rgr (version 1.1.0)

xyplot.eda7: Display a Third Variable in a X-Y Plot using Tukey Boxplot Symbology

Description

Displays a third variable where the data are represented by symbols using Tukey boxplot-based symbology. Tukey boxplots divide data into 7 groups, the middle 50%, and three lower and higher groupings, see Details below. The computation of the fences used to subdivide the data may be carried out following a logarithmic transformation of the data. The colours of the symbols may be optionally changed.

Usage

xyplot.eda7(xx, yy, zz, sfact = 1, xlim = NULL, ylim = NULL,  
	log = NULL, logz = FALSE, xlab = deparse(substitute(xx)), 
	ylab = deparse(substitute(yy)), zlab = deparse(substitute(zz)), 
	main = "", ifgrey = FALSE, symcolr = NULL, ...)

Arguments

xx

name of the x-axis variable.

yy

name of the y-axis variable.

zz

name of the third variable to be plotted.

sfact

controls the absolute size of the plotted symbols, by default sfact = 1. Increasing sfact results in larger symbols.

xlim

user defined limits for the x-axis, see Details below.

ylim

user defined limits for the y-axis, see Details below.

log

if it is required to display the data with logarithmic axis scaling, set log = "x" for a logarithmically scaled x-axis, log = "y" for a logarithmically scaled y-axis, and log = "xy" for both axes logarithmically scal

logz

if it is required to undertake the Tukey Boxplot computations after a logarithmic data transform, set logz = TRUE.

xlab

the x-axis title, by default the variable name, deparse(substitute(xx)). It is often desirable to replace the default x-axis title of the input variable name text string with a more informative title, e.g., xlab = "Fe (mg/kg) in stream

ylab

the y-axis title, by default the variable name, deparse(substitute(yy)). It is often desirable to replace the default y-axis title of the input variable name text string with a more informative title, e.g., ylab = "Mn (mg/kg) in stream

zlab

by default, zlab = deparse(substitute(zz)), a plot title is generated by appending the input variable name text string to Proportional Symbol Plot for. Alternative titles may be generated, see Details below.

main

an alternative plot title, see Details below.

ifgrey

set ifgrey = TRUE if a grey-scale plot is required, see Details below.

symcolr

the default is a colour plot and default colours are provided, deeper blues for lower values, green for the middle 50% of the data, and oranges and reds for higher values. A set of alternate symbol colours can be provided by defining symcolr

...

further arguments to be passed to methods. For example, if it is required to make the plot title smaller, add cex.main = 0.9 to reduce the font size by 10%.

Details

Tukey boxplots divide data into 7 groups, the middle 50%, and three lower and high groupings: within the whisker, near outliers and far outliers, respectively. Symbols for values below the first quartile (Q1) are plotted as increasingly larger circles, while symbols for values above the third quartile are plotted as increasingly larger squares. For the higher groupings, the whisker contains values >Q3 and <(q3 +="" 1.5="" *="" hw)<="" code="">, where HW = (Q3 - Q1), the interquartile range; near outliers lie between (Q3 + 1.5 * HW) and (Q3 + 3 * HW); and far outliers have values >(Q3 + 3 * HW). For the lower groupings the group boundaries, fences, fall similarly spaced below Q1. The computation of the fences used to subdivide the data may be carried out following a logarithmic transformation of the data, set logz = TRUE. A summary table of the values of the symbol intervals, the number of values plotting as each symbol, and symbol shapes, sizes and colours is displayed on the current device. If zlab and main are undefined a default a plot title is generated by appending the input variable name text string to EDA Tukey Boxplot-Based Plot for. If no plot title is required set zlab = "", and if some user defined plot title is required it should be defined in main, e.g. main = "Plot Title Text". If the grey-scale option is chosen the symbols are plotted 100% black for the far outliers, 85% black for the near outliers, 70% black for values within the whiskers, and 60% black for values falling within the middle 50% of the data. The default colours, symcolr = c(25, 22, 20, 13, 6, 4, 1), are selected from the rainbow(36) pallette, and alternate colour schemes need to be selected from the same palette. See display.rainbow for the available colours. It is essential that 7 colours be provided, e.g., symcolr = c(27, 24, 22, 12, 5, 3, 36), if exactly 7 are not provided the default colours will be displayed.

See Also

display.rainbow, ltdl.fix.df, remove.na

Examples

## Make test data available
data(sind)
attach(sind)

## Plot a default Tukey boxplot-based display
xyplot.eda7(Fe, Mn, Zn)

## Plot with logarithmically scaled boxplot fences and more
## appropriate axis scaling and labelling with a user specified title
xyplot.eda7(Fe, Mn, Zn, sfact = 2, log = "y", logz = TRUE,
	xlab = "Fe (pct) in stream sediment", 
	ylab = "Mn (mg/kg) in stream sediment",
	main = "Howarth & Sinding-Larsen Test Data
Log10(Zn) (mg/kg)") 

## Display a grey-scale equivalent of the above plot
xyplot.eda7(Fe, Mn, Zn, sfact = 2, log = "y", logz = TRUE, ifgrey = TRUE,
	xlab = "Fe (pct) in stream sediment", 
	ylab = "Mn (mg/kg) in stream sediment",
	main = "Howarth & Sinding-Larsen Test Data
Log10(Zn) (mg/kg)") 

## Plot the same display with an alternate colour scheme
xyplot.eda7(Fe, Mn, Zn, sfact = 2, log = "y", logz = TRUE,
	xlab = "Fe (pct) in stream sediment", 
	ylab = "Mn (mg/kg) in stream sediment",
	main = "Howarth & Sinding-Larsen Test Data
Log10(Zn) (mg/kg)",
	symcolr = c(27, 24, 22, 12, 5, 3, 36)) 

## Detach test data
detach(sind)