strat.plot: Plot a stratigraphic diagram

Description

Plots a diagram of multiple biological, physical or chemical parameters agains depth or time, as used in geology & palaeoecology.

Usage

strat.plot (d, yvar=NULL, scale.percent=FALSE, graph.widths=1, minmax=NULL, 
            scale.minmax=TRUE, xLeft=0.07, xRight=1, yBottom=0.07, 
            yTop=0.8, title="", cex.title=1.8, y.axis=TRUE, x.axis=TRUE,
            min.width=5, ylim=NULL, y.rev=FALSE, y.tks=NULL, y.tks.labels=NULL, 
            ylabel="", cex.ylabel=1, cex.yaxis=0.8, xSpace=0.01, x.pc.inc=10, 
            x.pc.lab=TRUE, x.pc.omit0=TRUE, wa.order="none", plot.line=TRUE, 
            col.line="black", lwd.line=1, col.symb="black", plot.bar=TRUE, 
            lwd.bar=1, col.bar="grey", sep.bar=FALSE, bar.back=FALSE,
            plot.poly=FALSE, col.poly="grey", col.poly.line=NA, lwd.poly=1,
            plot.symb=FALSE, symb.pch=19, symb.cex=1, x.names=NULL, cex.xlabel=1.1, 
            srt.xlabel=90, mgp=NULL, ylabPos=2, cex.axis=.8, clust=NULL, clust.width=0.1,
            orig.fig=NULL, exag=FALSE, exag.mult=5, col.exag="grey90", exag.alpha=0.2, 
            col.bg=NULL, fun1=NULL, fun2=NULL, add=FALSE, omitMissing=TRUE, ...)
addZone (x, upper, lower=NULL, ...)
addClustZone(x, clust, nZone, ...)

Value

Returns (invisibly) a list containing the following objects:

box: Vector of 4 values giving the coordinates of the left, right, bottom and top of the plotting area, in relative units.
usr: Ranges of the plotting area, in data units.
yvar: Variable used for the y-axis.
ylim: Limits of the y-axis.
figs: list of coordinates of each curve, in relative units.

Arguments

d: a matrix or data frame of variables to plot.
yvar: a vector of depths or ages to use for the y-axis (defaults to sample number).
scale.percent: logical to scale x-axes for (biological) percentage data.
graph.widths: a vector of relative widths for each curve, used if scale.percent=FALSE.
minmax: 2 * nvar matrix of min and max values to scale each curve if scale.percent=FALSE.
scale.minmax: logical to show only min and max values on x-axes (to avoid label crowding).
xLeft, xRight, yBottom, yTop: x, y position of plot on page, in relative units.
title: main title for plot.
x.names: character vector of names for each graph, of same length as ncol(d).
cex.title: size of label for title.
y.axis: logical to control drawing of left-hand y-axis scale. Defaults to TRUE.
x.axis: logical or logical vector to control drawing of x-axes. Defaults to TRUE.
min.width: minimum upper value of x-axis when scaled for percent data.
ylim: numeric vector of 2 values to control limist of y-axis. Defaults to data range.
y.rev: logical to reverse y-axis. Defaults to FALSE.
y.tks: numerical vector listing values of y-axis ticks.
y.tks.labels: character vector listing values of y-axis labels.
ylabel: label for y-axis.
ylabPos: position for y-axis label.
cex.ylabel, cex.yaxis: text size for y-axis labels and values.
xSpace: space between graphs, in relative units.
x.pc.inc: increment for x-axis values when scale.percent is TRUE.
x.pc.lab: logical to control drawing of x-axis values when scale.percent is TRUE.
x.pc.omit0: logical to omit initial zero x-axis label when scale.percent is TRUE.
wa.order: "none", "topleft" or "bottomleft", to sort variables according to the weighted average with y.
plot.line, plot.poly, plot.bar, plot.symb: logical flags to plot graphs as lines, silhouettes, bars or symbols.
col.line, col.poly.line: colour of lines and silhouette outlines. Can be a single colour or a vector of colours, one for each graph.
col.poly: silhouette fill colour. Can be a single colour or a vector of colours, one for each graph.
lwd.line, lwd.poly, lwd.bar: line widths for line, silhouette or bar graphs.
col.bar: colour of bars in a bar graph. col.bar can be a vector to specify colours of individual bars or graphs.
col.symb: symbol colour.
sep.bar: If true, colours in col.bar are applied to individual bars, otherwise individual graphs.
bar.back: logical to plot bars behind (TRUE) or on top (FALSE: default) of curves.
cex.xlabel: size of label for variable names.
srt.xlabel: rotation angle for variable names.
symb.pch, symb.cex: symbol type / size.
exag: logical to add exaggerated curves when plot.poly=TRUE. Can be a single value or a vector to add exaggeration to individual curves.
exag.mult: multiplier for exaggerated curves. Can be a single value or a vector to control exaggeration to individual curves.
col.exag: colour for exaggerated curves. Can be a single value, a vector to control colour of individual curves, or "auto" for transparent version of main curve.
exag.alpha: alpha channel for transparent exaggerated curves when col.exag="auto".
mgp: value of mgp for x-axes. See par for details.
cex.axis: text size for x-axis labels. See par for details.
clust: an constrained classification object of class chclust to add to plot.
fun1, fun2: custom functions to add additional features to curve. Can be a single function applied to all curves or a vector to apply individual functions to individual curves. fun1 draws behind curves, fun2 draws on top of curves.
clust.width: width of dendrogram to add to right of plot, in relative units.
orig.fig: fig values to specify area of window in which to place diagram. See par for details. Defaults to whole window.
add: logical to contol drawing of new page. See par for details. Defaults to FALSE in which a call to strat.plot will start a new diagram. Set to TRUE to add a diagram to an existing plot.
x: a stratigraphic diagram object produced by strat.plot.
upper, lower: upper and (optional) lower limits of a zone to add to an existing stratigraphic diagram.
nZone: number of zones to draw.
omitMissing: remove missing values before plotting. Defaults to TRUE.
col.bg: background colour for each curve.
...: further graphical arguments.

Author

Steve Juggins

Details

strat.plot plots a series of variables in a stratigraphic diagram. Diagrams can be plotted as line graphs and / or bar charts. Samples are plotted on the y-axis by sample number by default but may be plotted against sample age or depth by specifying a variable for yvar. Margins of the plotting area can be changed using xLeft, xRight, yBottom and yTop. A dendrogram produced by chclust can be added to the right of the diagram.

The function addZone can be used to add a horizontal line or box to an existing plot, and addClustZone will add a specified number of zones from a dendrogram (see examples).

The function uses fig to split the screen and may be incompatible with par(mfrow) and split.screen.

Examples

Run this code

library(vegan) ## decorana
data(RLGH)
if (FALSE) {
# create appropriately sized graphics window
windows(width=12, height=7) # quartz() on Mac, X11 on linux
}
# remove less abundant taxa
mx <- apply(RLGH$spec, 2, max)
spec <- RLGH$spec[, mx > 3]
depth <- RLGH$depths$Depth
#basic stratigraphic plot
strat.plot(spec, y.rev=TRUE)
#scale for percentage data
strat.plot(spec, y.rev=TRUE, scale.percent=TRUE)
# plot by sample depth
strat.plot(spec, yvar = depth, y.rev=TRUE, scale.percent=TRUE,
title="Round Loch of Glenhead", ylabel="Depth (cm)")
# add a dendromgram from constrained cluster analysis
diss <- dist(sqrt(RLGH$spec/100)^2)
clust <- chclust(diss, method="coniss")
# broken stick model suggest 3 significant zones
bstick(clust)
x <- strat.plot(spec, yvar = depth, y.rev=TRUE,
scale.percent=TRUE, title="Round Loch of Glenhead", ylabel="Depth (cm)",
clust=clust)
# add zones
addClustZone(x, clust, 3, col="red")
# use fig to contol diagram size and position
x <- strat.plot(spec, xRight = 0.7, yvar = depth, y.rev=TRUE,
scale.percent=TRUE, title="Round Loch of Glenhead", ylabel="Depth (cm)")
# add curves for first two DCA components of diatom data
dca <- decorana(spec, iweigh=1)
sc <- scores(dca, display="sites", choices=1:2)
strat.plot(sc, xLeft = 0.7, yvar = depth, y.rev=TRUE, xRight=0.99,
y.axis=FALSE, clust=clust, clust.width=0.08, add=TRUE)

# Use custom function to add smooth to curve

sm.fun <- function(x, y, i, nm) {
  tmp <- data.frame(x=y, y=x)
  tmp <- na.omit(tmp)
  lo <- lowess(tmp, f=0.3)
  lines(lo$y, lo$x, col="red", lwd=1)
}

x <- strat.plot(spec, yvar = depth, y.rev=TRUE, scale.percent=TRUE, 
title="Round Loch of Glenhead", ylabel="Depth (cm)", fun1=sm.fun)

# Pollen diagram using built-in Abernethy Forest dataset
data(aber)
depth <- aber$ages$Age
spec <- aber$spec

# basic silhouette plot
strat.plot(spec, yvar = depth, y.rev=TRUE, scale.percent=TRUE, ylabel="Depth (cm)", 
plot.poly=TRUE, col.poly="darkgreen", col.poly.line=NA)

# now with horizontal lines at sample positions
strat.plot(spec, yvar = depth, y.rev=TRUE, scale.percent=TRUE, ylabel="Depth (cm)", 
plot.poly=TRUE, col.poly="darkgreen", plot.bar="Full", col.poly.line=NA)

# add exaggerated curves
strat.plot(spec, yvar = depth, y.rev=TRUE, scale.percent=TRUE, ylabel="Depth (cm)", 
plot.poly=TRUE, col.poly="darkgreen", plot.bar="Full", col.poly.line=NA, exag=TRUE)

# use different colours for trees
xx <- 1:ncol(spec)
cc <- ifelse(xx < 8, "darkgreen", "darkred")
strat.plot(spec, yvar = depth, y.rev=TRUE, scale.percent=TRUE, ylabel="Depth (cm)", 
plot.poly=TRUE, col.poly=cc, plot.bar="Full", col.poly.line=NA, exag=TRUE, col.exag="auto")

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