Plot echosounder data.
Simple linear approximation is used when a newx value is specifie
with the which=2 method, but arguably a gridding method should be
used, and this may be added in the future.
# S4 method for echosounder
plot(x, which = 1, beam = "a", newx, xlab, ylab,
xlim, ylim, zlim, type = "l", col = oce.colorsJet, lwd = 2,
despike = FALSE, drawBottom, ignore = 5, drawTimeRange = FALSE,
drawPalette = TRUE, radius, coastline, adorn = NULL,
mgp = getOption("oceMgp"), mar = c(mgp[1] + 1, mgp[1] + 1, mgp[1] + 1,
mgp[1] + 1), atTop, labelsTop, tformat, debug = getOption("oceDebug"), ...)An echosounder object, e.g. as read by
read.echosounder, or created by as.echosounder.
list of desired plot types: which=1 or which="zt
image" gives a z-time image, which=2 or which="zx image"
gives a z-distance image, and which=3 or which="map" gives a
map showing the cruise track. In the image plots, the display is of
log10 of amplitude, trimmed to zero for any amplitude values
less than 1 (including missing values, which equal 0). Add 10 to the
numeric codes to get the secondary data (non-existent for single-beam files,
a more detailed specification of the data to be plotted. For
single-beam data, this may only be "a". For dual-beam data, this may
be "a" for the narrow-beam signal, or "b" for the wide-beam
signal. For split-beam data, this may be "a" for amplitude,
"b" for x-angle data, or "c" for y-angle data.
optional vector of values to appear on the horizontal axis if
which=1, instead of time. This must be of the same length as the
time vector, because the image is remapped from time to newx using
approx.
optional labels for the horizontal and vertical axes; if
not provided, the labels depend on the value of which.
optional range for x axis.
optional range for y axis.
optional range for colour scale.
type of graph, "l" for line, "p" for points, or
"b" for both.
colour scale for image, a function
line width (ignored if type="p")
remove vertical banding by using smooth to
smooth across image columns, row by row.
optional flag used for section images. If TRUE,
then the bottom is inferred as a smoothed version of the ridge of highest
image value, and data below that are grayed out after the image is drawn.
If drawBottom is a colour, then that colour is used, instead of
white. The bottom is detected with findBottom, using the
ignore value described next.
optional flag specifying the thickness in metres of a surface
region to be ignored during the bottom-detection process. This is ignored
unless drawBottom=TRUE.
if TRUE, the time range will be drawn at the
top. Ignored except for which=2, i.e. distance-depth plots.
if TRUE, the palette will be drawn.
radius to use for maps; ignored unless which=3 or
which="map".
coastline to use for maps; ignored unless which=3 or
which="map".
(Defunct)
An expression or vector of expressions that contain
R code that is to be executed immediately after each panel of the plot.
If the number of expressions matches the number of panels, then the
expressions are used for the corresponding panels; otherwise, the
expression list is extended to match the number of panels (i.e.
to obtain length(which) elements). Note that adorn
is a dangerous argument, because if the expressions contained
therein set up local storage, there is a chance of entirely
disrupting the plotting. For this reason, adorn was
marked as defunct in June 2016, and will be removed entirely
after the July CRAN release. Users with existing code that uses
adorn should simply plot the panels individually, and
use conventional R functions, e.g. lines etc.,
after each panel, to achieve the desired effect. (See
oce-defunct for notes on other deprecated or
defunct oce features.)
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.
value to be used with par("mar").
optional vector of time values, for labels at the top of the
plot produced with which=2. If labelsTop is provided, then it
will hold the labels. If labelsTop is not provided, the labels will
be constructed with the format function, and these may be
customized by supplying a format in the … arguments.
optional vector of character strings to be plotted above
the atTop times. Ignored unless atTop was provided.
set to an integer exceeding zero, to get debugging information during processing.
optional arguments passed to plotting functions. For example,
for maps, it is possible to specify the radius of the view in kilometres,
with radius.
A list is silently returned, containing xat and yat,
values that can be used by oce.grid to add a grid to the plot.
Other things related to echosounder data: [[,echosounder-method,
[[<-,echosounder-method,
as.echosounder,
echosounder-class,
echosounder, findBottom,
read.echosounder,
subset,echosounder-method,
summary,echosounder-method
# NOT RUN {
# }
# NOT RUN {
library(oce)
data(echosounder)
plot(echosounder, which=c(1,2), drawBottom=TRUE)
# }
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