SPC-plotting: Profile Plot

In aqp: Algorithms for Quantitative Pedology

Description

Generate a simple diagram of a soil profile, with annotated horizon names.

Usage

plotSPC(x, color='soil_color', width=0.2, name=NULL, label=idname(x),
alt.label=NULL, alt.label.col='black', cex.names=0.5, 
cex.depth.axis=cex.names, cex.id=cex.names+(0.2*cex.names), 
print.id=TRUE, id.style='auto', plot.order=1:length(x), add=FALSE, 
scaling.factor=1, y.offset=0, x.idx.offset=0, n=length(x),
max.depth=max(x), n.depth.ticks=5, shrink=FALSE, 
shrink.cutoff=3, abbr=FALSE, abbr.cutoff=5, divide.hz=TRUE, 
hz.distinctness.offset=NULL, hz.distinctness.offset.col='black', 
hz.distinctness.offset.lty=2, axis.line.offset=-2.5, 
plot.depth.axis=TRUE, density=NULL, col.label=color, 
col.palette = rev(brewer.pal(10, 'Spectral')), lwd=1, lty=1, 
default.color=grey(0.95), ...)

Arguments

x	a SoilProfileCollection object
color	the name of the column containing R-compatible color descriptions, or a column containing numeric data; see details
width	scaling of profile widths
name	the name of the (horizon-level) attribute containing horizon designation labels
label	the name of the (site-level) attribute used to identify profiles in the plot
alt.label	the name of a (site-level) attribute used for seconary annotation
alt.label.col	color used when printing secondary annotation
cex.names	character scaling applied to horizon names
cex.depth.axis	character scaling applied to depth scale
cex.id	character scaling applied to profile id
print.id	should the profile id be printed above each profile? (TRUE)
id.style	profile ID printing style: 'auto' (default) = simple heuristic used to select from: 'top' = centered above each profile, 'side' = 'along the top-left edge of profiles'
plot.order	a vector describing the order in which individual SoilProfile objects from the parent should be plotted
add	add to an existing figure
scaling.factor	vertical scaling of the profile heights
y.offset	vertical offset for top of profiles
x.idx.offset	integer specifying horizontal offset from 0
n	integer describing amount of space along x-axis to allocate, defaults to length(x)
max.depth	suggested lower depth boundary of plot
n.depth.ticks	suggested number of ticks in depth scale
shrink	should long horizon names be shrunk by 80% ?
shrink.cutoff	character length defining long horizon names
abbr	should the profile ID be abbreviated?
abbr.cutoff	suggested minimum length for abbreviated IDs
divide.hz	should horizons be divided with a thin black line? (default is TRUE)
hz.distinctness.offset	column name containing vertical offsets used to depict horizon boundary distinctness (same units as profiles)
hz.distinctness.offset.col	color used to encode horizon distinctness (default is 'black')
hz.distinctness.offset.lty	line style used to encode horizon distinctness (default is 2)
axis.line.offset	horizonatal offset applied to depth axis (default is -2.5)
plot.depth.axis	plot depth axis? (default is TRUE)
density	fill density used for horizon color shading, either a single integer or a column name containing integer values (default is NULL, no shading)
col.label	text printed above the color-coded legend
col.palette	color palette used to plot numeric data
lwd	single numeric value: line width multiplier
lty	single integert: line style
default.color	default horizon fill color used when 'color' attribute is NA
...	other arguments passed into lower level plotting functions

Details

Depth limits (max.depth) and number of depth ticks (n.depth.ticks) are *suggestions* to the pretty function. You may have to tinker with both parameters to get what you want.

The 'side' id.style is useful when plotting a large collection of profiles, and/or, when profile IDs are long.

If the column containing horizon designations is not specified (the name argument), a column (presumed to contain horizon designation labels) is guessed based on regular expression matching of the pattern 'name'– this usually works, but it is best to manual specify the name of the column containing horizon designations.

The color argument can either name a column containing R-compatible colors, possibly created via munsell2rgb, or column containing numeric values. In the second case, numeric values are converted into colors and displayed along with a simple legend above the plot. Note that this functionality makes several assumptions about plot geometry and is most useful in an interactive setting.

The x.idx.offset argument can be used to shift a collection of pedons from left to right in the figure. This can be useful when plotting several different SoilProfileCollection objects within the same figure. Space must be pre-allocated in the first plotting call, with an offset specified in the second call. See examples below.

Value

A new plot of soil profiles is generated, or optionally added to an existing plot.

Methods

signature(x = "SoilProfileCollection")

Author(s)

Dylan E. Beaudette

References

http://casoilresource.lawr.ucdavis.edu/

See Also

SoilProfileCollection-class, pretty, hzDistinctnessCodeToOffset, addBracket, profileGroupLabels

Examples

data(sp1)

# usually best to adjust margins
par(mar=c(0,0,3,0))

# add color vector
sp1$soil_color <- with(sp1, munsell2rgb(hue, value, chroma))

# promote to SoilProfileCollection
depths(sp1) <- id ~ top + bottom

# plot profiles
plot(sp1, id.style='side')

# title, note line argument:
title('Sample Data 1', line=1, cex.main=0.75)

# plot profiles without horizon-line divisions
plot(sp1, divide.hz=FALSE)

# add dashed lines illustrating horizon boundary distinctness
sp1$hzD <- hzDistinctnessCodeToOffset(sp1$bound_distinct)
plot(sp1, hz.distinctness.offset='hzD')

# plot horizon color according to some property
data(sp4)
depths(sp4) <- id ~ top + bottom
plot(sp4, color='clay')

# another example
data(sp2)
depths(sp2) <- id ~ top + bottom
site(sp2) <- ~ surface

# label with site-level attribute: `surface`
plot(sp2, label='surface', plot.order=order(sp2$surface))

# plot two SPC objects in the same figure
par(mar=c(1,1,1,1))
# plot the first SPC object and 
# allocate space for the second SPC object
plot(sp1, n=length(sp1) + length(sp2))
# plot the second SPC, starting from the first empty space
plot(sp2, x.idx.offset=length(sp1), add=TRUE)

Example output

This is aqp 1.25

Attaching package: ‘aqp’

The following object is masked from ‘package:stats’:

    filter

aqp documentation built on May 2, 2019, 4:51 p.m.