plot.ctd {oce} | R Documentation

## Plot seawater CTD data

### Description

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.

### Usage

    ## S4 method for signature '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,
         clongitude, clatitude, span, showHemi=TRUE,
         lonlabel=NULL, latlabel=NULL, sides=NULL,
         projection=NULL, parameters=NULL, orientation=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='l',
         adorn=NULL,
         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, e.g. as read by `read.ctd`, or a list containing items named `salinity` and `temperature`.

`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 `x@metadata$deploymentType=="profile"` or if that item is non extant). If the deployment type is `"moored"` or `"thermosalinograph"`, the default will be `c(30, 3, 31, 5)`. If it is `"towyo"`, `c(30, 31, 32, 3)` will be used.

- `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`, 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

`col` | colour of lines or symbols
`fill` | a legacy parameter that will be permitted only temporarily; see “History”.
`borderCoastline` | colour of coastlines and international borders, passed to `plot.coastline` if a map is included in `which`.
`colCoastline` | fill colour of coastlines and international borders, passed to `plot.coastline` if a map is included in `which`. Set to `NULL` to avoid filling.
`eos` | 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` to load it on every call. So, if `plot.coastline` 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
`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
`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.
`lonlabel,latlabel,sides` | optional vectors of longitude and latitude to label on the indicated sides of plot, passed to `plot.coastline`. Using these arguments permits reasonably simple customization. If they are are not provided, reasonable defaults will be used.

`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.

`parameters` | parameters for map, as for `projection`.
`orientation` | orientation for map, as for `projection`.
`latlon.pch` | pch for sample location (ignored if no map plotted)
`latlon.cex` | cex for sample location (ignored if no map plotted)
`latlon.col` | col 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` | type of plot to draw, using the same scheme as `plot`.
`adorn` | list of expressions to be executed for the panels in turn, e.g. to adorn the plots. If the number matches the number of panels, then the strings are applied to the appropriate panels, as they are drawn from top-left to bottom-right. If only a single expression is provided, it is used for all panels. (See “Examples”.)
`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")`.
`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` | 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` | set to a positive value to get debugging information during processing.
`...` | 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 panels are controlled by the `which` argument. Normally, 4 panels are specified with the `which`, but it can also be useful to specify less than 4 panels, and then to draw other panels after this call.

If only 2 panels are requested, they will be drawn side by side.

If more than one panel is drawn, then on exit from `plot.ctd`, the value of `par` will be reset to the value it had before the function call. However, if only one panel is drawn, the adjustments to `par` made within `plot.ctd` are left in place, so that further additions may be made to the plot.

### History

Until February, 2016, `plot.cctd` relied on a now-defunct argument `fill` to control colours; `colCoastline` is to be used now, instead. Also, now it is possible to set the edge of coasts and international boundaries, with `borderCoastline`.

### Author(s)

Dan Kelley

### See Also

The documentation for `ctd-class` explains the structure of CTD objects, and also outlines the other functions dealing with them.

### Examples

    library(oce)
    data(ctd)
    plot(ctd)

[Package oce version 0.9-18 Index]