Add depth-wise brackets to an existing plot of a SoilProfileCollection object.

addBracket(top, bottom=NULL, idx=NULL, label=NULL, label.cex=0.75,
tick.length = 0.05, arrow.length = 0.05, offset = -0.3,
missing.bottom.depth = 25,
...)

Arguments

top

numeric vector of bracket top depths

bottom

numeric vector of bracket bottom depths

idx

optional integer index, associating bracket with profile

label

optional vector of labels for brackets

label.cex

scaling factor for label font

tick.length

length of bracket "tick" mark

arrow.length

length of arrowhead

offset

numeric, length of left-hand offset from each profile

missing.bottom.depth

distance (in depth units) to extend brackets that are missing a lower depth

…

further arguments passed on to segments or arrows

Details

The optional argument idx can be used to manually specify which profile a given bracket will be associated with. When idx is NULL, an integer sequence associated with plotting order (via plotSPC) is used. See examples below.

Note

This is a `low-level` plotting function: you must first plot a SoilProfileCollection object before using this function.

See also

plotSPC

Examples

# sample data
data(sp1)

# add color vector
sp1$soil_color <- with(sp1, munsell2rgb(hue, value, chroma))

# promote to SoilProfileCollection
depths(sp1) <- id ~ top + bottom

# plot profiles
plot(sp1)

# extract top/bottom depths associated with all A horizons
f <- function(i) {
  h <- horizons(i)
  idx <- grep('^A', h$name)
  c(min(h$top[idx]), max(h$bottom[idx], na.rm=TRUE))
}

# apply function to sp1, result is a list
a <- profileApply(sp1, f, simplify=FALSE)
# convert list into matrix
a <- do.call('rbind', a)

# plot
plot(sp1)
# annotate with brackets
# note that plotting order is derived from the call to `plot(sp1)`
addBracket(a[, 1], a[, 2], col='red')

# more interesting example using diagnostic horizons
if(require(soilDB)) {
  # load some sample data with diagnostic horizons
  data(loafercreek)

  # extract first 15 profiles
  x <- loafercreek[1:15, ]
  s <- site(x)

  # plot
  par(mar=c(0,0,0,0))
  plot(x, name='hzname', id.style='top')

  # add brackets describing the argillic horizon
  addDiagnosticBracket(x, 'argillic horizon', col='red')
  # add brackets describing paralithic contact
  addDiagnosticBracket(x, 'paralithic contact', col='blue')
}