R: Plot a stratigraphic diagram

strat.plot {rioja}

R Documentation

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

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")

[Package rioja version 1.0-6 Index]