plotTransect: Arrange Profiles along a Transect

In sharpshootR: A Soil Survey Toolkit

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,
  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),
  ...
)

Arguments

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.

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.

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

Note

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

Author(s)

D.E. Beaudette

Examples

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('x_std', 'y_std'))
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 = 'pedon_id', 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 = '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, xy, grad.var.name = 'elev_field',
             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, xy, 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, xy, 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')

par(op)
  
}

sharpshootR documentation built on Aug. 24, 2023, 5:07 p.m.