introduction
latticeExtra is an R package (i.e. a package for the R statistical computing environment), providing functions for generating statistical graphics. It extends the Lattice framework (lattice package), which is an implementation of Trellis graphics in R.
Many of the functions and datasets in latticeExtra are described in Deepayan Sarkar's book, Lattice: Multivariate Data Visualization with R. The book web site also includes figures and code.
This site serves as a reference for the R functions and datasets in the package. The help pages for all functions are also available as a PDF document -- the "Reference manual" -- from any CRAN mirror (see link below).
The package is maintained by Deepayan Sarkar and Felix Andrews.
For more information, see
index
| ancestry | Modal ancestry by County according to US 2000 Census |
| as.layer | Overlay panels of Trellis plots on same or different scales |
| biocAccess | Hourly access attempts to Bioconductor website |
| combineLimits | Combine axis limits across margins |
| c.trellis | Merge trellis objects, using same or different scales |
| custom.theme | Create a lattice theme based on specified colors |
| dendrogramGrob | Create a Grob Representing a Dendrogram |
| doubleYScale | Draw two plot series with different y scales |
| EastAuClimate | Climate of the East Coast of Australia |
| ecdfplot | Trellis Displays of Empirical CDF |
| ggplot2like | A ggplot2-like theme for Lattice |
| gvhd10 | Flow cytometry data from five samples from a patient |
| horizonplot | Plot many time series in parallel |
| layer | Add layers to a lattice plot, optionally using a new data source |
| mapplot | Trellis displays on Maps a.k.a. Choropleth maps |
| marginal.plot | Display marginal distributions |
| panel.2dsmoother | Plot a smooth approximation of z over x and y. |
| panel.3dmisc | Miscellanous panel utilities for three dimensional Trellis Displays |
| panel.ablineq | Draw a line with a label, by default its equation |
| panel.ellipse | Lattice panel function to fit and draw a confidence ellipsoid from bivariate data. |
| panel.key | Draw a simple key inside a panel of a lattice plot. |
| panel.levelplot.points | Panel functions for level-coded irregular points |
| panel.quantile | Plot a quantile regression line with standard error bounds. |
| panel.scaleArrow | Draw a scale bar as an arrow, labelled with its length in plot units. |
| panel.smoother | Plot a smoothing line with standard error bounds. |
| panel.tskernel | Calculate and plot smoothed time series. |
| panel.xblocks | Plot contiguous blocks along x axis. |
| panel.xyarea | Plot series as filled polygons. |
| postdoc | Reasons for Taking First Postdoctoral Appointment |
| resizePanels | Resize panels to match data scales |
| rootogram | Trellis Displays of Tukey's Hanging Rootograms |
| scale.components | Custom lattice axis scales |
| SeatacWeather | Daily Rainfall and Temperature at the Seattle-Tacoma Airport |
| segplot | Plot segments using the Trellis framework |
| style example | This is a sample plot to demonstrate different graphical settings (themes). |
| theEconomist.theme | Generate plots with style like The Economist. |
| tileplot | Plot a spatial mosaic from irregular 2D points |
| USAge | US national population estimates |
| USCancerRates | Rate of Death Due to Cancer in US Counties |
| useOuterStrips | Put Strips on the Boundary of a Lattice Display |
| xyplot.stl | Display stl fits with Lattice |
general statistical plots
rootogram
Trellis Displays of Tukey's Hanging Rootograms
One example:
rootogram(~x, dfun = function(x) dpois(x, lambda = 50))
segplot
Plot segments using the Trellis framework
One example:
segplot(reorder(factor(county), rate.male) ~ LCL95.male +
UCL95.male, data = subset(USCancerRates, state ==
"Washington"), draw.bands = FALSE, centers = rate.male)
ecdfplot
Trellis Displays of Empirical CDF
One example:
ecdfplot(~height | voice.part, data = singer)
marginal.plot
Display marginal distributions
One example:
marginal.plot(enviro[, 1:5], data = enviro, groups = is.windy,
auto.key = list(lines = TRUE))
functions of one variable
xyplot.stl
Display stl fits with Lattice
One example:
xyplot(stl(log(co2), s.window = 21), main = "STL decomposition of CO2 data")
panel.smoother
Plot a smoothing line with standard error bounds.
One example:
xyplot(y + y2 ~ x, xy) + glayer(panel.smoother(...))
panel.quantile
Plot a quantile regression line with standard error bounds.
One example:
update(xyplot(y ~ x, xy) + layer(panel.quantile(x,
y, tau = c(0.5, 0.9, 0.1), superpose = TRUE)),
auto.key = list(text = paste(c(50, 90, 10), "% quantile"),
points = FALSE, lines = TRUE))
panel.xblocks
Plot contiguous blocks along x axis.
One example:
xyplot(flow ~ flowdates, type = "l") + layer_(panel.xblocks(x,
months, col = c("lightgray", "#e6e6e6"), border = "darkgray"))
panel.xyarea
Plot series as filled polygons.
One example:
xyplot(ts.union(data = sunspot.year, lag10 = lag(sunspot.year,
10)), aspect = "xy", cut = list(n = 3, overlap = 0),
superpose = TRUE, panel = panel.superpose, panel.groups = function(...,
group.number) {
if (group.number ==....
panel.tskernel
Calculate and plot smoothed time series.
One example:
xyplot(sunspot.year) + layer(panel.tskernel(x, y,
width = 20, c = 3, col = 1, lwd = 2))
horizonplot
Plot many time series in parallel
One example:
horizonplot(dat, horizonscale = 10, colorkey = TRUE,
layout = c(1, 12), strip.left = FALSE, ylab = list(rev(colnames(dat)),
rot = 0, cex = 0.7)) + layer_(panel.fill(col = "gray90"),
panel.xblocks(..., col = "white"))
functions of two variables
mapplot
Trellis displays on Maps a.k.a. Choropleth maps
One example:
mapplot(county ~ log10(population), ancestry, map = county.map,
colramp = NULL)
tileplot
Plot a spatial mosaic from irregular 2D points
One example:
tileplot(z ~ x * y, xyz, border = "black", col.regions = grey.colors(100),
pch = ifelse(is.na(xyz$z), 4, 21), panel = function(...) {
panel.fill("hotpink")
panel.voronoi(...)
})
panel.levelplot.points
Panel functions for level-coded irregular points
One example:
levelplot(depth ~ long + lat | Magnitude, data = quakes.ordered,
panel = panel.levelplot.points, type = c("p",
"g"), aspect = "iso", prepanel = prepanel.default.xyplot)
panel.2dsmoother
Plot a smooth approximation of z over x and y.
One example:
levelplot(z ~ x * y, xyz, panel = panel.levelplot.points,
cex = 1.2) + layer_(panel.2dsmoother(..., n = 200))
panel.ellipse
Lattice panel function to fit and draw a confidence ellipsoid from bivariate data.
One example:
xyplot(Sepal.Length ~ Petal.Length, groups = Species,
data = iris, scales = "free", par.settings = list(superpose.symbol = list(pch = c(15:17)),
superpose.line = list(lwd = 2, lty = 1:3)),
panel = function(x, y, ...) {
pane....
dendrogramGrob
Create a Grob Representing a Dendrogram
One example:
levelplot(x[row.ord, col.ord], aspect = "fill", scales = list(x = list(rot = 90)),
colorkey = list(space = "left"), legend = list(right = list(fun = dendrogramGrob,
args = list(x = dd.col, ord = col.ord, side = "right",
si....
utilities
useOuterStrips
Put Strips on the Boundary of a Lattice Display
One example:
xyplot(mpg ~ disp | HP + factor(cyl), mtcars, layout = dimx,
par.strip.text = list(lines = 0.5), strip = new.strip,
strip.left = new.strip.left, par.settings = par.settings)
resizePanels
Resize panels to match data scales
One example:
dotplot(state.name ~ Frost | reorder(state.region,
Frost), data = state, layout = c(1, 4), scales = list(y = list(relation = "free")),
par.settings = list(layout.heights = list(panel = h),
layout.widths = list(panel = w)))
combineLimits
Combine axis limits across margins
One example:
xyplot(Price ~ EngineSize | reorder(AirBags, Price) +
Cylinders, data = Cars93, subset = Cylinders !=
"rotary" & Cylinders != "5", scales = list(relation = "free",
y = list(log = FALSE, tick.number = 3, rot = 0)),
xlab = "Engine S....
scale.components
Custom lattice axis scales
One example:
xyplot((1:200)/20 ~ (1:200)/20, type = c("p", "g"),
scales = list(x = list(log = 2), y = list(log = 10)),
xscale.components = xscale.components.fractions,
yscale.components = yscale.components.log10ticks)
panel.ablineq
Draw a line with a label, by default its equation
One example:
update(xyplot(ysim ~ xsim) + layer(panel.ablineq(lm(y ~
x), r.sq = TRUE, rot = TRUE, at = 0.8, pos = 3),
style = 1) + layer(panel.ablineq(lm(y ~ x + 0),
r.sq = TRUE, rot = TRUE, at = 0.8, pos = 1),
style = 2), auto.key = list(text....
panel.scaleArrow
Draw a scale bar as an arrow, labelled with its length in plot units.
One example:
xyplot(EuStockMarkets) + layer(panel.scaleArrow(x = 0.99,
append = " units", col = "grey", srt = 90, cex = 0.8))
panel.3dmisc
Miscellanous panel utilities for three dimensional Trellis Displays
One example:
cloud(VADeaths, panel.3d.cloud = panel.3dbars, xbase = 0.4,
ybase = 0.4, zlim = c(0, max(VADeaths)), scales = list(arrows = FALSE,
just = "right"), xlab = NULL, ylab = NULL,
col.facet = level.colors(VADeaths, at = do.breaks(range(....
panel.key
Draw a simple key inside a panel of a lattice plot.
One example:
xyplot(ozone ~ wind | equal.count(temperature, 2),
data = environmental) + layer(panel.loess(x,
y, span = 0.5), style = 1) + layer(panel.loess(x,
y, span = 1), style = 2) + layer(panel.key(c("span = 0.5",
"span = 1.0"), corner = c....
extended trellis framework
layer
Add layers to a lattice plot, optionally using a new data source
One example:
qua + layer_(panel.contourplot(x = gridlon, y = gridlat,
z = dist, contour = TRUE, subscripts = TRUE),
data = newdat)
as.layer
Overlay panels of Trellis plots on same or different scales
One example:
xyplot(fdeaths ~ mdeaths) + as.layer(bwplot(~mdeaths,
box.ratio = 0.2), y.same = FALSE)
doubleYScale
Draw two plot series with different y scales
One example:
doubleYScale(obj1 = obj1, obj2 = obj2, add.ylab2 = TRUE)
c.trellis
Merge trellis objects, using same or different scales
One example:
update(c(xyplot(lat ~ long | equal.count(depth, 3),
quakes, aspect = "iso", pch = ".", cex = 2, xlab = NULL,
ylab = NULL), histogram(quakes$depth), x.same = FALSE,
y.same = FALSE, layout = c(4, 1)), scales = list(at = list(NULL,
N....
styles
style example
This is a sample plot to demonstrate different graphical settings (themes).
One example:
xyplot(Sepal.Length + Sepal.Width ~ Petal.Length +
Petal.Width, iris, type = c("p", "r"), jitter.x = TRUE,
jitter.y = TRUE, factor = 5, auto.key = list(lines = TRUE,
rectangles = TRUE), legend = list(right = list(fun = "draw.color....
custom.theme
Create a lattice theme based on specified colors
One example:
xyplot(Sepal.Length + Sepal.Width ~ Petal.Length +
Petal.Width, iris, type = c("p", "r"), jitter.x = TRUE,
jitter.y = TRUE, factor = 5, auto.key = list(lines = TRUE,
rectangles = TRUE), legend = list(right = list(fun = "draw.color....
ggplot2like
A ggplot2-like theme for Lattice
One example:
bwplot(voice.part ~ height, data = singer)
theEconomist.theme
Generate plots with style like The Economist.
One example:
trellis.last.object() + layer_(panel.xblocks(x, x >=
1980, col = "#6CCFF6", alpha = 0.5)) + layer(panel.text(1988,
180, "Forecast", font = 3, pos = 2))
data
USAge
US national population estimates
One example:
xyplot(Population ~ Age | factor(Year), USAge.df,
groups = Sex, type = c("l", "g"), auto.key = list(points = FALSE,
lines = TRUE, columns = 2), aspect = "xy",
ylab = "Population (millions)", subset = Year %in%
seq(1905, 19....
USCancerRates
Rate of Death Due to Cancer in US Counties
One example:
mapplot(rownames(USCancerRates) ~ log(rate.male) +
log(rate.female), data = USCancerRates, map = map("county",
plot = FALSE, fill = TRUE, projection = "mercator"))
postdoc
Reasons for Taking First Postdoctoral Appointment
One example:
barchart(prop.table(postdoc, margin = 1), auto.key = TRUE,
xlab = "Proportion")
biocAccess
Hourly access attempts to Bioconductor website
One example:
xyplot(stl(ts(biocAccess$counts[1:(24 * 30)], frequency = 24),
"periodic"))
gvhd10
Flow cytometry data from five samples from a patient
One example:
histogram(~log2(FSC.H) | Days, gvhd10, xlab = "log Forward Scatter",
type = "density", nint = 50, layout = c(2, 4))
SeatacWeather
Daily Rainfall and Temperature at the Seattle-Tacoma Airport
One example:
doubleYScale(obj1 = temp, obj2 = rain, style1 = 0,
style2 = 3, add.ylab2 = TRUE, text = c("min. T",
"max. T", "rain"), columns = 3)
EastAuClimate
Climate of the East Coast of Australia
One example:
segplot(Latitude ~ WinterMinTemp + SummerMaxTemp,
EastAuClimate, main = "Average daily temperature ranges n of coastal Australian sites",
ylab = "Latitude", xlab = "Temperature (degrees C)",
par.settings = simpleTheme(lwd = 3, alpha ....