aqp (version 1.18)

SoilProfileCollection-plotting-methods: Profile Plot

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), font.id=2, 
print.id=TRUE, id.style='auto', plot.order=1:length(x), 
relative.pos=1:length(x), add=FALSE, 
scaling.factor=1, y.offset=0, x.idx.offset=0, n=length(x),
max.depth=ifelse(is.infinite(max(x)), 200, 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')), col.legend.cex=1,
n.legend=8,
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 or categorical 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

font.id

font style applied to profile id, default is 2 (bold)

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

relative.pos

a vector of relative positions along the x-axis, within {1, n}, ignores plot.order see details

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

col.legend.cex

scaling of color legend

n.legend

approximate number of classes used in numeric legend, max number of items per row in categorical legend

lwd

single numeric value: line width multiplier

lty

single integer: line style

default.color

default horizon fill color used when `color` attribute is NA

…

other arguments passed into lower level plotting functions

Value

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

Methods

signature(x = "SoilProfileCollection")

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 either numeric or categorical (either factor or character) values. In the second case, 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.

Adjustments to the legend can be specified via col.label (legend title), col.palette (palette of colors, automatically expanded), col.legend.cex (legend scaling), and n.legend (approximate number of classes for numeric variables, or, maximum number of legend items per row for categorical variables). Currently, plotSPC will only generate two rows of legend items. Consider reducing the number of classes if two rows isn't enough room.

Profile sketches can be added according to relative positions along the x-axis (vs. integer sequence) via relative.pos argument. This should be a vector of positions within {1,n} that are used for horizontal placement. Default values are 1:length(x). Care must be taken when both plot.order and relative.pos are used simultaneously: relative.pos specifies horizontal placement after sorting. addDiagnosticBracket and addVolumeFraction use the relative.pos values for subsequent annotation.

Relative positions that are too close will result in overplotting of sketches. Adjustments to relative positions such that overlap is minimized can be performed with fixOverlap(pos), where pos is the original vector of relative positions.

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.

References

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

See Also

fixOverlap, explainPlotSPC, SoilProfileCollection-class, pretty, hzDistinctnessCodeToOffset, addBracket, profileGroupLabels

Examples

# NOT RUN {
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))

# example using a categorical attribute
plot(sp2, color = "plasticity")

# 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)


##
## demonstrate adaptive legend
##

data(sp3)
depths(sp3) <- id ~ top + bottom

# make some fake categorical data
horizons(sp3)$fake.data <- sample(letters[1:15], size = nrow(sp3), replace=TRUE)

# better margins
par(mar=c(0,0,3,1))

# note that there are enough colors for 15 classes (vs. previous limit of 10)
# note that the legend is split into 2 rows when length(classes) > n.legend argument
plot(sp3, color='fake.data', name='fake.data', cex.names=0.8)

# make enough room in a single legend row
plot(sp3, color='fake.data', name='fake.data', cex.names=0.8, n.legend=15)

# }