Lattice Panel Function for Soil Profiles
Panel function for plotting grouped soil property data, along with upper and lower estimates of uncertainty.
This function can be used to replace panel.superpose when plotting
depth function data. When requested, contributing fraction data are printed
using colors the same color as corresponding depth function lines unless a
single color value is given via cf.col.
This function is not able to apply transformations (typically log = 10) applied in the scales argument to xyplot to upper/lower bounds. These will have to be manually applied. See examples.
panel.depth_function( x, y, id, upper = NA, lower = NA, subscripts = NULL, groups = NULL, sync.colors = FALSE, cf = NA, cf.col = NA, cf.interval = 20, ... )
x |
x values (generated by calling lattice function) |
y |
y values (generated by calling lattice function) |
id |
vector of id labels, same length as x and y–only required when plotting segments (see Details section) |
upper |
vector of upper confidence envelope values |
lower |
vector of lower confidence envelope values |
subscripts |
paneling indices (generated by calling lattice function) |
groups |
grouping data (generated by calling lattice function) |
sync.colors |
optionally sync the fill color within the region bounded by (lower–upper) with the line colors |
cf |
optionally annotate contributing fraction data at regular depth
intervals see |
cf.col |
optional color for contributing fraction values, typically used to override the line color |
cf.interval |
number of depth units to space printed contributing fraction values |
... |
further arguments to lower-level lattice plotting functions, see below |
D.E. Beaudette
library(lattice)
data(sp1)
# 1. plotting mechanism for step-functions derived from soil profile data
xyplot(
cbind(top, bottom) ~ prop,
data = sp1,
id = sp1$id,
panel = panel.depth_function,
ylim = c(250, -10),
scales = list(y = list(tick.number = 10)),
xlab = 'Property',
ylab = 'Depth (cm)',
main = 'panel.depth_function() demo'
)
# 1.1 include groups argument to leverage lattice styling framework
sp1$group <- factor(sp1$group, labels = c('Group 1', 'Group2'))
xyplot(
cbind(top, bottom) ~ prop,
groups = group,
data = sp1,
id = sp1$id,
panel = panel.depth_function,
ylim = c(250, -10),
scales = list(y = list(tick.number = 10)),
xlab = 'Property',
ylab = 'Depth (cm)',
main = 'panel.depth_function() demo',
auto.key = list(
columns = 2,
points = FALSE,
lines = TRUE
),
par.settings = list(superpose.line = list(col = c(
'Orange', 'RoyalBlue'
)))
)
# more complex examples, using step functions with grouped data
# better looking figures with less customization via tactile package
if(requireNamespace('tactile')) {
library(data.table)
library(lattice)
library(tactile)
# example data
data(sp6)
# a single profile
x <- sp6[1:5, ]
# wide -> long format
x.long <- melt(
data.table(x),
id.vars = c('id', 'top', 'bottom'),
measure.vars = c('sand', 'silt', 'clay')
)
# (optional) convert back to data.frame
x.long <- as.data.frame(x.long)
# three variables sharing a common axis
# factor levels set by melt()
xyplot(
cbind(top, bottom) ~ value | id,
groups = variable,
data = x.long,
id = x.long$id,
ylim = c(200, -5), xlim = c(10, 60),
scales = list(alternating = 1, y = list(tick.number = 10)),
par.settings = tactile.theme(superpose.line = list(lwd = 2)),
xlab = 'Sand, Silt, Clay (%)',
ylab = 'Depth (cm)',
panel = panel.depth_function,
auto.key = list(columns = 3, lines = TRUE, points = FALSE),
asp = 1.5
)
# all profiles
x <- sp6
# wide -> long format
x.long <- melt(
data.table(x),
id.vars = c('id', 'top', 'bottom'),
measure.vars = c('sand', 'silt', 'clay')
)
# (optional) convert back to data.frame
x.long <- as.data.frame(x.long)
# three variables sharing a common axis
# factor levels set by melt()
xyplot(
cbind(top, bottom) ~ value | id,
groups = variable,
data = x.long,
id = x.long$id,
ylim = c(200, -5), xlim = c(0, 70),
scales = list(alternating = 1, y = list(tick.number = 10)),
par.settings = tactile.theme(superpose.line = list(lwd = 2)),
xlab = 'Sand, Silt, Clay (%)',
ylab = 'Depth (cm)',
panel = panel.depth_function,
auto.key = list(columns = 3, lines = TRUE, points = FALSE),
as.table = TRUE
)
xyplot(
cbind(top, bottom) ~ value,
groups = variable,
data = x.long,
id = x.long$id,
ylim = c(200, -5), xlim = c(0, 70),
scales = list(alternating = 1, y = list(tick.number = 10)),
par.settings = tactile.theme(superpose.line = list(lwd = 2)),
xlab = 'Sand, Silt, Clay (%)',
ylab = 'Depth (cm)',
panel = panel.depth_function,
auto.key = list(columns = 3, lines = TRUE, points = FALSE),
as.table = TRUE
)
xyplot(
cbind(top, bottom) ~ value | variable,
groups = variable,
data = x.long,
id = x.long$id,
ylim = c(200, -5), xlim = c(0, 70),
scales = list(alternating = 1, y = list(tick.number = 10)),
par.settings = tactile.theme(superpose.line = list(lwd = 2)),
xlab = 'Sand, Silt, Clay (%)',
ylab = 'Depth (cm)',
panel = panel.depth_function,
auto.key = list(columns = 3, lines = TRUE, points = FALSE),
as.table = TRUE
)
xyplot(
cbind(top, bottom) ~ value | variable,
data = x.long,
id = x.long$id,
ylim = c(200, -5), xlim = c(0, 70),
scales = list(alternating = 1, y = list(tick.number = 10)),
par.settings = tactile.theme(superpose.line = list(lwd = 2)),
xlab = 'Sand, Silt, Clay (%)',
ylab = 'Depth (cm)',
panel = panel.depth_function,
auto.key = list(columns = 3, lines = TRUE, points = FALSE),
as.table = TRUE
)
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