Plot CTD data, by default in a four-panel display showing (a) profiles of salinity and temperature, (b) profiles of density and the square of buoyancy frequency, (c) a TS diagram and (d) a coastline diagram indicating the station location.

# S4 method for ctd
plot(
x,
which,
col = par("fg"),
fill,
borderCoastline = NA,
colCoastline = "lightgray",
eos = getOption("oceEOS", default = "gsw"),
ref.lat = NaN,
ref.lon = NaN,
grid = TRUE,
coastline = "best",
Slim,
Clim,
Tlim,
plim,
densitylim,
N2lim,
Rrholim,
dpdtlim,
timelim,
lonlim,
latlim,
drawIsobaths = FALSE,
clongitude,
clatitude,
span,
showHemi = TRUE,
lonlabels = TRUE,
latlabels = TRUE,
projection = NULL,
latlon.pch = 20,
latlon.cex = 1.5,
latlon.col = "red",
cex = 1,
cex.axis = par("cex.axis"),
pch = 1,
useSmoothScatter = FALSE,
df,
keepNA = FALSE,
type,
mgp = getOption("oceMgp"),
mar = c(mgp[1] + 1.5, mgp[1] + 1.5, mgp[1] + 1.5, mgp[1] + 1),
inset = FALSE,
debug = getOption("oceDebug"),
...
)

## Arguments

x a ctd object. List of desired plot types, as given below. If which is not supplied, a default will be used. This default will be c(1,2,3,5) if the CTD is in profiling mode (i.e. if deploymentType in the metadata slot equals "profile", or is missing) or "moored"/"thermosalinograph", the default will be c(30, 3, 31, 5). If it is "towyo", c(30, 31, 32, 3) will be used. Details are as follows. which=1 or which="salinity+temperature" gives a combined profile of temperature and salinity which=2 or which="density+N2" gives a combined profile of $$\sigma_\theta$$ and $$N^2$$ which=3 or which="TS" gives a TS plot which=4 or which="text" gives a textual summary of some aspects of the data which=5 or which="map" gives a map plotted with plot,coastline-method(), with a dot for the station location. Notes near the top boundary of the map give the station number, the sampling date, and the name of the chief scientist, if these are known. Note that the longitude will be converted to a value between -180 and 180 before plotting. (See also notes about span.) which=5.1 as for which=5, except that the file name is drawn above the map which=6 or which="density+dpdt" gives a profile of density and $$dP/dt$$, which is useful for evaluating whether the instrument is dropping properly through the water column which=7 or which="density+time" gives a profile of density and time which=8 or which="index" gives a profile of index number (especially useful for ctdTrim()) which=9 or which="salinity" gives a salinity profile which=10 or which="temperature" gives a temperature profile which=11 or which="density" gives a density profile which=12 or which="N2" gives an $$N^2$$ profile which=13 or which="spice" gives a spiciness profile which=14 or which="tritium" gives a tritium profile which=15 or which="Rrho" gives an Rrho profile which=16 or which="RrhoSF" gives an RrhoSF profile which=17 or which="conductivity" gives a conductivity profile which=20 or which="CT" gives a Conservative Temperature profile which=21 or which="SA" gives an Absolute Salinity profile which=30 gives a time series of Salinity which=31 gives a time series of Temperature which=32 gives a time series of pressure which=33 gives a time series of sigmaTheta Color of lines or symbols. A legacy parameter that will be permitted only temporarily; see “History”. Color of coastlines and international borders, passed to plot,coastline-method() if a map is included in which. Fill color of coastlines and international borders, passed to plot,coastline-method() if a map is included in which. Set to NULL to avoid filling. String indicating the equation of state to be used, either "unesco" or "gsw". Latitude of reference point for distance calculation. Longitude of reference point for distance calculation. Set TRUE to get a grid on all plots. A specification of the coastline to be used for which="map". This may be a coastline object, whether built-in or supplied by the user, or a character string. If the later, it may be the name of a built-in coastline ("coastlineWorld", "coastlineWorldFine", or "coastlineWorldCoarse"), or "best", to choose a suitable coastline for the locale, or "none" to prevent the drawing of a coastline. There is a speed penalty for providing coastline as a character string, because it forces plot,coastline-method() to load it on every call. So, if plot,coastline-method() is to be called several times for a given coastline, it makes sense to load it in before the first call, and to supply the object as an argument, as opposed to the name of the object. Optional limits of salinity axes. Optional limits of conductivity axes. Optional limits of temperature axes. Optional limits of pressure axes. Optional limits of density axis, whether that axis be horizontal or vertical. Optional limits of $$N^2$$ axis. Optional limits of $$R_rho$$ axis. Optional limits of dP/dt axis. Optional limits of delta-time axis. Optional limits of longitude axis of map (ignored if no map plotted) DEPRECATED 2014-01-07. Optional limits of latitude axis of map (ignored if no map plotted) DEPRECATED 2014-01-07. An indication of whether to draw depth contours on maps, in addition to the coastline. The argument has no effect except for panels in which the value of which equals "map" or the equivalent numerical code, 5. If drawIsobaths is FALSE, then no contours are drawn. If drawIsobaths is TRUE, then contours are selected automatically, using pretty(c(0,300)) if the station depth is under 100m or pretty(c(0,5500)) otherwise. If drawIsobaths is a numerical vector, then the indicated depths are drawn. For plots drawn with projection set to NULL, the contours are added with contour() and otherwise mapContour() is used. To customize the resultant contours, e.g. setting particular line types or colors, users should call these functions directly (see e.g. Example 2). Center longitude. Center latitude. Optional span of map, in km. If not given, this will be determined as a small multiple of the distance to the nearest point of land, in an attempt to show some coastline in the plot. Logical indicating whether to show hemisphere in axis tick labels. Values that control the labelling of longitude and latitude along the sides of the plot, used only if projection is not NULL. See mapPlot() for details. Projection for map, if desired. If this is NULL, no projection will be used; the map will simply show longitude and latitude in a cartesian frame, scaled to retain shapes at the centre. If this is the string "automatic", then either a Mercator or Stereographic projection will be used, depending on whether the CTD station is within 70 degrees of the equator or at higher latitudes. Finally, if this is a string in the format used by mapPlot(), then it is is passed to that function. Symbol code for sample location (ignored if no map plotted). Symbol expansion factor for sample location (ignored if no map plotted). Color of symbol for sample location (ignored if no map plotted). Size to be used for plot symbols (see par()). Size factor for axis labels (see par()). Code for plotting symbol (see par()). Boolean, set to TRUE to use smoothScatter() instead of plot() to draw the plot. Optional argument that is ignored except for plotting buoyancy frequency; in that case, it is passed to swN2() as the argument named df. Flag indicating whether to keep NA values in linegraphs, which will yield breaks in the lines. The type of plot to draw, using the same scheme as plot(). If supplied, this is increased to be the same length as which, if necessary, and then supplied to each of the individual plot calls. If it is not supplied, then those plot calls use defaults (e.g. using a line for plotProfile(), using dots for plotTS(), etc). Three-element numerical vector specifying axis-label geometry, passed to par(). The default establishes tighter margins than in the usual R setup. Four-element numerical vector specifying margin geometry, passed to par(). The default establishes tighter margins than in the usual R setup. Note that the value of mar is ignored for the map panel of multi-panel maps; instead, the present value of par("mar") is used, which in the default call will make the map plot region equal that of the previously-drawn profiles and TS plot. Set to TRUE for use within plotInset(). The effect is to prevent the present function from adjusting margins, which is necessary because margin adjustment is the basis for the method used by plotInset(). Logical, indication of whether to add to an existing plot. This only works if length(which)=1, and it will yield odd results if the value of which does not match that in the previous plots. 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 one function calls another, it usually reduces the value of debug first, so that a user can often obtain deeper debugging by specifying higher debug values. Optional arguments passed to plotting functions. A common example is to set df, for use in swN2() calculations.

## Details

Creates a multi-panel summary plot of data measured in a CTD cast. The default values of which and other arguments are chosen to be useful for quick overviews of data. However, for detailed work it is common to call the present function with just a single value of which, e.g. with four calls to get four panels. The advantage of this is that it provides much more control over the display, and also it permits the addition of extra display elements (lines, points, margin notes, etc.) to the individual panels.

Note that panels that draw more than one curve (e.g. which="salinity+temperature" draws temperature and salinity profiles in one graph), the value of par("usr") is established by the second profile to have been drawn. Some experimentation will reveal what this profile is, for each permitted which case, although it seems unlikely that this will help much ... the simple fact is that drawing two profiles in one graph is useful for a quick overview, but not useful for e.g. interactive analysis with locator() to flag bad data, etc.

## History

Until February, 2016, plot,ctd-method() relied on a now-defunct argument fill to control colors; colCoastline is to be used now, instead. Also, now it is possible to set the color of coasts and international boundaries, with borderCoastline.

The documentation for ctd explains the structure of CTD 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,gps-method, plot,ladp-method, plot,landsat-method, plot,lisst-method, plot,lobo-method, plot,met-method, plot,odf-method, plot,rsk-method, plot,satellite-method, plot,sealevel-method, plot,section-method, plot,tidem-method, plot,topo-method, plot,windrose-method, plot,xbt-method, plotProfile(), plotScan(), plotTS(), tidem-class

Other things related to ctd data: CTD_BCD2014666_008_1_DN.ODF.gz, [[,ctd-method, [[<-,ctd-method, as.ctd(), cnvName2oceName(), ctd-class, ctd.cnv, ctdDecimate(), ctdFindProfiles(), ctdRaw, ctdTrim(), ctd, d200321-001.ctd, d201211_0011.cnv, handleFlags,ctd-method, initialize,ctd-method, initializeFlagScheme,ctd-method, oceNames2whpNames(), oceUnits2whpUnits(), plotProfile(), plotScan(), plotTS(), read.ctd.itp(), read.ctd.odf(), read.ctd.odv(), read.ctd.sbe(), read.ctd.woce.other(), read.ctd.woce(), read.ctd(), setFlags,ctd-method, subset,ctd-method, summary,ctd-method, woceNames2oceNames(), woceUnit2oceUnit(), write.ctd()

## Examples

## 1. simple plot
library(oce)
data(ctd)
plot(ctd)
## 2. how to customize depth contours
par(mfrow=c(1,2))
data(section)
stn <- section[["station", 105]]
plot(stn, which='map', drawIsobaths=TRUE)
plot(stn, which='map')data(topoWorld)
tlon <- topoWorld[["longitude"]]
tlat <- topoWorld[["latitude"]]
tdep <- -topoWorld[["z"]]
contour(tlon, tlat, tdep, drawlabels=FALSE,
levels=seq(1000,6000,1000), col='lightblue', add=TRUE)contour(tlon, tlat, tdep, vfont=c("sans serif", "bold"),