util.plot: Functions to Create and Modify Plots

Description

Initialize a new plot window using preset parameters, open a postcript file for plotting, add an axis or title to a plot, generate labels for plot axes and for identification of subplots and physical and chemical conditions, add stability lines for water to a diagram.

Usage

thermo.plot.new(xlim, ylim, xlab, ylab, cex = par("cex"),
    mar = NULL, lwd = par("lwd"), side = c(1,2,3,4), 
    mgp = c(1.2, 0.3, 0), cex.axis = par("cex"), col = par("col"),
    yline = NULL, axs = "i", do.box = TRUE, ticks = NULL, las = 1,
    xline = NULL)
  thermo.postscript(file, family = "Helvetica", width = 8, 
    height = 6, horizontal = FALSE)
  thermo.axis(lab = "x-axis", side = 1, line = 1.5, cex = par("cex"),
    lwd = par("lwd"), T = NULL, col = par("col"))
  label.plot(x, xfrac = 0.95, yfrac = 0.9, cex = 1, paren = TRUE, 
    adj = 1)
  axis.label(lab, opt = NULL, do.state = TRUE, oldstyle = FALSE,
    do.upper = FALSE, mol = "mol")
  species.label(formula, do.state = FALSE, state = "", do.log = FALSE)
  water.lines(xaxis = "pH", yaxis = "Eh", T = 298.15, P = "Psat", 
    which = c("oxidation","reduction"), logaH2O = 0, lty = 2, 
    col = par("fg"), xpoints = NULL)
  mtitle(main, ...)

Arguments

xlim

numeric, limits of the $x$-axis.

ylim

numeric, limits of the $y$-axis.

xlab

character, $x$-axis label.

ylab

character, $y$-axis label.

cex

numeric, character expansion factor for labels.

mar

numeric, width (number of lines) of margins on each side of plot.

lwd

numeric, line width.

side

numeric, which sides of plot to draw axes.

mgp

numeric, sizes of margins of plot.

cex.axis

numeric, character expansion factor for names of axes.

col

character, line color.

yline

numeric, margin line on which to plot $y$-axis name.

axs

character, setting for axis limit calculation.

do.box

logical, draw a box around the plot?

ticks

numeric, same effect as side (retained for backwards compatibility).

las

numeric, style for axis labels

xline

numeric, margin line on which to plot $x$-axis name.

file

character, path to a file.

family

character, font family.

width

numeric, width of plot.

height

numeric, height of plot.

horizontal

logical, create plot in landscape mode?

lab

character, description of axis label.

line

numeric, margin line to plot axis label.

numeric, temperature (K).

character, label to place on plot.

xfrac

numeric, fractional location on $x$-axis for placement of label.

yfrac

numeric, fractional location on $y$-axis for placement of label.

paren

logical, add parentheses around label text?

adj

numeric, parameter for text alignment.

opt

character or numeric, options for axis labels.

do.state

logical, append state abbreviation to label?

oldstyle

logical, use old style of axis labels?

do.upper

logical, use uppercase letters in axis label?

mol

character, string to use as the denominator of units in axis label.

formula

character, representation of chemical formula.

state

character, designation of physical state.

do.log

logical, prepend a text indicating logarithm of activity or fugacity?

xaxis

character, description of $x$-axis.

yaxis

character, description of $y$-axis.

numeric, pressure (bar).

which

character, which of oxidation/reduction lines to plot.

logaH2O

numeric, logarithm of the activity of $\mathrm{H_2O}$.

lty

numeric, line type.

xpoints

numeric, points to plot on $x$ axis.

main

character, text for plot title.

...

further arguments passed to mtext.

Side Effects

These functions create or modify a plot.

Details

thermo.postscript calls postscript with some custom parameters used by the package author (and might be handy for other users of the package as well).

thermo.plot.new sets parameters for a new plot, creates a new plot using plot.new, and adds axes and major and minor ticks to the plot. Plot parameters (see par) including cex, mar, lwd, mgp and axs can be given, as well as a numeric vector in ticks identifying which sides of the plot receive tick marks. yline, if present, denotes the margin line (default par('mgp')[1]) where the y-axis name is plotted.

axis.label returns an expression to be used for plotting an axis label, which may be the symbol for a thermodynamic properties, chemical activity or fugacity, or one of T, P, Eh, pH, pe or logK. An expression for chemical activity or fugacity is returned if the first argument is the name of one of the basis species (e.g., O2). The expression in this case includes italic and subscripted symbols, unless oldstyle is TRUE, when labels with a simpler format (e.g. O2 (log f)) are returned. The default value of NULL of opt means to use the state this basis species is in, or if this basis species is not present to use the value in thermo$opt$state. Likewise, if x is T or P the units of temperature or pressure are determined using nuts (which also refers to thermo$opt). do.upper, if TRUE, tells the function to print the label using uppercase letters. Labels for properties can be generated by using e.g. DGf or DG0r as arguments. mol (default: mol) refers to the denominator of the units (default: molality); this can be changed to represent e.g. specific units, by setting mol to g. opt when generating labels for properties indicates the prefix to place on the units.

species.label is like axis.label but is specifically intended for generating expressions for the chemical formulas of species. The state (in parentheses) is included in the expression only if state is not NULL. If do.log is TRUE, the expression will contain a prefix in front of the formula that indicates chemical activity (like log_a or log_f).

water.lines plots lines representing the oxidation and reduction stability limits of water on yaxis-xaxis diagrams, where yaxis can be Eh or O2, and xaxis can be pH or T. which controls which lines (oxidation, reduction, or both (the default)) are drawn, logaH2O (default 0) denotes the logarithm of the activity of water, lty (default 2) the line type, col (default par('fg'), the foreground color), and xpoints an optional list of points on the x axis to which to restrict the plotting (default of NULL refers to the axis limits).

label.plot adds identifying text to the plot; the value given for x is made into a label like $(a)$. The location of the label is controlled by xfrac and yfrac (the fractional locations along the respective axes) as well as adj (the text alignment parameter, see text).

thermo.axis is used to add axes and axis labels to plots, with some default style settings (rotation of numeric labels) and conversions between oxidation-reduction scales (called by thermo.plot.new). It also adds minor tick marks.

mtitle can be used to add a multi-line title to a plot. It loops over each element of main and places it on a separate margin line using mtext. This function exists to facilitate using expressions in multiline titles (see revisit for an example.)