plot.adp: Plot ADP data

Description

Plot ADP data

Usage

## S3 method for class 'adp':
plot(x, which=1:dim(x@data$v)[3],
     mode=c("normal", "diagnostic"),
     col, breaks,
     zlim,
     titles,
     lwd=par('lwd'),
     type='l',
     ytype=c("profile", "distance"),
     adorn=NULL,
     drawTimeRange=getOption("oceDrawTimeRange"),
     useSmoothScatter,
     missingColor="gray",
     mgp=getOption("oceMgp"),
     mar=c(mgp[1]+1.5,mgp[1]+1.5,1.5,1.5),
     mai.palette=rep(0, 4),
     tformat,
     marginsAsImage=FALSE,
     cex=par("cex"), cex.axis=par("cex.axis"), cex.main=par("cex.main"),
     xlim, ylim, 
     control,
     useLayout=FALSE,
     coastline="coastlineWorld", span=300,
     main="",
     grid=FALSE, grid.col="darkgray", grid.lty="dotted", grid.lwd=1,
     debug=getOption("oceDebug"),
     ...)

Arguments

an adp object, e.g. as read by read.adp.

which

list of desired plot types. These are graphed in panels running down from the top of the page. See Details for the meanings of various values of which.

mode

a string indicating whether to plot the conventional signal (normal) or or, in the special case of Aquadopp single-bin profilers, possibly the diagnostic signal. This argument is ignored except in the case of A

col

optional indication of colour(s) to use. If not provided, the default for images is oce.colorsPalette(128,1), and for lines and points is black.

breaks

optional breaks for colour scheme

zlim

a range to be used as the zlim parameter to the imagep call that is used to create the image. If omitted, zlim is set for each panel individually, to encompass the data

titles

optional vector of character strings to be used as labels for the plot panels. For images, these strings will be placed in the right hand side of the top margin. For timeseries, these strings are ignored. If this is provided, its length

lwd

if the plot is of a time-series or scattergraph format with lines, this is used in the usual way; otherwise, e.g. for image formats, this is ignored.

type

if the plot is of a time-series or scattergraph format, this is used in the usual way, e.g. "l" for lines, etc.; otherwise, as for image formats, this is ignored.

ytype

character string controlling the type of the y axis for images (ignored for time series). If "distance", then the y axis will be distance from the sensor head, with smaller distances nearer the bottom of the graph. If "pro

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 onl

drawTimeRange

boolean that applies to panels with time as the horizontal axis, indicating whether to draw the time range in the top-left margin of the plot.

useSmoothScatter

boolean that indicates whether to use smoothScatter in various plots, such as which="uv". If not provided a default is used, with s

missingColor

colour used to indicate NA values in images (see imagep); set to NULL to avoid this indication.

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").

mai.palette

margins, in inches, to be added to those calculated for the palette; alter from the default only with caution

tformat

optional argument passed to oce.plot.ts, for plot types that call that function. (See strptime for the format used.)

marginsAsImage

boolean, TRUE to put a wide margin to the right of time-series plots, even if there are no images in the which list. (The margin is made wide if there are some images in the sequence.)

cex

size of labels on axes; see par("cex").

cex.axis

see par("cex.axis").

cex.main

see par("cex.main").

xlim

optional 2-element list for xlim, or 2-column matrix, in which case the rows are used, in order, for the panels of the graph.

ylim

optional 2-element list for ylim, or 2-column matrix, in which case the rows are used, in order, for the panels of the graph.

control

optional list of parameters that may be used for different plot types. Possibilities are drawBottom (a boolean that indicates whether to draw the bottom) and bin (a numeric giving the index of the bin on which to ac

useLayout

set to FALSE to prevent using layout to set up the plot. This is needed if the call is to be part of a sequence set up by e.g. par(mfrow).

coastline

a coastline object, or a character string naming one. This is used only for which="map". See notes at plot.ctd for more information on built-in coastlines.

span

approximate span of map in km

main

main title for plot, used just on the top panel, if there are several panels.

grid

if TRUE, a grid will be drawn for each panel. (This argument is needed, because calling grid after doing a sequence of plots will not result in useful results for the individual

grid.col

colour of grid

grid.lty

line type of grid

grid.lwd

line width of grid

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 plotting functions. For example, supplying despike=TRUE will cause time-series panels to be de-spiked with despike. Another common action is to set

Value

A list is silently returned, containing xat and yat, values that can be used by oce.grid to add a grid to the plot.

Details

Creates a summary plot of data measured by an acoustic doppler profiler. This may have one or more panels, with the content being controlled by the which argument.

which=1:4(orwhich="u1"to"u4") yield a distance-time image plot of a velocity component. Ifxis inbeamcoordinates (signalled byx@metadata$oce.coordinate=="beam"), this will be the beam velocity, labelledb[1]etc. Ifxis in xyz coordinates (sometimes called frame coordinates, or ship coordinates), it will be the velocity component to the right of the frame or ship (labelleduetc). Finally, ifxis in"enu"coordinates, the image will show the the eastward component (labelledeast). Ifxis in"other"coordinates, it will be component corresponding to east, after rotation (labelledu'). Note that the coordinate is set byread.adp, or bybeamToXyzAdp,xyzToEnuAdp, orenuToOtherAdp.
which=5:8(orwhich="a1"to"a4") yield distance-time images of backscatter intensity of the respective beams. (For data derived from Teledyn-RDI instruments, this is the item called ``echo intensity.'')
which=9:12(orwhich="q1"to"q4") yield distance-time images of signal quality for the respective beams. (For RDI data derived from instruments, this is the item called ``correlation magnitude.'')
which=60orwhich="map"draw a map of location(s).
which=70:73(orwhich="g1"to"g4") yield distance-time images of percent-good for the respective beams. (For data derived from Teledyne-RDI instruments, which are the only instruments that yield this item, it is called ``percent good.'')
which=13(orwhich="salinity") yields a time-series plot of salinity.
which=14(orwhich="temperature") yields a time-series plot of temperature.
which=15(orwhich="pressure") yields a time-series plot of pressure.
which=16(orwhich="heading") yields a time-series plot of instrument heading.
which=17(orwhich="pitch") yields a time-series plot of instrument pitch.
which=18(orwhich="roll") yields a time-series plot of instrument roll.
which=19yields a time-series plot of distance-averaged velocity for beam 1, rightward velocity, eastward velocity, or rotated-eastward velocity, depending on the coordinate system.
which=20yields a time-series of distance-averaged velocity for beam 2, foreward velocity, northward velocity, or rotated-northward velocity, depending on the coordinate system.
which=21yields a time-series of distance-averaged velocity for beam 3, up-frame velocity, upward velocity, or rotated-upward velocity, depending on the coordinate system.
which=22yields a time-series of distance-averaged velocity for beam 4, forbeamcoordinates, or velocity estimate, for other coordinates. (This is ignored for 3-beam data.)
which=23yields a progressive-vector diagram in the horizontal plane, plotted withasp=1. Normally, the depth-averaged velocity components are used, but if thecontrollist contains an item namedbin, then the depth bin will be used (with an error resulting if the bin is out of range).
which=24yields a time-averaged profile of the first component of velocity (seewhich=19for the meaning of the component, in various coordinate systems).
which=25as for 24, but the second component.
which=26as for 24, but the third component.
which=27as for 24, but the fourth component (if that makes sense, for the given instrument).
which=28or"uv"yields velocity plot in the horizontal plane, i.e. u[2] versus u[1]. If the number of data points is small, a scattergraph is used, but if it is large,smoothScatteris used.
which=29or"uv+ellipse"as the"uv"case, but with an added indication of the tidal ellipse, calculated from the eigen vectors of the covariance matrix.
which=30or"uv+ellipse+arrow"as the"uv+ellipse"case, but with an added arrow indicating the mean current.
which=40or"bottomRange"for average bottom range from all beams of the instrument.
which=41to44(or"bottomRange1"to"bottomRange4") for bottom range from beams 1 to 4.
which=50or"bottomVelocity"for average bottom velocity from all beams of the instrument.
which=51to54(or"bottomVelocity1"to"bottomVelocity4") for bottom velocity from beams 1 to 4.
which=55(or"heaving") for time-integrated, depth-averaged, vertical velocity, i.e. a time series of heaving.
which=100(or"soundSpeed") for a time series of sound speed.

In addition to the above, there are some groupings defined:

which="velocity"equivalent towhich=1:3(velocity components)
which="amplitude"equivalent towhich=5:7(backscatter intensity components)
which="quality"equivalent towhich=9:11(quality components)
which="hydrography"equivalent towhich=14:15(temperature and pressure)
which="angles"equivalent towhich=16:18(heading, pitch and roll)

The colour scheme for image plots (which in 1:12) is provided by the col argument, which is passed to image to do the actual plotting. See Examples for some comparisons.

A common quick-look plot to assess mooring movement is to use which=15:18 (pressure being included to signal the tide, and tidal currents may dislodge a mooring or cause it to settle).

By default, plot.adp uses a zlim value for the image that is constructed to contain all the data, but to be symmetric about zero. This is done on a per-panel basis, and the scale is plotted at the top-right corner, along with the name of the variable being plotted. You may also supply zlim as one of the ...arguments, but be aware that a reasonable limit on horizontal velocity components is unlikely to be of much use for the vertical component.

A good first step in the analysis of measurements made from a moored device (stored in d, say) is to do plot(d, which=14:18). This shows time series of water properties and sensor orientation, which is helpful in deciding which data to trim at the start and end of the deployment, because they were measured on the dock or on the ship as it travelled to the mooring site.

Examples

Run this code

library(oce)
data(adp)
plot(adp, which=1:3)
plot(adp, which=5, missingColor='gray',
adorn=expression({
    lines(x[["time"]], x[["pressure"]], lwd=3, col='blue')
    }))
plot(adp, which='temperature', tformat='%H:%M')