stat_find_wls {ggspectra}

Find wavelength for target quantity value.

Description

stat_find_wls finds at which x positions values equal to a target are located.

Usage

stat_find_wls(
  mapping = NULL,
  data = NULL,
  geom = "point",
  target = "half.maximum",
  interpolate = TRUE,
  chroma.type = "CMF",
  label.fmt = "%.3g",
  x.label.fmt = label.fmt,
  y.label.fmt = label.fmt,
  position = "identity",
  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

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

character string giving a format definition for converting values into character strings by means of function sprintf.

x.label.fmt

character string giving a format definition for converting $x$-values into character strings by means of function sprintf.

y.label.fmt

character string giving a format definition for converting $y$-values into character strings by means of function sprintf.

position

The position adjustment to use for overlapping points on this layer

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.

...

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

Details

These stats use geom_point by default as it is the geom most likely to work well in almost any situation without need of tweaking. The default aesthetics set by these stats allow their direct use with geom_text, geom_label, geom_line, geom_rug, geom_hline and geom_vline. The formatting of the labels returned can be controlled by the user.

Value

A data frame with one row for each match to target found in the data.

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

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.

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")