sharpshootR (version 1.8)

plotTransect: Arrange Profiles along a Transect

Description

Plot a collection of Soil Profiles linked to their position along some gradient (e.g. transect).

Usage

plotTransect(
  s,
  grad.var.name,
  grad.var.order = order(site(s)[[grad.var.name]]),
  transect.col = "RoyalBlue",
  tick.number = 7,
  y.offset = 100,
  scaling.factor = 0.5,
  distance.axis.title = "Distance Along Transect (km)",
  crs = NULL,
  grad.axis.title = NULL,
  dist.scaling.factor = 1000,
  spacing = c("regular", "relative"),
  fix.relative.pos = list(thresh = 0.6, maxIter = 5000),
  ...
)

Arguments

s

SoilProfileCollection object

grad.var.name

the name of a site-level attribute containing gradient values

grad.var.order

optional indexing vector used to override sorting along grad.var.name

transect.col

color used to plot gradient (transect) values

tick.number

number of desired ticks and labels on the gradient axis

y.offset

vertical offset used to position profile sketches

scaling.factor

scaling factor applied to profile sketches

distance.axis.title

a title for the along-transect distances

crs

an optional CRS object (sp package) used to convert coordinates into a projected coordinate reference system

grad.axis.title

a title for the gradient axis

dist.scaling.factor

scaling factor (divisor) applied to linear distance units, default is conversion from m to km (1000)

spacing

profile sketch spacing style: "regular" (profiles aligned to an integer grid) or "re lative" (relative distance along transect)

fix.relative.pos

adjust relative positions in the presence of overlap, FALSE to suppress, otherwise list of arguments to aqp::fixOverlap

...

further arguments passed to aqp::plotSPC.

Value

An invisibly-returned data.frame object:

• scaled.grad: scaled gradient values

• scaled.distance: cumulative distance, scaled to the interval of 0.5, nrow(coords) + 0.5

• distance: cumulative distance computed along gradient, e.g. transect distance

• variable: sorted gradient values

• x: x coordinates, ordered by gradient values

• y: y coordinate, ordered by gradient values

• grad.order: a vector index describing the sort order defined by gradient values

Details

Depending on the nature of your SoilProfileCollection and associated gradient values, it may be necessary to tinker with figure margins, y.offset and scaling.factor.

Examples

# NOT RUN {
# }
# NOT RUN {
if(require(aqp) & 
require(sp) &
  require(soilDB)
) {
  
  # sample data
  data("mineralKing", package = "soilDB")
  
  # quick overview
  par(mar=c(1,1,2,1))
  groupedProfilePlot(mineralKing, groups='taxonname', print.id=FALSE)
  
  # init coords and CRS
  coordinates(mineralKing) <- ~ x_std + y_std
  proj4string(mineralKing) <- '+proj=longlat +datum=NAD83'
  
  # projected CRS, units of meters
  crs.utm <- CRS('+proj=utm +zone=11 +datum=NAD83')
  
  # adjust margins
  par(mar=c(4.5,4,4,1))
  
  # standard transect plot, profile sketches arranged along integer sequence
  plotTransect(mineralKing, grad.var.name='elev_field', crs=crs.utm, 
               grad.axis.title='Elevation (m)', label='pedon_id', name='hzname')
  
  # default behavior, attempt adjustments to prevent over-plot and preserve relative spacing
  # use set.seed() to fix outcome
  plotTransect(mineralKing, grad.var.name='elev_field', crs=crs.utm, 
               grad.axis.title='Elevation (m)', label='pedon_id', 
               name='hzname', width=0.15, spacing = 'relative')
  
  # attempt relative positioning based on scaled distances, no corrections for overlap
  # profiles are clustered in space and therefore over-plot
  plotTransect(mineralKing, grad.var.name='elev_field', crs=crs.utm, 
               grad.axis.title='Elevation (m)', label='pedon_id', name='hzname', 
               width=0.15, spacing = 'relative', fix.relative.pos = FALSE)
  
  # customize arguments to aqp::fixOverlap()
  plotTransect(mineralKing, grad.var.name='elev_field', crs=crs.utm, 
               grad.axis.title='Elevation (m)', label='pedon_id', name='hzname', 
               width=0.15, spacing = 'relative', 
               fix.relative.pos = list(maxIter=6000, adj=0.2, thresh=0.7))
  
  plotTransect(mineralKing, grad.var.name='elev_field', crs=crs.utm, 
               grad.axis.title='Elevation (m)', label='pedon_id', name='hzname', 
               width=0.2, spacing = 'relative', 
               fix.relative.pos = list(maxIter=6000, adj=0.2, thresh=0.6),
               name.style = 'center-center')
  
}
# }
# NOT RUN {

# }