plotProfile {oce} | R Documentation

## Plot a profile, with decreasing pressure on the y axis

### Description

Plot a profile, showing variation of some quantity (or quantities) with pressure, using the oceanographic convention of putting lower pressures nearer the top of the plot. This works for any `oce` object that has a pressure column in its `data` slot.

### Usage

    plotProfile(x,
        xtype="salinity+temperature",
        ytype=c("pressure", "z", "depth", "sigmaTheta"),
        eos=getOption("oceEOS", default="gsw"),
        lty=1,
        xlab=NULL, ylab=NULL,
        col="black",
        col.salinity="darkgreen",
        col.temperature="red",
        col.rho="blue",
        col.N2="brown",
        col.dpdt="darkgreen",
        col.time="darkgreen",
        pt.bg="transparent",
        grid=TRUE,
        col.grid="lightgray",
        lty.grid="dotted",
        Slim, Clim, Tlim, densitylim, N2lim, Rrholim, dpdtlim, timelim, plim, ylim,
        lwd=par("lwd"),
        xaxs="r", yaxs="r",
        cex=1, pch=1,
        useSmoothScatter=FALSE,
        df,
        keepNA=FALSE,
        type='l',
        mgp=getOption("oceMgp"),
        mar=c(1 + if (length(grep('\\+', xtype))) mgp[1] else 0,
              mgp[1]+1.5, mgp[1]+1.5, mgp[1]),
        add=FALSE, inset=FALSE,
        debug=getOption("oceDebug"),
        ...)

### Arguments

`x` | A `ctd` object, e.g. as read by `read.ctd`.

`xtype`

Item(s) plotted on the x axis, either a vector of length equal to that of `x@data$pressure` or a text code from the list below.

`"salinity"`

  Profile of salinity.

`"conductivity"`

  Profile of conductivity.

`"temperature"`

  Profile of in-situ temperature.

`"theta"`

  Profile of potential temperature.

`"density"`

  Profile of density (expressed as sigma_theta).

`"index"`

  Index of sample (very useful for working with `ctdTrim`).

`"salinity+temperature"`

  Profile of salinity and temperature within a single axis frame.

`"N2"`

  Profile of square of buoyancy frequency N^2, calculated with `swN2` with an optional argument setting of `df=length(x[["pressure"]])/4` to do some smoothing.

`"density+N2"`

  Profile of sigma-theta and the square of buoyancy frequency within a single axis frame.

`"density+dpdt"`

  Profile of sigma-theta and dP/dt for the sensor. The latter is useful in indicating problems with the deployment. It is calculated by first differencing pressure and then using a smoothing spline on the result (to avoid grid-point wiggles that result because the SBE software only writes 3 decimal places in pressure). Note that dP/dt may be off by a scale factor; this should not be a problem if there is a `time` column in the `data` slot, or a `sample.rate` in the `metadata` slot.

`"spice"`

  Profile of spice

`"Rrho"`

  Profile of Rrho, defined in the diffusive sense

`"RrhoSF"`

  Profile of Rrho, defined in the salt-finger sense

an expression

  an expression to be evaluated, in the calling environment, for some quantity; in this case, it makes sense to specify also `xlab`.

`ytype` | variable to use on y axis; note that `z` is the negative of `depth`.
`eos` | equation of state to be used, either `"unesco"` or `"gsw"`.
`xlab` | optional label for x axis (at top of plot).
`ylab` | optional label for y axis. Set to `""` to prevent labelling the axis.
`lty` | line type for the profile.
`col` | colour for a general profile.
`col.salinity` | colour for salinity profile (see “Details”).
`col.temperature` | colour for temperature (see “Details”).
`col.rho` | colour for density (see “Details”).
`col.N2` | colour for square of buoyancy frequency (see “Details”).
`col.dpdt` | colour for dP/dt.
`col.time` | colour for delta-time.
`pt.bg` | inside colour for symbols with `pch` in 21:25
`grid` | logical, set to `TRUE` to get a grid.
`col.grid` | colour for grid.
`lty.grid` | line type for grid.
`Slim` | Optional limit for S axis
`Clim` | Optional limit for conductivity axis
`Tlim` | Optional limit for T axis
`densitylim` | Optional limit for density axis
`N2lim` | Optional limit for N2 axis
`Rrholim` | Optional limit for Rrho axis
`dpdtlim` | Optional limit for dp/dt axis
`timelim` | Optional limit for delta-time axis
`plim` | Optional limit for pressure axis, ignored unless `ytype=="pressure"`, in which case it takes precedence over `ylim`.
`ylim` | Optional limit for y axis, which can apply to any plot type, although is overridden by `plim` if `ytype=="pressure"`.
`lwd` | lwd value for data line
`xaxs` | value of `par` `xaxs` to use
`yaxs` | value of `par` `yaxs` to use
`cex` | size to be used for plot symbols (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, passed to `swN2` if provided, and if a plot using N^2 is requested.
`keepNA` | FALSE
`type` | type of plot to draw, using the same scheme as `plot`.
`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")`.
`add` | a flag that controls whether to add to an existing plot. (It makes sense to use `add=TRUE` in the `panel` argument of a `coplot`, for example.)
`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`.
`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 other functions. A common example is to set `df`, for use in swN2 calculations.

### Details

The colours (`col.salinity`, etc.) are ony used if two profiles appear on a plot.

### Value

None.

### Author(s)

Dan Kelley

### See Also

`read.ctd` scans ctd information from a file, `plot.ctd` is a general plotting function for `ctd` objects, and `plotTS` plots a temperature-salinity diagrams.

### Examples

    library(oce)
    data(ctd)
    plotProfile(ctd, xtype="temperature")

[Package oce version 0.9-18 Index]