AquaEnv (version 1.0-4)

plot.aquaenv: plot.aquaenv

Description

PUBLIC function: high level plot function for objects of class aquaenv

Arguments

x

object of class aquaenv

xval

only valid if bjerrum=FALSE: a vector of the (maximal) length of the elements of aquaenv against which they are to be plotted

what

a list of names of the elements of aquaenv that are to be plotted, if not supplied and bjerrum=FALSE and cumulative=FALSE: all elements are plotted, if not supplied and bjerrum=TRUE then what is set to be c("CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH", "H3PO4", "H2PO4", "HPO4", "PO4", "SiOH4", "SiOOH3", "SiO2OH2", "H2S", "HS", "S2min", "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F", "HNO3", "NO3", "HNO2", "NO2"), needs to be supplied for cumulative=TRUE

bjerrum

flag: TRUE = a bjerrum plot is done (by calling bjerrumplot)

cumulative

flag: TRUE = a cumulative plot is done (by calling cumulativeplot)

newdevice

flag: if TRUE, new plot device is opened

setpar

flag: if TRUE parameters are set with the function par

xlab

x axis label

log

only valif if bjerrum=TRUE: should the plot be on a logarithmic y axis?

total

only valid if cumulative=TRUE: should the sum of all elements specified in what be plotted as well?

device

the device to plot on; default: "x11" (can also be "eps" or "pdf")

filename

filename to be used if "eps" or "pdf" is selected for device

size

the size of the plot device; default: 12 (width) by 10 (height) inches

ylim

standard plot parameter; if not supplied it will be calculated by range() of the elements to plot

lwd

standard plot parameter; width of the lines in the plot

mgp

standard plot parameter; default: axis title on line 1.8, axis labels on line 0.5, axis on line 0

mar

standard plot parameter; default: margin of 3 lines bottom and left and 0.5 lines top and right

oma

standard plot parameter; default: no outer margin

palette

only valid if bjerrum=TRUE or cumulative=TRUE: a vector of colors to use in the plot (either numbers or names given in colors())

legendposition

only valid if bjerrum=TRUE or cumulative=TRUE: position of the legend

legendinset

only valid if bjerrum=TRUE or cumulative=TRUE: standard legend parameter inset

legendlwd

only valid if bjerrum=TRUE or cumulative=TRUE: standard legend parameter lwd: line width of lines in legend

bg

only valid if bjerrum=TRUE or cumulative=TRUE: standard legend parameter: default background color: white

y.intersp

standard legend parameter; if cumulative=TRUE then default: 1.2 lines space between the lines in the legend

...

further arguments are passed on to the plot function

Details

Top level generic usage is

plot.aquaenv(x, xval, what=NULL, bjerrum=FALSE,
             cumulative=FALSE, newdevice=TRUE, setpar=TRUE,
	     device="x11", ...)

Generic usages for standard plotting are

plot.aquaenv(x, xval, ...)

plot.aquaenv(x, xval, what, mfrow=c(1,1), size=c(7,7), ...)

Generic usage for creating a bjerrum plot is

plot.aquaenv(x, what, log=FALSE, palette=NULL,
             device="x11", filename="aquaenv",
             size=c(12,10), ylim=NULL, lwd=2, xlab="free scale pH",
	     mgp=c(1.8, 0.5, 0), mar=c(3,3,0.5,0.5), oma=c(0,0,0,0),
	     legendposition="bottomleft", legendinset=0.05,
	     legendlwd=4, bg="white", newdevice=TRUE, setpar=TRUE,
	     device="x11",...)

Generic usage for creating a cumulative plot is

plot.aquaenv(x, xval, what, total=TRUE, palette=NULL,
             device="x11", filename="aquaenv", size=c(12,10), ylim=NULL,
             lwd=2, mgp=c(1.8, 0.5, 0), mar=c(3,3,0.5,0.5), oma=c(0,0,0,0),
             legendposition="bottomleft", legendinset=0.05, legendlwd=4,
             bg="white", y.intersp=1.2, newdevice=TRUE, setpar=TRUE,
	     device="x11",...)