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,
  add = FALSE,
  debug = getOption("oceDebug"),
  ...
)

Arguments

x

a ctd object.

which

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

col

Color of lines or symbols.

fill

A legacy parameter that will be permitted only temporarily; see “History”.

borderCoastline

Color of coastlines and international borders, passed to plot,coastline-method() if a map is included in which.

colCoastline

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.

eos

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

ref.lat

Latitude of reference point for distance calculation.

ref.lon

Longitude of reference point for distance calculation.

grid

Set TRUE to get a grid on all plots.

coastline

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.

Slim

Optional limits of salinity axes.

Clim

Optional limits of conductivity axes.

Tlim

Optional limits of temperature axes.

plim

Optional limits of pressure axes.

densitylim

Optional limits of density axis, whether that axis be horizontal or vertical.

N2lim

Optional limits of \(N^2\) axis.

Rrholim

Optional limits of \(R_rho\) axis.

dpdtlim

Optional limits of dP/dt axis.

timelim

Optional limits of delta-time axis.

lonlim

Optional limits of longitude axis of map (ignored if no map plotted) DEPRECATED 2014-01-07.

latlim

Optional limits of latitude axis of map (ignored if no map plotted) DEPRECATED 2014-01-07.

drawIsobaths

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).

clongitude

Center longitude.

clatitude

Center latitude.

span

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.

showHemi

Logical indicating whether to show hemisphere in axis tick labels.

lonlabels, latlabels

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

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.

latlon.pch

Symbol code for sample location (ignored if no map plotted).

latlon.cex

Symbol expansion factor for sample location (ignored if no map plotted).

latlon.col

Color of symbol for sample location (ignored if no map plotted).

cex

Size to be used for plot symbols (see par()).

cex.axis

Size factor for axis labels (see par()).

pch

Code for plotting symbol (see par()).

useSmoothScatter

Boolean, set to TRUE to use smoothScatter() instead of plot() to draw the plot.

df

Optional argument that is ignored except for plotting buoyancy frequency; in that case, it is passed to swN2() as the argument named df.

keepNA

Flag indicating whether to keep NA values in linegraphs, which will yield breaks in the lines.

type

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).

mgp

Three-element numerical vector specifying axis-label geometry, passed to par(). The default establishes tighter margins than in the usual R setup.

mar

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.

inset

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().

add

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.

debug

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.

See also

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"), levels=stn[['waterDepth']], col='red', lwd=2, add=TRUE)