stat_wb_irrad: Integrate irradiance for wavebands.

In ggspectra: Extensions to 'ggplot2' for Radiation Spectra

Integrate irradiance for wavebands.

Description

stat_wb_irrad integrates the area under a spectral irradiance curve, yielding energy or photon irradiance. The range(s) of wavelengths to integrate are set with a list of waveband objects. x-scale transformations and axis flipping are currently not supported.

Usage

stat_wb_irrad(
  mapping = NULL,
  data = NULL,
  geom = "text",
  position = "identity",
  ...,
  w.band = NULL,
  time.unit,
  unit.in,
  label.qty = "total",
  label.mult = 1,
  chroma.type = "CMF",
  label.fmt = "%.3g",
  ypos.mult = 1.07,
  ypos.fixed = NULL,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

stat_wb_e_irrad(
  mapping = NULL,
  data = NULL,
  geom = "text",
  position = "identity",
  ...,
  w.band = NULL,
  time.unit = "second",
  unit.in = "energy",
  label.qty = "total",
  label.mult = 1,
  chroma.type = "CMF",
  label.fmt = "%.3g",
  ypos.mult = 1.07,
  ypos.fixed = NULL,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

stat_wb_q_irrad(
  mapping = NULL,
  data = NULL,
  geom = "text",
  position = "identity",
  ...,
  w.band = NULL,
  time.unit = "second",
  unit.in = "photon",
  label.qty = "total",
  label.mult = 1,
  chroma.type = "CMF",
  label.fmt = "%.3g",
  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.
time.unit	character or lubridate::duration
unit.in	character One of "photon","quantum" or "energy"
label.qty	character
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 irrad, e_irrad or q_irrad to the data.

y.label

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

x

w.band-midpoint

wb.xmin

w.band minimum

wb.xmax

w.band maximum

wb.ymin

data$y minimum

wb.ymax

data$y maximum

wb.yeff

weighted irradiance if w.band describes a BSWF

wb.yint

not weighted irradiance for the range of w.band

wb.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

BW.color

black_or_white(wb.color)

Default aesthetics

Set by the statistic and available to geoms.

label

..y.label..

x

..x..

xmin

..wb.xmin..

xmax

..wb.xmax..

ymin

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

ymax

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

yintercept

..wb.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_contribution(), stat_wb_hbar(), 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 for energy irradiance in W m-2
ggplot(sun.spct) +
  stat_wb_column(w.band = PAR(), alpha = 0.5) +
  stat_wb_e_irrad(w.band = PAR(), ypos.fixed = 0.32) +
  geom_line() +
  scale_fill_identity() + scale_color_identity()

# using defaults for photon irradiance in umol m-2 s-1
ggplot(sun.spct, unit.out = "photon") +
  stat_wb_column(w.band = PAR(), alpha = 0.5) +
  stat_wb_q_irrad(w.band = PAR(), ypos.fixed = 1.5e-6, label.mult = 1e6) +
  geom_line() +
  scale_fill_identity() + scale_color_identity()

# modify label format and position
ggplot(sun.spct) +
  stat_wb_column(w.band = VIS_bands(), alpha = 0.7) +
  stat_wb_e_irrad(w.band = VIS_bands(),
                  angle = 90, size = 3, hjust = "left",
                  label.fmt = "%2.0f~~W~m^{-2}", parse = TRUE,
                  ypos.fixed = 0.1) +
  geom_line() +
  scale_fill_identity() + scale_color_identity()

# Changing label mapping
ggplot(sun.spct) +
  stat_wb_column(w.band = VIS_bands(), alpha = 0.5) +
  stat_wb_e_irrad(w.band = VIS_bands(),
               label.fmt = "%.2f",
               angle = 90, color = "black", ypos.fixed = 0.1,
               hjust = "left", size = 3,
               mapping = aes(label = after_stat(paste(wb.name, ": ",
                                                signif(wb.yint, 3),
                                                sep = "")))) +
  geom_line() +
  scale_fill_identity() + scale_color_identity() +
  theme_bw()

ggspectra documentation built on April 4, 2025, 2:19 a.m.