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

In rgr: Applied Geochemistry EDA

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. The x-y plot axes may be optionally displayed with logarithmic (base 10) scaling. Optionally a legend may be added to the plot.

Where the x-y data are parts from a composition they should be plotted as symmetric coordinates, and the third variable as a log-ratio if it is from the same composition.

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, iflgnd = FALSE,
	title = deparse(substitute(zz)), cex.lgnd = 0.8, ...)

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 scaled.
logz	if it is required to undertake the Tukey Boxplot computations after a logarithmic data transform, set logz = TRUE.
xlab	by default the character string for xx is used for the x-axis title. An alternate title can be displayed with xlab = "text string", see Examples.
ylab	by default the character string for yy is used for the x-axis title. An alternate title can be displayed with ylab = "text string", see Examples.
zlab	by default the character string for zz is appended to the text string “EDA Tukey Boxplot Based Plot for” for the plot title

. An alternate title can be displayed with zlab = "text string", 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, see Details below.
iflgnd	the default is no legend. If a legend is required set iflgnd = TRUE, following the plotting of the data the cursor will be activated, locate that at the top left corner of the desired legend position and ‘left button’ on the pointing device.
title	a short title for the legend, e.g., title = "Zn (mg/kg)". The default is the character string for zz.
cex.lgnd	controls the scaling of the legend box and text, but not the symbols so that they match those on the plot, the default is cex.lgnd = 0.8.
...	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 higher 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, a ‘+’ is used to plot the data falling in the middle 50%. For the higher groupings, the whisker contains values >Q3 and <(Q3 + 1.5 * HW), 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.

For compositional data the function gx.symm.coords.mat is required, and arguments xx and yy are replaced by a call to that function which returms the symmetric coordinated for those parts of the composition, and the axes are labelled appropriately. See example below.

Note

Any less than detection limit values represented by negative values, or zeros or other numeric codes representing blanks in the data, must be removed prior to executing this function, see ltdl.fix.df.

Any data vectors including NAs are removed prior to displaying the plot.

Author(s)

Robert G. Garrett

See Also

display.rainbow, ltdl.fix.df, remove.na, gx.symm.coords.mat

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\nLog10(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\nLog10(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\nLog10(Zn) (mg/kg)",
	symcolr = c(27, 24, 22, 12, 5, 3, 36)) 

## Detach test data
detach(sind)
rm(sind)

## More appropriately for compositional data
data(nockolds)
attach(nockolds)

## Plot a minor element log ratio against the symmetric coordinates for
## Si and Al
xyplot.eda7(gx.symm.coords.mat(nockolds, 1, 2), log(P/Ti))

## Detach test data
detach(nockolds)
rm(nockolds)

Example output

Loading required package: MASS
Loading required package: fastICA

	Cut Levels	  No. of Symbols   Symbol - size - Colour
	Log = FALSE 				sfact = 1.00 

			       0 	     Circle  2.00    25 
	 -135 
			       0 	     Circle  1.50    22 
	 -51 
			       7 	     Circle  1.00    20 
	 33 
			       12 	     Cross   0.50    13 
	 89 
			       2 	     Square  1.00    6 
	 173 
			       0 	     Square  1.50    4 
	 257 
			       4 	     Square  2.00    1 
Warning messages:
1: In par(old.par) : graphical parameter "cin" cannot be set
2: In par(old.par) : graphical parameter "cra" cannot be set
3: In par(old.par) : graphical parameter "csi" cannot be set
4: In par(old.par) : graphical parameter "cxy" cannot be set
5: In par(old.par) : graphical parameter "din" cannot be set
6: In par(old.par) : graphical parameter "page" cannot be set

	Cut Levels	  No. of Symbols   Symbol - size - Colour
	Log = TRUE 				sfact = 2.00 

			       0 	     Circle  4.00    25 
	 1.68 
			       0 	     Circle  3.00    22 
	 7.45 
			       7 	     Circle  2.00    20 
	 33 
			       12 	     Cross   1.00    13 
	 89 
			       3 	     Square  2.00    6 
	 394.19 
			       3 	     Square  3.00    4 
	 1745.9 
			       0 	     Square  4.00    1 
Warning messages:
1: In par(old.par) : graphical parameter "cin" cannot be set
2: In par(old.par) : graphical parameter "cra" cannot be set
3: In par(old.par) : graphical parameter "csi" cannot be set
4: In par(old.par) : graphical parameter "cxy" cannot be set
5: In par(old.par) : graphical parameter "din" cannot be set
6: In par(old.par) : graphical parameter "page" cannot be set

	Cut Levels	  No. of Symbols   Symbol - size - Colour
	Log = TRUE 				sfact = 2.00 

			       0 	     Circle  4.00    #000000 
	 1.68 
			       0 	     Circle  3.00    #262626 
	 7.45 
			       7 	     Circle  2.00    #4D4D4D 
	 33 
			       12 	     Cross   1.00    #666666 
	 89 
			       3 	     Square  2.00    #4D4D4D 
	 394.19 
			       3 	     Square  3.00    #262626 
	 1745.9 
			       0 	     Square  4.00    #000000 
Warning messages:
1: In par(old.par) : graphical parameter "cin" cannot be set
2: In par(old.par) : graphical parameter "cra" cannot be set
3: In par(old.par) : graphical parameter "csi" cannot be set
4: In par(old.par) : graphical parameter "cxy" cannot be set
5: In par(old.par) : graphical parameter "din" cannot be set
6: In par(old.par) : graphical parameter "page" cannot be set

	Cut Levels	  No. of Symbols   Symbol - size - Colour
	Log = TRUE 				sfact = 2.00 

			       0 	     Circle  4.00    27 
	 1.68 
			       0 	     Circle  3.00    24 
	 7.45 
			       7 	     Circle  2.00    22 
	 33 
			       12 	     Cross   1.00    12 
	 89 
			       3 	     Square  2.00    5 
	 394.19 
			       3 	     Square  3.00    3 
	 1745.9 
			       0 	     Square  4.00    36 
Warning messages:
1: In par(old.par) : graphical parameter "cin" cannot be set
2: In par(old.par) : graphical parameter "cra" cannot be set
3: In par(old.par) : graphical parameter "csi" cannot be set
4: In par(old.par) : graphical parameter "cxy" cannot be set
5: In par(old.par) : graphical parameter "din" cannot be set
6: In par(old.par) : graphical parameter "page" cannot be set
  ** Are the data/parts all in the same measurement units? **

	Cut Levels	  No. of Symbols   Symbol - size - Colour
	Log = FALSE 				sfact = 1.00 

			       0 	     Circle  2.00    25 
	 -3.56 
			       1 	     Circle  1.50    22 
	 -2.68 
			       3 	     Circle  1.00    20 
	 -1.8 
			       8 	     Cross   0.50    13 
	 -1.21 
			       3 	     Square  1.00    6 
	 -0.33 
			       1 	     Square  1.50    4 
	 0.55 
			       0 	     Square  2.00    1 
Warning messages:
1: In par(old.par) : graphical parameter "cin" cannot be set
2: In par(old.par) : graphical parameter "cra" cannot be set
3: In par(old.par) : graphical parameter "csi" cannot be set
4: In par(old.par) : graphical parameter "cxy" cannot be set
5: In par(old.par) : graphical parameter "din" cannot be set
6: In par(old.par) : graphical parameter "page" cannot be set

rgr documentation built on May 2, 2019, 6:09 a.m.