plot.adp {oce} | R Documentation |
Plot ADP data
## S4 method for signature '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"), ...)
x |
an |
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
|
mode |
a string indicating whether to plot the conventional signal
( |
col |
optional indication of colour(s) to use. If not provided,
the default for images is |
breaks |
optional breaks for colour scheme |
zlim |
a range to be used as the |
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 |
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. |
ytype |
character string controlling the type of the y axis for
images (ignored for time series). If |
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”.) |
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
|
missingColor |
colour used to indicate |
mgp |
3-element numerical vector to use for |
mar |
value to be used with |
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 |
marginsAsImage |
boolean, |
cex |
size of labels on axes; see |
cex.axis |
see |
cex.main |
see |
xlim |
optional 2-element list for |
ylim |
optional 2-element list for |
control |
optional list of parameters that may be used for
different plot types. Possibilities are |
useLayout |
set to |
coastline |
a |
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 |
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 |
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
(or which="u1"
to "u4"
) yield a
distance-time image plot of a velocity component. If x
is
in beam
coordinates (signalled by
x@metadata$oce.coordinate=="beam"
), this will be the beam
velocity, labelled b[1]
etc. If x
is in xyz
coordinates (sometimes called frame coordinates, or ship
coordinates), it will be the velocity component to the right of
the frame or ship (labelled u
etc). Finally, if x
is in "enu"
coordinates, the image will show the the
eastward component (labelled east
). If x
is in
"other"
coordinates, it will be component corresponding to
east, after rotation (labelled u\'
). Note that the
coordinate is set by read.adp
, or by
beamToXyzAdp
, xyzToEnuAdp
, or
enuToOtherAdp
.
which=5:8
(or which="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
(or which="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=60
or which="map"
draw a map of location(s).
which=70:73
(or which="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
(or which="salinity"
) yields a
time-series plot of salinity.
which=14
(or which="temperature"
) yields a
time-series plot of temperature.
which=15
(or which="pressure"
) yields a
time-series plot of pressure.
which=16
(or which="heading"
) yields a
time-series plot of instrument heading.
which=17
(or which="pitch"
) yields a time-series
plot of instrument pitch.
which=18
(or which="roll"
) yields a time-series
plot of instrument roll.
which=19
yields 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=20
yields a time-series of distance-averaged
velocity for beam 2, foreward velocity, northward velocity, or
rotated-northward velocity, depending on the coordinate system.
which=21
yields 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=22
yields a time-series of distance-averaged
velocity for beam 4, for beam
coordinates, or velocity
estimate, for other coordinates. (This is ignored for 3-beam
data.)
which=23
yields a progressive-vector diagram in the
horizontal plane, plotted with asp=1
. Normally, the
depth-averaged velocity components are used, but if the
control
list contains an item named bin
, then the
depth bin will be used (with an error resulting if the bin is out
of range).
which=24
yields a time-averaged profile of the first
component of velocity (see which=19
for the meaning of the
component, in various coordinate systems).
which=25
as for 24, but the second component.
which=26
as for 24, but the third component.
which=27
as for 24, but the fourth component (if that
makes sense, for the given instrument).
which=28
or "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,
smoothScatter
is used.
which=29
or "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=30
or "uv+ellipse+arrow"
as the
"uv+ellipse"
case, but with an added arrow indicating the
mean current.
which=40
or "bottomRange"
for average bottom range
from all beams of the instrument.
which=41
to 44
(or "bottomRange1"
to
"bottomRange4"
) for bottom range from beams 1 to 4.
which=50
or "bottomVelocity"
for average bottom velocity
from all beams of the instrument.
which=51
to 54
(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 to which=1:3
(velocity components)
which="amplitude"
equivalent to which=5:7
(backscatter intensity components)
which="quality"
equivalent to which=9:11
(quality components)
which="hydrography"
equivalent to which=14:15
(temperature and pressure)
which="angles"
equivalent to which=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.
A list is silently returned, containing xat
and yat
,
values that can be used by oce.grid
to add a grid to the
plot.
Dan Kelley
The documentation for adp-class
explains the structure
of ADP objects, and also outlines the other functions dealing with them.
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')