# Formula Input - dividing by chromosome
chr.data <- data.frame(
    x = microarray$Chr,
    y = microarray[,1]
    );

create.histogram(
    # filename = tempfile(pattern = 'Histogram_Formula_Input', fileext = '.tiff'),
    x = y ~ x,
    data = chr.data,
    main = 'Formula input',
    description = 'Histogram created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Axes and Labels
create.histogram(
    # filename = tempfile(pattern = 'Histogram_Axes_Labels', fileext = '.tiff'),
    x = microarray[,1],
    main = 'Axes & labels',
    # Customizing the axes and labels
    xlab.label = 'Bins',
    ylab.label = 'Counts',
    xlimits = c(0, 16),
    xat = seq(0,15,5),
    # set break points for bins
    breaks = seq(floor(min(microarray[,1])), ceiling(max(microarray[,1])), 1),
    description = 'Histogram created by BoutrosLab.plotting.general',
    resolution = 100
    );


# Colour change
create.histogram(
    # filename = tempfile(pattern = 'Histogram_Colours', fileext = '.tiff'),
    x = microarray[,1],
    main = 'Colours',
    xlab.label = 'Bins',
    ylab.label = 'Counts',
    xlimits = c(0, 16),
    xat = seq(0,15,5),
    breaks = seq(floor(min(microarray[,1])), ceiling(max(microarray[,1])), 1),
    # Colours
    col = 'lightgrey',
    description = 'Histogram created by BoutrosLab.plotting.general',
    resolution = 100
    );

# Line type
create.histogram(
    # filename = tempfile(pattern = 'Histogram_Line_Type', fileext = '.tiff'),
    x = microarray[,1],
    main = 'Line type',
    xlab.label = 'Bins',
    ylab.label = 'Counts',
    xlimits = c(0, 16),
    xat = seq(0,15,5),
    breaks = seq(floor(min(microarray[,1])), ceiling(max(microarray[,1])), 1),
    col = 'lightgrey',
    # Changing the line type
    lty = 2,
    description = 'Histogram created by BoutrosLab.plotting.general',
    resolution = 200
    );

# Nature style
create.histogram(
    # filename = tempfile(pattern = 'Histogram_Nature_style', fileext = '.tiff'),
    x = microarray[,1],
    main = 'Nature style',
    xlimits = c(0, 16),
    xat = seq(0,15,5),
    breaks = seq(floor(min(microarray[,1])), ceiling(max(microarray[,1])), 1),
    col = 'lightgrey',

    # 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 = 'Histogram created by BoutrosLab.plotting.general',
    resolution = 200
    );

[Package BoutrosLab.plotting.general version 7.1.0 Index]