User Guide
Package ‘photobiologyPlants’ 0.5.0
Pedro J. Aphalo
2024-04-02
Introduction
This package provides data sets and functions relevant to the
photobiology of plants. It is part of a suite, which has package
‘photobiology’ at its core. Please visit (http://www.r4photobiology.info/) for more details. For
more details on plotting spectra, please consult the documentation for
package ‘ggspectra’, and for information on the calculation of summaries
and maths operations between spectra, please, consult the documentation
for package ‘photobiology’.
See the User Guide for packages ‘photobiology’ and ‘ggspectra’ for
instructions on how to work with spectral data. As package ‘ggspectra’
is only suggested, in this vignette it is loaded an used conditionally
on its availability.
library(photobiology)
library(photobiologyPlants)
library(photobiologyWavebands)
eval_plots <- requireNamespace("ggspectra", quietly = TRUE)
if (eval_plots) library(ggspectra)
theme_set(theme_bw())
Photon ratios relevant to plants
R_FR(), B_G(), UVB_UV(),
UVA_UV(), UV_PAR(), UVB_PAR(),
UVA_PAR() are convenience functions implemented using
function q_ratio() from package ‘photobiology’ and waveband
definitions from package ‘photobiiologyWavebands’ with defaults as
commonly used in the field of plant photobiology.
## R:FR[q:q]
## 1.266704
## attr(,"radiation.unit")
## [1] "q:q ratio"
Calculating the phytochrome photoequilibrium
In the examples below we use the solar spectral data included in
package ‘photobiology’ as a data frame in object
sun.spct.
We can calculate the phytochrome photoequilibrium from spectral
irradiance data contained in a source_spct object as
follows.
## [1] 0.68341
We can also calcualte the red:far-red photon ratio, in this second
example, for the same spectrum as above
## R:FR[q:q]
## 1.266704
## attr(,"radiation.unit")
## [1] "q:q ratio"
which is equivalent to calculating it using package ‘photobiology’
directly
q_ratio(sun.spct, Red("Smith10"), Far_red("Smith10"))
## R:FR[q:q]
## 1.266704
## attr(,"radiation.unit")
## [1] "q:q ratio"
We can, and should whenever spectral data are available, calculate
the photoequilibrium as above, directly from these data. It is possible
to obtain and approximation in case of the solar spectrum and other
broad spectra, using the red:far-red photon ratio. The calculation,
however, is only strictly valid, for di-chromatic illumination with red
plus far-red light.
Pfr_Ptot_R_FR(R_FR(sun.spct))
## R:FR[q:q]
## 0.7051691
Here we calculated the R:FR ratio from spectral data, but in practice
one would use this function only when spectral data is not available as
when a R plus FR sensor is used. We can see that in such a case the
photoequilibrium calculated is only a rough approximation. For sunlight,
in the example above when using spectral data we obtained a value of
0.683 in contrast to 0.705 when using the R:FR photon ratio. For other
light sources differences can be much larger. Furthermore, here we used
the true R:FR ratio calculated from the spectrum, while broad-band
red:far-red sensors guive only an approximation, which is good for
sunlight, but which will be innacurate for artifical light, unless a
special calibration is done for each type of lamp.
In the case of monochromatic light we can still use the same
functions, as the defaults are such that we can use a single value as
the ‘w.length’ argument, to obtain the Pfr:P ratio. For monochromatic
light, irradiance is irrelevant for the photoequilibrium
(steady-state).
## [1] 0.869649
## [1] 0.01749967
## [1] 0.86964902 0.01749967
## [1] 0.3859998
We can also plot Pfr:Ptot as a function of wavelength (nm) of
monochromatic light. The default is to return a vector for short input
vectors, and a response_spct object otherwise, but this can
be changed through argument spct.out.
autoplot(Pfr_Ptot(300:770), norm = NULL, unit.out = "photon",
w.band = Plant_bands(),
annotations = c("colour.guide", "labels", "boxes")) +
labs(y = "Phytochrome photoequilibrium, Pfr:Ptot ratio")
It is, of course, also possible to use base R plotting functions, or
as shown here functions from package ‘ggplot2’
ggplot(data = Pfr_Ptot(300:770), aes(w.length, s.q.response)) +
geom_line() +
labs(x = "Wavelength (nm)",
y = "Phytochrome photoequilibrium, Pfr:Ptot ratio")
In the case of dichromatic illumination with red (660 nm) and far-red
(730 nm) light, we can use a different function that takes the R:FR
photon ratio as argument.
These computations are valid only for true mixes of light at
these two wavelengths but not valid for broad spectra like sunlight and
especially inaccurate for plant growth lamps with peaks in their output
spectrum, such as most discharge lamps (sodium, mercury, multi-metal,
fluorescent tubes) and many LED lamps.
## [1] 0.6919699
## [1] 0.04747996
Pfr_Ptot_R_FR(c(1.15,0.01))
## [1] 0.69196990 0.04747996
It is also easy to plot Pfr:P ratio as a function of R:FR photon
ratio. However we have to remember that such values are exact only for
dichromatic light, and only a very rough approximation for wide-spectrum
light sources. For wide-spectrum light sources, the photoequilibrium
should, if possible, be calculated from spectral irradiance data.
ex6.data <- data.frame(r.fr=seq(0.01, 5.0, length.out=100), Pfr.p=numeric(100))
ex6.data$Pfr.p <- Pfr_Ptot_R_FR(ex6.data$r.fr)
ggplot(data=ex6.data, aes(r.fr, Pfr.p)) +
geom_line() +
labs(x ="R:FR photon ratio",
y = "Phytochrome photoequilibrium, Pfr:Ptot ratio")
Calculating reaction rates
with(clip_wl(sun.spct, c(300,770)), Phy_reaction_rates(w.length, s.e.irrad))
## $k1
## [1] 1.25935
##
## $k2
## [1] 0.5833947
##
## $nu
## [1] 1.842745
Calculating the absorption cross section at given wavelengths
The phytochrome photoequilibrium cannot be calculated from the
absorptance spectra of Pr and Pfr, because Pr and Pfr have different
quantum yields for the respective phototransformations. We need to use
action spectra, which in this context are usually called
absorption cross-sections'. They can be calculated as the product of absorptance and quantum yield. The values in these spectra, in the case of Phy are calledSigma’.
Here we reproduce Figure 3 in Mancinelli (1994), which gives the
‘Relative photoconversion cross-sections’ of Pr (\(\sigma_R\)) and Pfr (\(\sigma_{FR}\)). The values are expressed
relative to \(\sigma_R\) at its maximum
at \(\lambda = 666\) nm.
ex7.data <- data.frame(w.length=seq(300, 770, length.out=100))
ex7.data$sigma.r <- Phy_Sigma_R(ex7.data$w.length)
ex7.data$sigma.fr <- Phy_Sigma_FR(ex7.data$w.length)
ex7.data$sigma <- Phy_Sigma(ex7.data$w.length)
ggplot(ex7.data, aes(x = w.length)) +
geom_line(aes(y = sigma.r/ max(sigma.r)), colour = "red") +
geom_line(aes(y = sigma.fr/ max(sigma.r))) +
labs(x = "Wavelength (nm)", y = expression(sigma[R]~"and"~sigma[FR]))
Spectral absorbance of cryptochromes
## [1] "CRY1_dark" "CRY1_light" "CRY2_dark" "CRY2_light" "CRY3_dark"
Here we approximate Figure 1.B from Banerjee et al. (2007).
A_as_default()
autoplot(interpolate_wl(CRYs.mspct$CRY2_dark, 300:500))
autoplot(CRYs.mspct[c("CRY2_dark", "CRY2_light")])
autoplot(CRYs.mspct[c("CRY1_dark", "CRY1_light")])
autoplot(CRYs.mspct["CRY3_dark"], range = c(300,700))
ggplot(CRYs.mspct[c("CRY1_dark", "CRY2_dark", "CRY3_dark")]) +
geom_line(aes(linetype = spct.idx)) +
expand_limits(x = 300)
Spectral absorbance of phototropins
## [1] "PHOT1_fluo" "PHOT2_fluo" "PHOT1_dark" "PHOT1_light"
autoplot(PHOTs.mspct[c("PHOT1_fluo", "PHOT2_fluo")]) +
expand_limits(x = 300)
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
autoplot(PHOTs.mspct[c("PHOT1_dark", "PHOT1_light")])
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
UVR8 absorbance
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
Spectral absorbance of zeitloupe proteins
## [1] "ZTL_dark" "ZTL_light"
autoplot(ZTLs.mspct) +
expand_limits(x = 300)
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
Photosynthesis action spectra
names(McCree_photosynthesis.mspct)
## [1] "amaranth" "oats"
autoplot(McCree_photosynthesis.mspct)
Carotenoids
## [1] "beta_carotene" "dihydro_lycopene" "lycopene" "lutein"
## [5] "phytoene" "phytofluene" "violaxanthin" "zeaxanthin"
autoplot(carotenoids.mspct[1:4],
annotations = c("-", "labels", "boxes"))
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
autoplot(carotenoids.mspct[5:length(carotenoids.mspct)],
annotations = c("-", "labels", "boxes"))
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
Chlorophylls
names(chlorophylls.mspct)
## [1] "Chl_a_MethOH" "Chl_a_DME" "Chl_b_DME"
autoplot(chlorophylls.mspct[c("Chl_a_DME", "Chl_b_DME")])
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
## Warning in normalize_spct(spct = T2A(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
{r}, eval = eval_plots autoplot(chlorophylls.mspct[c("Chl_a_DME", "Chl_a_MethOH")])
Fluorescence
names(chlorophylls_fluorescence.mspct)
## [1] "Chl_a_MethOH" "Chl_a_DME" "Chl_b_DME"
autoplot(chlorophylls_fluorescence.mspct[c("Chl_a_DME", "Chl_b_DME")])
## Warning in normalize_spct(spct = e2q(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
## Warning in normalize_spct(spct = e2q(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
autoplot(chlorophylls_fluorescence.mspct[c("Chl_a_DME", "Chl_a_MethOH")])
## Warning in normalize_spct(spct = e2q(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
## Warning in normalize_spct(spct = e2q(x, action = "replace.raw"), range = range,
## : Normalization not updated: action not supported for objects created with
## 'photobiology' (<= 0.10.9).
Optical properties of leaves
names(Solidago_altissima.mspct)
## [1] "lower_adax" "lower_abax" "upper_adax" "upper_abax"
autoplot(Solidago_altissima.mspct$lower_adax)
autoplot(Solidago_altissima.mspct$lower_abax)
autoplot(as.filter_mspct(Betula_ermanii.mspct))
autoplot(as.reflector_mspct(Betula_ermanii.mspct))
