Creates a summary plot for a CTD section, with one panel for each value of
which.
# S4 method for section
plot(x, which = c(1, 2, 3, 99), eos, at = NULL,
labels = TRUE, grid = FALSE, contourLevels = NULL,
contourLabels = NULL, stationIndices, coastline = "best", xlim = NULL,
ylim = NULL, zlim = NULL, map.xlim = NULL, map.ylim = NULL,
clongitude, clatitude, span, projection = NULL, xtype = "distance",
ytype = "depth", ztype = "contour", zbreaks = NULL, zcol = NULL,
legend.loc = "bottomright", adorn = NULL, showStations = FALSE,
showStart = TRUE, showBottom = TRUE, axes = TRUE, mgp, mar, col, cex,
pch, debug, ...)a section object, e.g. as created by as.section
or read.section.
a list of desired plot types, as explained in “Details”.
There may be up to four panels in total, and the desired plots are placed in
these panels, in reading order. If only one panel is plotted, par is
not adjusted, which makes it easy to add to the plot with subsequent plotting
commands.
Character indication of the seawater equation of state
to use. The permitted choices are "gsw" and "unesco".
If eos is not supplied, it defaults to
getOption("oceEOS", default="gsw").
If NULL (the default), the x axis will indicate the distance
of the stations from the first in the section. (This may give errors in the
contouring routine, if the stations are not present in a geographical order.)
If a list, then it indicates the values at which stations will be plotted.
Either a logical, indicating whether to put labels on the x axis,
or a vector that is a list of labels to be placed at the x positions indicated
by at.
If TRUE, points are drawn at data locations.
Optional contour levels.
Optional contour labels.
Optional list of the indices of stations to use. Note
that an index is not a station number, e.g. to show the first 4
stations, use station.indices=1:4.
String giving the coastline to be used in a station map
The permitted choices are "best" (the default) to pick
a variant that suits the scale, "coastlineWorld" for the coarse
version that is provided by oce,
"coastlineWorldMedium" or "coastlineWorldFine" for two
coastlines provided by the ocedata package, or "none", to avoid
drawing a coastline.
Optional limit for x axis (only in sections, not map).
Optional limit for y axis (only in sections, not map)
Optional two-element numerical vector specifying the
limit on the plotted field. This is used only if ztype="image";
see also zbreaks and zcol.
Optional limits for station map; map.ylim is
ignored if map.xlim is provided.
Optional map centre position and span (km).
Parameter specifying map
projection; see mapPlot. If projection="automatic",
however, a projection is devised from the data, with stereographic if
the mean latitude exceeds 70N and mollweide otherwise.
Type of x axis, for contour plots, either "distance" for
distance (in km) to the first point in the section, "track" for distance
along the cruise track, "longitude", "latitude", or
"time". Note that if the x values are not in order, they will be put in
order (which may make no sense) and a warning will be printed.
Type of y axis for contour plots, either "pressure" for
pressure (in dbar, with zero at the surface) or "depth" for depth (in m
below the surface, calculated from pressure with swDepth).
String indicating whether to how to indicate the "z"
data (in the R sense, i.e. this could be salinity, temperature, etc; it does
not mean the vertical coordinate) The choices are: "contour" for
contours, "image" for an image (drawn with imagep with
filledContours=TRUE), or "points" to draw points.
In the first two cases, the data must be gridded, with identical pressures at
each station.
Indication of breaks and colours to be used if ztype="points" or
"image". If not provided, reasonable default are used. If zlim
is given but breaks is not given, then breaks is computed to
run from zlim[1] to zlim[2]. If zcol is a function,
it will be invoked with an argument equal to
1+length(zbreaks).
Location of legend, as supplied to legend, or
set to the empty string to avoid plotting a legend.
(Defunct)
An expression or vector of expressions that contain
R code that is to be executed immediately after each panel of the plot.
If the number of expressions matches the number of panels, then the
expressions are used for the corresponding panels; otherwise, the
expression list is extended to match the number of panels (i.e.
to obtain length(which) elements). Note that adorn
is a dangerous argument, because if the expressions contained
therein set up local storage, there is a chance of entirely
disrupting the plotting. For this reason, adorn was
marked as defunct in June 2016, and will be removed entirely
after the July CRAN release. Users with existing code that uses
adorn should simply plot the panels individually, and
use conventional R functions, e.g. lines etc.,
after each panel, to achieve the desired effect. (See
oce-defunct for notes on other deprecated or
defunct oce features.)
Logical indicating whether to draw station numbers on maps.
Logical indicating whether to indicate the first station with a different symbol than the others.
Logical indicating whether to draw the bottom, or a character
string indicating the method for plotting the bottom. The allowed methods are:
polygon, which fills the space to the bottom, or lines, which
draws lines from stations to the bottom, or points, which draws points
at the bottom.
Logical value indicating whether to draw axes.
A 3-element numerical vector to use for par(mgp), and also for
par(mar), computed from this. If not provided, this defaults to
getOption("oceMgp").
Value to be used with par("mar"). If not provided,
a default is set up.
Colour, which defaults to par("col").
Numerical character-expansion factor, which defaults to par("cex").
Indication of symbol type; defaults to par("pch").
an integer specifying whether debugging information is
to be printed during the processing. This is a general parameter that
is used by many oce functions. Generally, setting debug=0
turns off the printing, while higher values suggest that more information
be printed. If debug is not supplied, it defaults to
getOption("oceDebug").
Optional arguments passed to the contouring function, e.g. using
labcex=1 will increase the size of contour labels.
If the original section was gridded, the return value is that section. Otherwise, the gridded section that was constructed for the plot is returned. In both cases, the value is returned silently. The purpose of returning the section is to enable subsequent processing of the grid, including adding elements to the plot.
The type of plot is governed by which, as follows.
which=1 or "temperature" for temperature contours (the default)
which=2 or "salinity" for salinity contours
which=3 or "sigmaTheta" for sigma-theta contours
which=4 or "nitrate" for nitrate concentration contours
which=5 or "nitrite" for nitrite concentration contours
which=6 or "oxygen" for oxygen concentration contours
which=7 or "phosphate" for phosphate concentration contours
which=8 or "silicate" for silicate concentration contours
which=9 or "u" for eastward velocity
which=10 or "uz" for vertical derivative of eastward velocity
which=11 or "v" for northward velocity
which=12 or "vz" for vertical derivative of northward velocity
which=20 or "data" for a dot for each data location
which=99 or "map" for a location map
The y-axis for the contours is pressure, plotted in the conventional reversed
form, so that the water surface appears at the top of the plot. The x-axis is
more complicated. If at is not supplied, then the routine calculates x
as the distance between the first station in the section and each of the other
stations. (This will produce an error if the stations are not ordered
geographically, because the contour routine cannot handle
non-increasing axis coordinates.) If at is specified, then it is taken
to be the location, in arbitrary units, along the x-axis of labels specified by
labels; the way this works is designed to be the same as for
axis.
The documentation for section-class explains the
structure of section objects, and also outlines the other functions dealing
with them.
Other functions that plot oce data: plot,adp-method,
plot,adv-method,
plot,amsr-method,
plot,argo-method,
plot,bremen-method,
plot,cm-method,
plot,coastline-method,
plot,ctd-method,
plot,gps-method,
plot,ladp-method,
plot,lisst-method,
plot,lobo-method,
plot,met-method,
plot,odf-method,
plot,rsk-method,
plot,satellite-method,
plot,sealevel-method,
plot,tidem-method,
plot,topo-method,
plot,windrose-method,
plotProfile, plotScan,
plotTS, tidem-class
Other things related to section data: [[,section-method,
[[<-,section-method,
as.section,
handleFlags,section-method,
read.section, section-class,
sectionAddStation,
sectionGrid, sectionSmooth,
sectionSort, section,
subset,section-method,
summary,section-method
# NOT RUN {
library(oce)
data(section)
sg <- sectionGrid(section)
## 1. AO3 section, default fields.
plot(section)
## 2. Gulf Stream
GS <- subset(section, 109<=stationId&stationId<=129)
GSg <- sectionGrid(GS, p=seq(0, 2000, 100))
plot(GSg, which=c(1, 99), map.ylim=c(34, 42))
par(mfrow=c(2, 1))
plot(GS, which=1, ylim=c(2000, 0), ztype='points',
zbreaks=seq(0,30,2), pch=20, cex=3)
plot(GSg, which=1, ztype='image', zbreaks=seq(0,30,2))
par(mfrow=c(1, 1))
## 3. Image, with coloured dots to indicate grid-data mismatch.
plot(GSg, which=1, ztype='image')
T <- GS[['temperature']]
col <- oce.colorsJet(100)[rescale(T, rlow=1, rhigh=100)]
points(GS[['distance']],GS[['depth']],pch=20,cex=3,col='white')
points(GS[['distance']],GS[['depth']],pch=20,cex=2.5,col=col)
# }
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