scatterplot: Create a scatter plot with error ellipses or crosses

In pvermees/IsoplotR: Statistical Toolbox for Radiometric Geochronology

Create a scatter plot with error ellipses or crosses

Description

Takes bivariate data with (correlated) uncertainties as input and produces a scatter plot with error ellipses or crosses as output. (optionally) displays the linear fit on this diagram, and can show a third variable as a colour scale.

Usage

scatterplot(
  xy,
  oerr = 3,
  show.numbers = FALSE,
  show.ellipses = 1,
  levels = NA,
  clabel = "",
  ellipse.fill = c("#00FF0080", "#FF000080"),
  ellipse.stroke = "black",
  fit = NULL,
  add = FALSE,
  empty = FALSE,
  ci.col = "gray80",
  line.col = "black",
  lwd = 1,
  hide = NULL,
  omit = NULL,
  omit.fill = NA,
  omit.stroke = "grey",
  addcolourbar = TRUE,
  bg,
  cex,
  xlim = NULL,
  ylim = NULL,
  xlab,
  ylab,
  asp = NA,
  log = "",
  taxis = FALSE,
  box = !taxis,
  xaxt = ifelse(taxis, "n", "s"),
  ...
)

Arguments

xy	matrix with columns X, sX, Y, sY(, rXY)
oerr	indicates whether the analytical uncertainties of the output are reported as: 1: 1\sigma absolute uncertainties. 2: 2\sigma absolute uncertainties. 3: absolute (1-\alpha)% confidence intervals, where \alpha equales the value that is stored in settings('alpha'). 4: 1\sigma relative uncertainties (\%). 5: 2\sigma relative uncertainties (\%). 6: relative (1-\alpha)% confidence intervals, where \alpha equales the value that is stored in settings('alpha').
show.numbers	logical flag (TRUE to show grain numbers)
show.ellipses	show the data as: 0: points 1: error ellipses 2: error crosses
levels	a vector with additional values to be displayed as different background colours within the error ellipses.
clabel	label for the colour scale
ellipse.fill	Fill colour for the error ellipses. This can either be a single colour or multiple colours to form a colour ramp. Examples: a single colour: rgb(0,1,0,0.5), '#FF000080', 'white', etc.; multiple colours: c(rbg(1,0,0,0.5), rgb(0,1,0,0.5)), c('#FF000080','#00FF0080'), c('blue','red'), c('blue','yellow','red'), etc.; a colour palette: rainbow(n=100), topo.colors(n=100,alpha=0.5), etc.; or a reversed palette: rev(topo.colors(n=100,alpha=0.5)), etc. For empty ellipses, set ellipse.col=NA
ellipse.stroke	the stroke colour for the error ellipses. Follows the same formatting guidelines as ellipse.fill
fit	the output of york() (optional).
add	if TRUE, adds the points and lines to the existing plot.
empty	set up an empty plot with the right axis limits to fit the data
ci.col	the fill colour for the confidence interval of the intercept and slope.
line.col	colour of the regression line
lwd	line width of the regression line
hide	vector with indices of aliquots that should be removed from the plot.
omit	vector with indices of aliquots that should be plotted but omitted from the isochron age calculation.
omit.fill	fill colour that should be used for the omitted aliquots.
omit.stroke	stroke colour that should be used for the omitted aliquots.
addcolourbar	add a colour bar to display the colours used to levels
bg	background colour for the plot symbols (only used if show.ellipses=0).
cex	plot symbol magnification.
xlim	(optional) two-element vector with the x-axis limits
ylim	(optional) two-element vector with the y-axis limits
xlab	(optional) x-axis label (only used when add=FALSE)
ylab	(optional) y-axis label (only used when add=FALSE)
asp	the y/x aspect ratio, see ‘plot.window’.
log	same as the eponymous argument to the generic plot function.
taxis	logical. If TRUE, replaces the x-axis of an inverse isochron with a time scale. Only used if inverse=TRUE.
box	logical. If TRUE, draws a frame around the plot.
xaxt	see ?par
...	optional arguments to format the points and text.

Examples

X <- c(1.550,12.395,20.445,20.435,20.610,24.900,
       28.530,50.540,51.595,86.51,106.40,157.35)
Y <- c(.7268,.7809,.8200,.8116,.8160,.8302,
       .8642,.9534,.9617,1.105,1.230,1.440)
sX <- X*0.02
sY <- Y*0.01
dat <- cbind(X,sX,Y,sY)
scatterplot(dat,fit=york(dat),show.ellipses=2)

pvermees/IsoplotR documentation built on Nov. 18, 2024, 1:02 a.m.