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(1.5, 0.3, 0), cex.axis = par("cex"), col = par("col"),
    yline = NULL, axs = "i", do.box = TRUE, ticks = NULL, las = 1,
    xline = NULL)
  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)
  water.lines(xaxis = "pH", yaxis = "Eh", T = 298.15, P = "Psat", 
    which = c("oxidation","reduction"), logaH2O = 0, lty = 2, lwd=1,
    col = par("fg"), xpoints = NULL, O2state="gas")
  mtitle(main, ...)
  residualsplot(residuals, property = "Cp", model = "big")

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

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

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

O2state

character, state of O2

main

character, text for plot title

...

further arguments passed to mtext

residuals

numeric, named vector of residuals to plot

property

character, name of property

model

character, name of model to use in plot title

Side Effects

These functions create or modify a plot.

Details

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. The very first time thermo.plot.new is called, it stores the existing value of par(no.readonly=TRUE) in thermo$opar so that the plot device can be reset to the previous state later on.

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 are drawn (oxidation, reduction, or both (the default)). logaH2O denotes the logarithm of the activity of water. With O2state set to gas (the default), the logarithm of oxygen fugacity is plotted. Change this to aq to plot the logarithm of oxygen activity (do not change it if plotting Eh). xpoints is 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.)

residualsplot produces a barchart with options useful for plotting residuals of group contribution models for thermodynamic properties. It plots horizontal bars stacked with largest on top. The names of the residuals argument (i.e., the names of model species) are plotted across from each respective bar. The axis title is taken from the property (probably Cp or V), and the plot title includes the model name. See the xadditivity vignette for examples of these plots.