oce (version 0.9-19)

plot,section-method: Plot a Section

Description

Creates a summary plot for a CTD section, with one panel for each value of which.

Usage

"plot"(x, which = c(1, 2, 3, 99), eos = getOption("oceEOS", default = "gsw"), at = NULL, labels = TRUE, grid = FALSE, contourLevels = NULL, contourLabels = NULL, stationIndices, coastline = c("best", "coastlineWorld", "coastlineWorldMedium", "coastlineWorldFine", "none"), xlim = NULL, ylim = NULL, map.xlim = NULL, map.ylim = NULL, clongitude, clatitude, span, projection = NULL, xtype = c("distance", "track", "longitude", "latitude", "time"), ytype = c("depth", "pressure"), ztype = c("contour", "image", "points"), zbreaks = NULL, zcol = NULL, legend.loc = "bottomright", adorn = NULL, showStations = FALSE, showStart = TRUE, showBottom = TRUE, axes = TRUE, mgp = getOption("oceMgp"), mar = c(mgp[1] + 1, mgp[1] + 1, mgp[2] + 1, mgp[2] + 0.5), col = par("col"), cex = par("cex"), pch = par("pch"), debug = getOption("oceDebug"), ...)

Arguments

x

a section object, e.g. as created by as.section or read.section.

which

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.

eos

Character string indicating the equation of state to be used, either "unesco" or "gsw".

at

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.

labels

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.

grid

If TRUE, points are drawn at data locations.

contourLevels

Optional contour levels.

contourLabels

Optional contour labels.

stationIndices

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.

coastline

String giving the coastline to be used in a station map, or "best" to pick the one with highest resolution, or "none" to avoid drawing the coastline.

xlim

Optional limit for x axis (only in sections, not map).

ylim

Optional limit for y axis (only in sections, not map)

map.xlim, map.ylim

Optional limits for station map; map.ylim is ignored if map.xlim is provided.

clongitude, clatitude, span

Optional map centre position and span (km).

projection

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.

xtype

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.

ytype

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).

ztype

String indicating whether to use contours, an image, or points. In the first two cases, the data must be gridded, with identical pressures at each station.

zbreaks, zcol

Breaks and colours to be used if ztype="points" or "image". If not provided, a reasonable default is chosen. If zcol is a function, it will be invoked with an argument equal to 1+length(zbreaks). If zbreaks is not given, it defaults to a vector of length 200, with values spanning the data range.

legend.loc

Location of legend, as supplied to legend, or set to the empty string to avoid plotting a legend.

adorn

(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.)

showStations

Logical indicating whether to draw station numbers on maps.

showStart

Logical indicating whether to indicate the first station with a different symbol than the others.

showBottom

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.

axes

Logical value indicating whether to draw axes.

mgp

3-element numerical vector to use for par(mgp), and also for par(mar), computed from this. The default is tighter than the R default, in order to use more space for the data and less for the axes.

mar

Value to be used with par("mar").

col

Colour, as in par("col").

cex

Value to be used with par("cex"), for any use of points, e.g. for which="data".

pch

Value to be used with par("pch") (see cex, above.)

debug

A flag that turns on debugging. Set to 1 to get a moderate amount of debugging information, or to 2 to get more.

...

Optional arguments passed to the contouring function, e.g. using labcex=1 will increase the size of contour labels.

Value

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.

Details

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.

See Also

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

Examples

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)