Find wavelength for target quantity value.

stat_find_wls finds at which x positions values equal to a target are located. Axis flipping is currently not supported.

Usage

stat_find_wls(
  mapping = NULL,
  data = NULL,
  geom = "point",
  position = "identity",
  ...,
  target = "half.maximum",
  interpolate = TRUE,
  chroma.type = "CMF",
  label.fmt = "%.3g",
  x.label.fmt = label.fmt,
  y.label.fmt = label.fmt,
  x.label.transform = function(x) {
     x
 },
  y.label.transform = function(x) {
     x
 },
  x.colour.transform = x.label.transform,
  na.rm = FALSE,
  show.legend = FALSE,
  inherit.aes = TRUE
)

Arguments

mapping

The aesthetic mapping, usually constructed with aes or aes_. Only needs to be set at the layer level if you are overriding the plot defaults.

data

A layer specific dataset - only needed if you want to override the plot defaults.

geom

The geometric object to use display the data

position

The position adjustment to use for overlapping points on this layer

...

other arguments passed on to layer. This can include aesthetics whose values you want to set, not map. See layer for more details.

target

numeric vector indicating the spectral quantity values for which wavelengths are to be searched and interpolated if need. The character strings "half.maximum" and "half.range" are also accepted as arguments. A list with numeric and/or character values is also accepted.

interpolate

logical Indicating whether the nearest wavelength value in x should be returned or a value calculated by linear interpolation between wavelength values stradling the target.

chroma.type

character one of "CMF" (color matching function) or "CC" (color coordinates) or a chroma_spct object.

label.fmt, x.label.fmt, y.label.fmt

character strings giving a format definition for construction of character strings labels with function sprintf from x and/or y values.

x.label.transform, y.label.transform, x.colour.transform

function Applied to x or y values when constructing the character labels or computing matching colours.

na.rm

a logical value indicating whether NA values should be stripped before the computation proceeds.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders.

Value

A data frame with one row for each match to the target subset from the data or linearly interpolated between the two nearest values available. As spectra are not monotonic in the spectral quantity, this statistic can return more than one row in data per target value.

Details

For each row in the subset of data matching target a colour definition is computed assuming that after transformation with x.colour.transform() the values in x are wavelengths expressed in nanometres. Labels are constructed from x and y values after applying to them x.label.transform and y.label.transform, respectively. In most cases the x.label.transform is used to back-transform the values in data to make them agree with those displayed on the axis guides.

These stats use geom_point by default as it is a geometry likely to work well in almost any situation. The additional default aesthetic mappings set by these statistics allow their direct use with geom_text, geom_label, geom_line, geom_rug, geom_hline and geom_vline. The format of the labels returned can be controlled by the user.

Note

These stats work nicely together with geoms geom_text_repel and geom_label_repel from package ggrepel to solve the problem of overlapping labels by displacing them. To discard overlapping labels use check_overlap = TRUE as argument to geom_text. By default the labels are character values suitable to be plotted as is, but with a suitable label.fmt labels suitable for parsing by the geoms (e.g. into expressions containing greek letters or super or subscripts) can be also easily obtained.

Computed variables

x

x-value at or nearest to the match to the target as numeric

y

target value or y-value nearest to the target as numeric

x.label

x-value at or nearest to the match formatted as character

y.label

target value or y-value nearest to the target formatted as character

wl.color

color definition calculated by assuming that x-values are wavelengths expressed in nanometres.

Default aesthetics

Set by the statistic and available to geoms.

label

..x.label..

xintercept

..x..

yintercept

..y..

fill

..wl.color..

Required aesthetics

Required by the statistic and need to be set with aes().

x

numeric, wavelength in nanometres

y

numeric, a spectral quantity

See also

find_peaks.

Other stats functions: stat_color(), stat_find_qtys(), stat_label_peaks(), stat_peaks(), stat_spikes(), stat_wb_box(), stat_wb_column(), stat_wb_contribution(), stat_wb_hbar(), stat_wb_irrad(), stat_wb_label(), stat_wb_mean(), stat_wb_relative(), stat_wb_sirrad(), stat_wb_total(), stat_wl_strip(), stat_wl_summary()

Examples

# ggplot() methods for spectral objects set a default mapping for x and y.
ggplot(yellow_gel.spct) +
  geom_line() +
  stat_find_wls(target = c(0.25, 0.5, 0.75))


ggplot(yellow_gel.spct) +
  geom_line() +
  stat_find_wls(target = "half.maximum", geom = "point", colour = "red") +
  stat_find_wls(target = "half.maximum", geom = "text", colour = "red",
             hjust = 1.1, label.fmt = "%3.0f nm")