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,
    scale.minmax = TRUE, xLeft = 0.07, xRight = 1,
    yBottom = 0.07, yTop = 0.8, title = "", cex.title=1.8,
    y.axis=TRUE, min.width = 5, ylim = NULL, y.rev = FALSE,
    y.tks=NULL, ylabel = "", cex.ylabel=1, cex.yaxis=1,
    xSpace = 0.01, wa.order = "none", plot.line = TRUE,
    col.line = "black", lwd.line = 1, plot.bar = TRUE,
    lwd.bar = 1, col.bar = "grey", sep.bar = FALSE,
    cex.xlabel = 1.1, mgp=c(3,.5, 0), cex.axis=.8, clust = NULL,
    clust.width=0.1, orig.fig=NULL, add=FALSE, ...)
    
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.
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.
cex.title size of label for title.
y.axis logical to control drawing to left-hand y-axis scale. 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 / labels.
ylabel label for y-axis.
cex.ylabel text size for y-axis label.
cex.yaxis text size for y-axis values.
xSpace space between graphs, in relative units.
wa.order "none", "topleft" or "bottomleft", to sort variables according to the weighted average with y.
plot.line logical flag to plot a line graph.
col.line colour of lines in line graph.
lwd.line line weight (thickness) in line graph.
plot.bar logical flag to plot bars or horizonal lines.
lwd.bar bar weight (thickness) bar graph.
col.bar colour of bars in a bar graph. Can be a vector to specify colours of individual bars or graphs.
sep.bar If true, colours applied to individual bars, otherwise individual graphs.
cex.xlabel size of label for variable names.
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.
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.
... 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 otr 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 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.

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$depth$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)

[Package rioja version 0.5-6 Index]