plot.adp {oce}R Documentation

Plot ADP data

Description

Plot ADP data.

Usage

## S3 method for class 'adp':
plot(x, which=1:dim(x$data$ma$v)[3],
     col=oce.colors.palette(128,1), zlim, 
     titles,
     ytype=c("profile", "distance"),
     adorn=NULL,
     draw.time.range=getOption("oce.draw.time.range"),
     mgp=getOption("oce.mgp"),
     mar=c(mgp[1],mgp[1]+1,1,1/4),
     margins.as.image=FALSE,
     cex=1,
     debug=getOption("oce.debug"),
     ...)

Arguments

x 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.
col color palette to use. The default oce.colors.two palette blends from blue for negative values, through white at zero, to red at positive values; see “Details”.
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 of the panel and to be centred around zero. If provided as a two-element vector, then that is used for each panel. If provided as a two-column matrix, then each panel of the graph uses the corresponding row of the matrix; for example, setting zlim=rbind(c(-1,1),c(-1,1),c(-.1,.1)) might make sense for which=1:3, so that the two horizontal velocities have one scale, and the smaller vertical velocity has another.
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 must equal that of which.
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 "profile", then this will still be true for upward-looking instruments, but the y axis will be flipped for downward-looking instruments, so that in either case, the top of the graph will represent the sample nearest the sea surface.
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”.)
draw.time.range 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.
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").
margins.as.image 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 value for the character-expansion parameter, used by par("cex").
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.

Details

Creates a multi-panel summary plot of data measured by an ADP cast. The panels are controlled by the which argument.

The color 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.

Author(s)

Dan Kelley

See Also

The data are normally read with read.oce, which is usually able to detect the type of instrument. If that fails, the user should try read.adp.rdi (for RDI files) or read.adp.nortek (for NorTek files). These files may be in beam coordinates, in xyz coordinates, or in enu coordinates. It is common in a scientific setting to use beam coordinates, and so this package offers functions adp.beam2xyz and adp.xyz2enu to take the intermediate steps, and adp.enu2other to go further, e.g. to rotate into a coordinate system aligned with the shoreline or with an isobath.

The beam stength may be corrected for R-squared spreading with adp.beam.attenuate.

Summaries of ADP data are provided by summary.adp.

ADP data may be plotted with plot.adp.

Examples

library(oce)
data(adp)
e <- adp.xyz2enu(adp.beam2xyz(adp))
plot(e, which=1:3)
# Illustrate adornment
plot(e, which=1:2,
     adorn=expression({
         abline(v=as.POSIXct('2008-06-26 06:00:00',tz='UTC'),col='green',lwd=3)
         lines(x$data$ts$time, x$data$ts$pressure, lwd=3, col='blue')
     }))

[Package oce version 0.1-80 Index]