This function allows to identify the spectrum and the wavelength of a point
in a plot produced by plotspc()
.
spc.identify( x, y = NULL, wavelengths = NULL, ispc = NULL, tol.wl = diff(range(x))/200, tol.spc = diff(range(y))/50, point.fn = spc.point.max, formatter = spc.label.default, ..., cex = 0.7, adj = c(0, 0.5), srt = 90, warn = TRUE ) spc.point.max(wl, spc, wlclick) spc.point.default(wl, spc, wlclick) spc.point.min(wl, spc, wlclick) spc.point.sqr(wl, spc, wlclick, delta = 1L) spc.label.default(ispc, wl, spc, digits = 3) spc.label.wlonly(ispc, wl, spc, digits = 3)
x | either the abscissa coordinates or the list returned by |
---|---|
y | the ordinate values. Giving |
wavelengths | the wavelengths for the data points.
Giving |
ispc | if a selection of spectra was plotted, their indices can be
given in |
tol.wl, tol.spc | tolerance in wavelength and spectral intensity to search around the clicked point. See details. |
point.fn |
|
formatter |
|
... | passed to |
cex, adj, srt | see |
warn | Should the user be warned if no point is in the considered
window? In addition, see the discussion of option If `FALSE`, the resulting data.frame will have a row of `NA`s instead. |
wl | the wavelength to label |
spc | the intensity to label |
wlclick | the clicked wavelength |
delta |
|
digits | how many digits of the wavelength should be displayed? |
a data.frame
with columns
spectra indices of the
identified points, i.e. the rows of the hyperSpec
object that was
plotted.If ispc
is given, ispc [i]
is returned rather than i
.
the wavelengths of the identified points
the intensities of the identified points
This function first finds the spectrum with a point closest to the clicked
position (see graphics::locator()
). The distance to the clicked
point is evaluated relative to the size of the tolerance window.
In a second step, max.fn
searches for the actual point to label
within the specified wavelength window of that spectrum. This allows to
label maxima (or minima) without demanding too precise clicks. Currently,
the following functions to determine the precise point:
spc.point.default | uses the clicked wavelength together with its spectral intensity |
spc.point.max | the point with the highest intensity in the wavelength window |
spc.point.min | the point with the lowest intensity in the wavelength window |
spc.point.sqr | maximum of a parabola fit throug the point with highest intensity and the two surrounding points |
point.fn
is called with the arguments
wl
containing the considered wavelength window, spc
the
respective intensities of the closest spectrum, and wlclick
the
wavelength that was clicked. They return a vector of two elements
(wavelength and intensity).
As a last step, a label for the point produced by formatter
and plotted
using graphics::text()
. Currently, the following formatter
s are
available:
spc.label.default | spectrum number, wavelength |
spc.label.wlonly | wavelength |
formatter
functions receive the number of the spectrum ispc
,
the wavelength wl
, and the spectral intensity spc
and produce
a character variable suitable for labelling. The predefined formatters
surround the label text by spaces in order to easily have an appropriate
offset from the point of the spectrum.
The warning issued if no spectral point is inside the tolerance window may
be switched of by warn = FALSE
. In that case, the click will produce
a row of NA
s in the resulting data.frame.
spc.identify
uses option debuglevel
to determine whether debugging output
should be produced. debuglevel == 2
will plot the tolerance window for
every clicked point, debuglevel == 1
will plot the tolerance window only
if no data point was inside. See hyperSpec options
for details about retrieving and setting
options.
You may want to adjust the plot's ylim
to ensure that the labels are
not clipped. As a dirty shortcut, xpd = NA
may help.
graphics::locator()
, plotspc()
,
hyperSpec options()
map.identify()
, map.sel.poly()
C. Beleites