aqp (version 1.4)

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='name', alt.label=NULL,
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, 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, ...)

Arguments

x

a SoilProfileCollection object

color

the name of the column containing R-compatible color descriptions

width

scaling of profile widths

name

the name of the column containing the horizon designation

alt.label

the name of a column in @site used for seconary 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

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)

...

other arguments passed into lower level plotting functions

Value

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

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.

References

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

See Also

SoilProfileCollection-class, pretty, hzDistinctnessCodeToOffset

Examples

data(sp1)

# 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)

# plot profiles, using alternate profile ID label style
plot(sp1, id.style='side')

# 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
# RColorBrewer helps with nice colors
if(require(RColorBrewer)) {
  data(sp3)
  
  # setup colors
  cols <- rev(brewer.pal(8, 'Spectral'))
  cr <- colorRamp(cols)
  
  library(scales)
  # assign color based on clay content, rescaled to {0,1}
  sp3$soil_color <- rgb(cr(rescale(sp3$clay)), max=255)
  depths(sp3) <- id ~ top + bottom
  plot(sp3)
}