strat.plot: Plot a stratigraphic diagram

In nsj3/rioja: Analysis of Quaternary Science Data

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, ...)

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.

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.

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.

Author(s)

Steve Juggins

See Also

chclust.

Examples

library(vegan) ## decorana
data(RLGH)
## Not run: 
# create appropriately sized graphics window
windows(width=12, height=7) # quartz() on Mac, X11 on linux

## End(Not run)
# 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")

nsj3/rioja documentation built on Oct. 24, 2023, 1:37 a.m.