sharpshootR (version 1.6)

plotTransect: Plot a collection of Soil Profiles linked to their position along some gradient (e.g. 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='regular',
fix.relative.pos=list(thresh = 0.6, trace = TRUE, maxIter = 5000),
...)

Arguments

s

a SoilProfileCollection object

grad.var.name

the name of a site-level attribute containing gradient values

grad.var.order

optional vector of indices 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 used to adjust profile sketches

distance.axis.title

a tital for the along-transect distances

crs

an optional CRS object used to convert coordinates into a planar system

grad.axis.title

a title for the gradient axis

dist.scaling.factor

scaling factor applied to linear distance units, default is conversion from m to km

spacing

regular (profiles aligned to an integer grid) or relative (relative distance along transect) spacing

fix.relative.pos

FALSE to suppress, otherwise list of arguments to aqp::fixOverlap

…

further arguments passed to 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 {
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, trace=TRUE, 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=0.15, spacing = 'relative', 
fix.relative.pos = list(maxIter=6000, trace=TRUE, adj=0.2, thresh=0.5))

}
# }