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Arrange Profiles along a Transect — plotTransect • sharpshootR

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

plotTransect(
  s,
  xy,
  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)",
  grad.axis.title = NULL,
  dist.scaling.factor = 1000,
  spacing = c("regular", "relative"),
  fix.relative.pos = list(thresh = 0.6, maxIter = 5000),
  ...
)

s

SoilProfileCollection object

xy

sf object, defining point coordinates of soil profiles, must be in same order as s, must be a projected coordinate reference system (UTM, AEA, etc.)

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

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 "relative" (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.

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

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.

This function is very much a work in progress, ideas welcome!

# \donttest{

if(require(aqp) & 
require(sf) &
  require(soilDB)
) {
   
library(aqp)
library(soilDB)
library(sf)


# sample data
data("mineralKing", package = "soilDB")

# device options are modified locally, reset when done
op <- par(no.readonly = TRUE)

# quick overview
par(mar=c(1,1,2,1))
groupedProfilePlot(mineralKing, groups='taxonname', print.id=FALSE)

# setup point locations
s <- site(mineralKing)
xy <- st_as_sf(s, coords = c('longstddecimaldegrees', 'latstddecimaldegrees'))
st_crs(xy) <- 4326

# convert to suitable projected cRS
# projected CRS, UTM z11 NAD83 (https://epsg.io/26911)
xy <- st_transform(xy, 26911) 

# adjust margins
par(mar = c(4.5, 4, 4, 1))

# standard transect plot, profile sketches arranged along integer sequence
plotTransect(mineralKing, xy, grad.var.name = 'elev_field',
             grad.axis.title = 'Elevation (m)', label = 'upedonid', name = 'hzname')

# default behavior, attempt adjustments to prevent over-plot and preserve relative spacing
# use set.seed() to fix outcome
plotTransect(mineralKing, xy, grad.var.name = 'elev_field',
             grad.axis.title = 'Elevation (m)', label = 'upedonid',
             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, xy, grad.var.name = 'elev_field',
             grad.axis.title = 'Elevation (m)', label = 'upedonid', name = 'hzname',
             width = 0.15, spacing = 'relative', fix.relative.pos = FALSE)

# customize arguments to aqp::fixOverlap()
plotTransect(mineralKing, xy, grad.var.name = 'elev_field', crs = crs.utm,
             grad.axis.title = 'Elevation (m)', label = 'upedonid', name = 'hzname',
             width = 0.15, spacing = 'relative',
             fix.relative.pos = list(maxIter=6000, adj=0.2, thresh=0.7))

plotTransect(mineralKing, xy, grad.var.name = 'elev_field', crs = crs.utm,
             grad.axis.title = 'Elevation (m)', label = 'upedonid', name = 'hzname',
             width = 0.2, spacing = 'relative',
             fix.relative.pos = list(maxIter = 6000, adj = 0.2, thresh = 0.6),
             name.style = 'center-center')

par(op)
  
}
#> Loading required package: sf
#> Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.4.0; sf_use_s2() is TRUE


#> 589 iterations


#> 980 iterations

#> 501 iterations

# }

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