R: Add Depth Brackets

addBracket {aqp}

R Documentation

Add Depth Brackets

Description

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

Usage

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.

Author(s)

D.E. Beaudette

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')

plot of chunk unnamed-chunk-1

# 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')
}