plotProfile: Plot a ctd Profile

In oce: Analysis of Oceanographic Data

Plot a ctd Profile

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. The colors (col.salinity, etc.) are only used if two profiles appear on a plot.

Usage

plotProfile(
  x,
  xtype = "salinity+temperature",
  ytype = "pressure",
  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,
  sigmalim,
  N2lim,
  Rrholim,
  dpdtlim,
  timelim,
  plim,
  xlim,
  ylim,
  lwd = par("lwd"),
  xaxs = "r",
  yaxs = "r",
  cex = 1,
  pch = 1,
  useSmoothScatter = FALSE,
  df,
  keepNA = FALSE,
  type = "l",
  mgp = getOption("oceMgp"),
  mar,
  add = FALSE,
  inset = FALSE,
  debug = getOption("oceDebug", 0),
  ...
)

Arguments

x	a ctd object.
xtype	item(s) to be plotted on the x axis, either a character value taken from the following list, or a numeric vector of length matching the pressure field stored in x. (In the second case, as of version 1.7-11, a label is auto-constructed, unless the user supplied a character value for xlab.) "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 (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 sigma0 and the square of buoyancy frequency within a single axis frame. "density+dpdt" Profile of sigma0 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. "sigma0", "sigma1", "sigma2", "sigma3" and "sigma4" Profile of potential density referenced to 0dbar (i.e. the surface), 1000dbar, 2000dbar, 3000dbar, and 4000dbar. "spice", "spiciness0" "spiciness1" or "spiciness2" Profile of named quantity. For spice, swSpice() is called with the eos argument set to "unesco". Otherwise, gsw::gsw_spiciness0()', gsw::gsw_spiciness1()' or gsw::gsw_spiciness2()' is called. "Rrho" Profile of Rrho, defined in the diffusive sense. "RrhoSF" Profile of Rrho, defined in the salt-finger sense.
ytype	variable to use on y axis. The valid choices are: "pressure" (the default), "z", "depth", "sigmaTheta" and "sigma0".
eos	equation of state to be used, either "unesco" or "gsw".
lty	line type for the profile.
xlab	optional label for x axis (at top of plot). If not provided, a label is inferred from the value of xtype. For the user-supplied case, bear in mind that the easy way to get units is to use an expression, e.g. xlab=expression("Acceleration ["*m/s^2*"]").
ylab	optional label for y axis. See xlab for a note on units. Setting ylab="" prevents labelling the axis.
col	color for a general profile.
col.salinity	color for salinity profile (see “Details”).
col.temperature	color for temperature (see “Details”).
col.rho	color for density (see “Details”).
col.N2	color for square of buoyancy frequency (see “Details”).
col.dpdt	color for dP/dt.
col.time	color for delta-time.
pt.bg	inside color for symbols with pch in 21:25
grid	logical, set to TRUE to get a grid.
col.grid	color for grid.
lty.grid	line type for grid.
Slim	optional limit for the salinity axis, which can either represent Practical Salinity or Absolute Salinity.
Clim	optional limit for the conductivity axis.
Tlim	optional limit for the temperature axis, which can represent in-situ temperature, potential temperature, or Conservative Temperature.
densitylim	optional limit for density axis.
sigmalim	optional limit for the density-anomaly axis, which can represent sigmaTheta, sigma0, sigma1, sigma2, sigma3 or sigma4.
N2lim	optional limit for the N2 axis.
Rrholim	optional limit for the density ratio axis.
dpdtlim	optional limit for the dp/dt axis.
timelim	optional limit for the delta-time axis.
plim	optional limit for the pressure axis, ignored unless ytype=="pressure", in which case it takes precedence over ylim.
xlim	optional limit for x axis, which can apply to any plot type. This is ignored if the plotted x variable is something for which a limit may be specified with an argument, e.g. xlim is ignored for a salinity profile, because Slim ought to be given in such a case.
ylim	optional limit for y axis, which can apply to any plot type, although is overridden by plim if ytype is "pressure" or by densitylim if ytype is "sigmaTheta".
lwd	line width 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	Four-element numerical value to be used to set the plot margins, with a call to par(mar) prior to the plot. If this is not supplied, a reasonable default will be set up.
add	A logical value 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	A logical value indicating whether to draw an inset plot. Setting this to TRUE will prevent the present function from adjusting the 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.

Value

None.

Author(s)

Dan Kelley

See Also

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

Other functions that plot oce data: download.amsr(), 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,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, 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, ctd-class, ctd.cnv.gz, ctdDecimate(), ctdFindProfiles(), ctdFindProfilesRBR(), ctdRaw, ctdRepair(), ctdTrim(), ctd_aml.csv.gz, d200321-001.ctd.gz, d201211_0011.cnv.gz, handleFlags,ctd-method, initialize,ctd-method, initializeFlagScheme,ctd-method, oceNames2whpNames(), oceUnits2whpUnits(), plot,ctd-method, plotScan(), plotTS(), read.ctd(), read.ctd.aml(), read.ctd.itp(), read.ctd.odf(), read.ctd.odv(), read.ctd.saiv(), read.ctd.sbe(), read.ctd.ssda(), read.ctd.woce(), read.ctd.woce.other(), setFlags,ctd-method, subset,ctd-method, summary,ctd-method, woceNames2oceNames(), woceUnit2oceUnit(), write.ctd()

Examples

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

oce documentation built on Sept. 11, 2024, 7:09 p.m.