Initialize a new plot window using preset parameters, add an axis or title to a plot, generate labels for axes and subplots, add stability lines for water, get colors for a set of numeric values.
thermo.plot.new(xlim, ylim, xlab, ylab, cex = par("cex"),
mar = NULL, lwd = par("lwd"), side = c(1,2,3,4),
mgp = c(1.7, 0.3, 0), cex.axis = par("cex"), col = par("col"),
yline = NULL, axs = "i", do.box = TRUE, las = 1,
xline = NULL, ...)
label.plot(x, xfrac = 0.05, yfrac = 0.95, paren = FALSE,
italic = FALSE, ...)
usrfig()
label.figure(x, xfrac = 0.05, yfrac = 0.95, paren = FALSE,
italic = FALSE, ...)
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", plot.it = TRUE)
mtitle(main, line=0, ...)
ZC.col(z)numeric, limits of the \(x\)-axis
numeric, limits of the \(y\)-axis
character, \(x\)-axis label
character, \(y\)-axis label
numeric, character expansion factor for labels
numeric, width (number of lines) of margins on each side of plot
numeric, line width
numeric, which sides of plot to draw axes
numeric, sizes of margins of plot
numeric, character expansion factor for names of axes
character, line color
numeric, margin line on which to plot \(y\)-axis name
character, setting for axis limit calculation
logical, draw a box around the plot?
numeric, style for axis labels
numeric, margin line on which to plot \(x\)-axis name
further arguments passed to par or mtext
numeric, temperature (K)
character, label to place on plot
numeric, fractional location on \(x\)-axis for placement of label
numeric, fractional location on \(y\)-axis for placement of label
logical, add parentheses around label text?
logical, italicize label text?
character, description of \(x\)-axis
character, description of \(y\)-axis
numeric, pressure (bar)
character, which of oxidation/reduction lines to plot
numeric, logarithm of the activity of \(\mathrm{H_2O}\)
numeric, line type
numeric, points to plot on \(x\) axis
character, state of O2
logical, plot the lines?
character, text for plot title
numeric, margin line to place title
numeric, set of values
thermo.plot.new sets parameters for a new plot, creates a new plot using plot.new, and adds axes and major and minor tick marks to the plot. Plot parameters (see par) including cex, mar, lwd, mgp and axs can be given, as well as a numeric vector in side 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.
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 and label.figure add identifying text within the plot region and figure region.
The value given for x is made into a label, optionally italicized and with parentheses (like ).
The location of the label is controlled by xfrac and yfrac (the fractional coordinates of either the plot or figure region), and ... can include other parameters such as cex and adj that are passed to text.
usrfig returns the limits of the figure region in “user” coordinates (i.e. the limits of the plot region, from par("usr")).
It is a supporting function for label.figure but is also useful for other circumstances where information must be added at a particular location in a figure.
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.
The spacing of the last (bottom) line from the edge of the plot is specified by line.
This function exists to facilitate using expressions in multiline titles (see revisit for an example.)
ZC.col uses colorspace) to generate colors from a diverging palette (red - light grey - blue) corresponding to the values in z.
Red is associated with lower values of z.
This function is intended to generate colors for distinguishing average oxidation state of carbon ZC, but any numeric values can be supplied.