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Integrate ranges under spectral curve.

Source: R/stat-wb-contribution.R
stat_wb_contribution.Rd

stat_wb_contribution integrates the area under a spectral curve. It first integrates the area under the curve for each waveband and for the whole curve and then expresses the integral for each band as a relative contribution to the area under the whole spectral curve. Sets suitable default aesthetics for "rect", "hline", "vline", "text" and "label" geoms displaying "contributions" per waveband to the total of the spectral integral. x-scale transformations and axis flipping are currently not supported.

Usage

stat_wb_contribution(
  mapping = NULL,
  data = NULL,
  geom = "text",
  position = "identity",
  ...,
  w.band = NULL,
  integral.fun = integrate_xy,
  label.mult = 1,
  chroma.type = "CMF",
  label.fmt = "%1.2f",
  ypos.mult = 1.07,
  ypos.fixed = NULL,
  na.rm = FALSE,
  show.legend = NA,
  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.

w.band

a waveband object or a list of waveband objects or numeric vector of at least length two.

integral.fun

function on $x$ and $y$.

label.mult

numeric Scaling factor applied to y-integral values before conversion into character strings.

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 y-integral values into character strings by means of function sprintf.

ypos.mult

numeric Multiplier constant used to scale returned y values.

ypos.fixed

numeric If not NULL used a constant value returned in y.

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 waveband object in the argument to w.band. Wavebeand outside the range of the spectral data are trimmed or discarded.

Computed variables

What it is named integral below is the result of appying integral.fun to the data, with default integrate_xy.

y.label

yint multiplied by label.mult and formatted according to label.fmt

x

w.band-midpoint

xmin

w.band minimum

xmax

w.band maximum

ymin

data$y minimum

ymax

data$y maximum

yint

data$y integral for w.band / data$y integral for whole range of data$x

xmean

yint divided by wl_expanse(w.band)

y

ypos.fixed or top of data, adjusted by ypos.mult

wb.color

color of the w.band

wb.name

label of w.band

Default aesthetics

Set by the statistic and available to geoms.

label

..y.label..

x

..x..

xmin

..xmin..

xmax

..xmax..

ymin

..y.. - (..ymax.. - ..ymin..) * 0.03

ymax

..y.. + (..ymax.. - ..ymin..) * 0.03

yintercept

..ymean..

fill

..wb.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

Other stats functions: stat_color(), stat_find_qtys(), stat_find_wls(), stat_label_peaks(), stat_peaks(), stat_spikes(), stat_wb_box(), stat_wb_column(), 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


library(photobiologyWavebands)
# ggplot() methods for spectral objects set a default mapping for x and y.

# Using defaults
ggplot(sun.spct) +
  geom_line() +
  stat_wb_box(w.band = VIS()) +
  stat_wb_contribution(w.band = VIS()) +
  scale_fill_identity() + scale_color_identity()


# Setting position and angle of the text
ggplot(sun.spct) +
  geom_line() +
  stat_wb_box(w.band = VIS_bands()) +
  stat_wb_contribution(w.band = VIS_bands(), angle = 90, size = 2.5) +
  scale_fill_identity() + scale_color_identity()


# Showing percentages, i.e., using a different format for numbers
ggplot(sun.spct) +
  geom_line() +
  stat_wb_box(w.band = VIS_bands()) +
  stat_wb_contribution(w.band = VIS_bands(), size = 2.5,
                       label.mult = 100, label.fmt = "%3.0f%%") +
  scale_fill_identity() + scale_color_identity()


# Including the name of the waveband, i.e., changing the mapping for label
ggplot(sun.spct, range = c(NA, 410)) +
  geom_line() +
  stat_wb_box(w.band = UV_bands(), color = "white") +
  stat_wb_contribution(w.band = UV_bands(), size = 2.5,
                       label.mult = 100, label.fmt = "%3.0f%%",
                       mapping = aes(label = after_stat(paste(wb.name, y.label)))) +
  scale_fill_identity() + scale_color_identity()