Package 'ggspectra' extends 'ggplot2' with stats, geoms, scales and
annotations suitable for light spectra. It also defines ggplot()
and
autoplot()
methods specialized for the classes defined in package
photobiology
for storing different types of spectral data. The
autoplot()
methods are described separately in vignette 'Autoplot
Methods'.
The new elements can be freely combined with methods and functions defined in packages 'ggplot2', 'scales' and extensions like 'ggrepel', 'cowplot', 'ggpp', 'gginnards' and 'patchwork'.
autoplot()
method specializations for?The autoplot()
generic method is defined in package 'ggplot2'. Package
'ggspectra' provides specializations of this method that construct fully
annotated plots as ggplot objects, which can be further manipulated if so
desired. These methods use the metadata stored in spectral objects of classes
defined in package 'photobiology' to automatically generate suitable axis
labels, scales and annotations. (Please, see vignette "Autoplot methods" for
details.)
ggplot
specializations for?The ggplot()
specializations set default aes
according to the type of
spectral object. They also add support for unit.out
arguments allowing
on-the-fly conversion of units of expression or spectral quantities.
These are only defaults and can be overridden by explicit use of aes()
to set the mapping of aesthetics.
The stats defined in this package help with with the generation of
annotations and decorations of plots of spectral data. They are meant to
be used only when the x aesthetic is mapped to a variable containing
wavelength values expressed in nanometres. They are designed to work
with spectral objects of the classes defined in package 'photobiology'.
Many of them also work well with any data frame as long as the x
aesthetic mapping fulfils the expectations. Package 'ggpmisc' contains
some equivalent stats which do not assume that x is mapped to
wavelength, accepting numeric
and datetime values.
| stat | default geom (used for) | other uses |
|:----------------|:----------------|:------------------------------------|
| stat_peaks
| point (highlight maxima) | wavelength label, spectral quantity label |
| stat_valleys
| point (highlight minima) | wavelength label, spectral quantity label |
| stat_label_peaks
| text (wavelength label) | spectral quantity label (support 'ggrepel') |
| stat_label_valleys
| text (wavelength label) | spectral quantity label (support 'ggrepel') |
| stat_find_wls
| point (highlight wls at qty) | wavelength label, spectral quantity label |
| stat_find_qtys
| point (highlight qty at wl) | wavelength label, spectral quantity label |
| stat_color
| color, fill | |
| stat_wb_label
| text (waveband name) | rect (showing range of waveband and its color) |
| stat_wb_total
| text (y integral) | label(s) with waveband integral |
| stat_wb_mean
| text (y mean) | label(s) with waveband mean |
| stat_wl_summary
| text (y mean) | label with wavelength range mean |
| stat_wb_contribution
| text (contribution) | label(s) with waveband integral / whole spectrum integral |
| stat_wb_relative
| text (relative) | label(s) with waveband integral / sum of integrals of all wavebands |
| stat_wb_e_irrad
| text (energy irradiance) | rect (showing range of waveband and its color) |
| stat_wb_q_irrad
| text (photon irradiance) | rect (showing range of waveband and its color) |
| stat_wb_e_sirrad
| text (spectral energy irradiance) | rect (showing range of waveband and its color) |
| stat_wb_q_sirrad
| text (spectral photon irradiance) | rect (showing range of waveband and its color) |
| stat_wl_strip
| rect (fill of wavelength or waveband) | text (label with waveband name) |
| stat_wb_box
| rect (fill of waveband) | |
| stat_wb_hbar
| errorbarh (color of waveband) | |
| stat_wb_column
| rect (fill of waveband) | |
geom_spct
useful for?The geom_spct
geometry is a special case of geom_area
, but with
the minimum of the y range fixed to 0, but with stacking not enabled.
The new scales are convenience wrapper functions built on top of the scales exported by package 'ggplot2', but with default arguments that are suitable for spectral data.
Functions for automatic generation of secondary x-axes in the case when a variable containing wavelength data (nm) is mapped to the x aesthetic simplify the task of adding an axis with frequencies or wave numbers to the plot of a spectrum.
| scale | unit.exponent | name | labels | breaks | |:-----------------|:-------------|:-------------|:-------------|:-------------| | scale_y_cps_continuous | 0 | cps_label() | SI_pl_format() | | | scale_y_counts_continuous | 3 | counts_label() | SI_pl_format() | | | scale_y_counts_tg_continuous | 3 | counts_label() | SI_tg_format() | | | scale_y_A_internal_continuous | 0 | A_internal_label() | SI_pl_format() | | | scale_y_A_total_continuous | 0 | A_total_label() | SI_pl_format() | | | scale_y_Tfr_internal_continuous | 0 | Tfr_internal_label() | SI_pl_format() | | | scale_y_Tfr_total_continuous | 0 | Tfr_total_label() | SI_pl_format() | | | scale_y_Rfr_internal_continuous | 0 | Rfr_internal_label() | SI_pl_format() | | | scale_y_Rfr_total_continuous | 0 | Rfr_total_label() | SI_pl_format() | | | scale_y_s.e.irrad_continuous | 0 | s.e.irrad_label() | SI_pl_format() | | | scale_y_s.q.irrad_continuous | -6 | s.q.irrad_label() | SI_pl_format() | | | scale_y_s.e.response_continuous | 0 | s.e.response_label() | SI_pl_format() | | | scale_y_s.q.response_continuous | 0 | s.q.response_label() | SI_pl_format() | | | scale_x_wl_continuous | -9 | w_length_label() | SI_pl_format() | pretty_breaks(n=7) | | scale_x_wavenumber_continuous | -6 | w_number_label() | SI_pl_format() | pretty_breaks(n=7) | | scale_x_energy_eV_continuous | 0 | w_energy_eV_label() | SI_pl_format() | pretty_breaks(n=7) | | scale_x_energy_J_continuous | -18 | w_energy_J_label() | SI_pl_format() | pretty_breaks(n=7) | | scale_x_frequency_continuous | 12 | w_frequency_label() | SI_pl_format() | pretty_breaks(n=7) |
In addition secondary axis definitions, sec_axis_w_number()
,
sec_axis_w_frequency()
, sec_axis_w_energy_eV()
, sec_axis_w_energy_J()
and
sec_axis_wl(), and SI system formatters SI_pl_format
, and SI_tg_format
are
exported, together with auxiliary functions for finding the nearest SI
multiplier based on an arbitrary exponent.
color_chart()
and black_or_white()
for?Function color_chart()
makes a color chart of rectangular tiles from a
vector R color definitions. The chart returned is a ggplot
object.
Function black_or_white()
accepts a vector of color definitions and
returns a vector with colors "white"
or "black"
depending on the
approximate luminosity of each color in the input. The main use is to
automatically achieve suitable contrast between text plotted on top of a
color background.
autotitle()
for?Function autotitle()
adds a title, subtitle and/or a caption to a
plot. The difference with ggtitle()
from package 'ggplot2' is that
autotitle()
automatically retrieves metadata from an spectral object
based on keys. It is used internally by all autoplot()
methods
defined in package 'ggspectra' and allowed syntax and key values are
described in User Guide 2: Autoplot Methods together with plot
annotations.
library(ggplot2) library(scales) library(photobiology) library(photobiologyWavebands) library(ggspectra) library(ggrepel)
library(knitr) opts_chunk$set(fig.align = 'center', fig.show = 'hold', fig.width = 7, fig.height = 4, cache = FALSE) options(warnPartialMatchArgs = FALSE)
Create a collection of two source_spct objects.
two_suns.mspct <- source_mspct(list(sun1 = sun.spct, sun2 = sun.spct / 2))
We bind the two spectra in the collection into a single spectral object.
This object includes an indexing factor, by default names spct.idx
. We
use this new object to later on demonstrate grouping in ggplots.
two_suns.spct <- rbindspct(two_suns.mspct)
We change the default theme.
theme_set(theme_bw())
The only difference between these specializations and the base
ggplot()
method is that the aesthetics for $x$ and $y$ have suitable
defaults. These are just defaults, so if needed they can still be
supplied with a mapping
argument with an user-defined aes()
.
ggplot(sun.spct) + geom_line()
It is possible to add to the defaults by means of +
and aes()
as
shown below.
ggplot(two_suns.spct) + aes(color = spct.idx) + geom_line()
If a mapping is supplied directly through ggplot
, $x$ and $y$ should
be included.
ggplot(two_suns.spct, aes(w.length, s.e.irrad, color = spct.idx)) + geom_line()
In the case of ggplot.source_spct()
an additional parameter allows
setting the type of units to use in the plot. This not only sets a
suitable aes()
for $y$ but also if needed converts the spectral data.
The two possible values are "energy"
and "photon"
and the default,
depends on option photobiology.radiation.unit
. This parameter has a
default value that can be modified through option
"photobiology.radiation.unit"
. Package 'photobiology' defines
convenience functions for this.
ggplot(sun.spct, unit.out = "photon") + geom_line()
After evaluation of photon_as_default()
, a new default is in effect,
but we can override it with an explicit argument if needed.
photon_as_default() ggplot(sun.spct) + geom_line() ggplot(sun.spct, unit.out = "energy") + geom_line()
This new default will remain active for the rest of the R session, unless changed. We can easily either unset this default, or all photobiology-package related user set defaults.
unset_user_defaults()
The next example is for spectral properties of filters.
ggplot(yellow_gel.spct) + geom_line()
In the case of ggplot.filter_spct()
the additional parameter is called
plot.qty
and allows choosing between "transmittance"
and
"absorbance"
.
ggplot(yellow_gel.spct, plot.qty = "absorbance") + geom_line()
In the case of ggplot.object_spct()
three values ("reflectance"
,
"transmittance"
and "all"
are accepted. Passing "all"
as argument
results in the spectral data being molten into a long form, using
value
and variable
as value and key columns, respectively. The
column variable
has three levels Tfr
, Rfr
and Afr
indexing the
Tfr
and Rfr
from the object_spct
object plus newly calculated
absorptance values.
This parameter has a default value that can be modified through option
"photobiology.filter.qty"
. Package 'photobiology' defines convenience
functions for this.
Afr_as_default() ggplot(yellow_gel.spct) + geom_line() unset_user_defaults()
The names of the additional parameters are consistent with those used in
the autoplot()
methods defined in this package.
The ggplot()
methods for collections of spectra work similarly to the
methods for spectra when used with an spectral object containing
concatenated spectra, as that shown in the previous section.
Plotting a collection of spectra using an aesthetic.
ggplot(two_suns.mspct) + aes(linetype = spct.idx) + wl_guide(ymax = -0.05) + geom_line()
Using facets.
ggplot(two_suns.mspct) + wl_guide(ymax = -0.05) + geom_spct() + geom_line() + facet_wrap(facets = vars(spct.idx), ncol = 1L)
ggplot(two_suns.mspct) + wl_guide(ymax = -0.05) + geom_spct() + geom_line() + facet_wrap(vars(spct.idx), ncol = 1L, scales = "free_y")
The scales provided are all wrappers of continuous scales from packages
'ggplot2' or 'scales'. All pass non-specific parameters to the wrapped
scales. The scales defined in 'ggspectra' compute suitable arguments for
name
and labels
and pass them to the wrapped scales. The default
text for the labels can be also set by the user by redefining a
function, in addition than overriding the defaults in individual calls.
This is a step towards multilingual support.
We present here, only once for all scales, examples of how to use features common to all of them. To start with we show the defaults for the scale for wavelengths and spectral energy irradiance that we will use for this examples.
ggplot(sun.spct) + geom_line() + scale_x_wl_continuous() + scale_y_s.e.irrad_continuous()
We can have also axis labels without symbols, either by passing an argument to
parameter axis.symbols
or by seeting R option ggspectra.axis.symbols
, which
sets the default.
ggplot(sun.spct) + geom_line() + scale_x_wl_continuous(axis.symbols = FALSE) + scale_y_s.e.irrad_continuous(axis.symbols = FALSE)
Here we change the unit.exponent
from its default value of -9
(nanometres) to -6
(micrometers) for wavelengths, and change 0
to -3
for irradiance. When they exist SI multipliers are used, and powers of
10 otherwise. This is not a transformation of the data, it only affects
the tick labels and the axis labels in coordination. Consequently
summary values will not be affected.
ggplot(sun.spct) + geom_line() + scale_x_wl_continuous(unit.exponent = -6) + scale_y_s.e.irrad_continuous(unit.exponent = -3)
ggplot(sun.spct) + geom_line() + scale_x_wl_continuous(unit.exponent = -7) + scale_y_s.e.irrad_continuous()
We can find the largest valid SI-scaling factor that is smaller or equal to an arbitrary power of 10.
nearest_SI_exponent(-4)
We can call this function on-the-fly.
ggplot(sun.spct) + geom_line() + scale_x_wl_continuous(unit.exponent = nearest_SI_exponent(-4)) + scale_y_s.e.irrad_continuous()
In addition to formatters defined in package 'scales', two additional formatters
are defined in package 'ggspectra', SI_pl_format()
and SI_tg_format()
. Most
of the new scales defined use SI_pl_format()
, but SI_tg_format()
can be
passed as an argument. When it is used as shown here, it is important to
remember that the axis label should not show scaled units, i.e., when using
SI_tg_format()
, unit.exponent
must be passed zero as argument. I have seen
this approach used in engineering related publications. (Recent updates to
packages 'ggplot2' and 'scales' have added similar functionality.)
ggplot(sun.spct) + geom_line() + scale_x_wl_continuous() + scale_y_s.e.irrad_continuous(unit.exponent = 0, labels = SI_tg_format(exponent = -3))
Transformation objects from package 'scales', or user defined, can be
passed as additional arguments. We replace zeros to avoid a warning
from the log10()
call, and as the scale limits
discards some
observations, we use na.rm = TRUE
to silence this additional warning.
temp.spct <- clean(sun.spct, range.s.data = c(1e-20, Inf), fill = 1e-20) ggplot(temp.spct) + geom_line(na.rm = TRUE) + scale_x_wl_continuous() + scale_y_s.e.irrad_continuous(unit.exponent = 0, trans = "log10", labels = trans_format("log10", math_format()), limits = c(1e-6, NA))
The default text used can be overridden. To keep only the symbol and
units pass ""
as argument (not shown).
ggplot(sun.spct) + geom_line() + scale_x_wl_continuous(label.text = "Longitud de onda,") + scale_y_s.e.irrad_continuous(label.text = "Irradiancia espectral,")
If the data are normalized, we can pass the normalization wavelength as an argument. In this example, we retrieve this wavelength from the metadata.
norm_sun.spct <- normalize(sun.spct) ggplot(norm_sun.spct) + geom_line() + scale_x_wl_continuous() + scale_y_s.e.irrad_continuous(normalized = getNormalized(norm_sun.spct))
If the data have been scaled, we can pass this information to the scale.
scaled_sun.spct <- fscale(sun.spct) ggplot(scaled_sun.spct) + geom_line() + scale_x_wl_continuous() + scale_y_s.e.irrad_continuous(scaled = is_scaled(scaled_sun.spct))
Name and labels can be passed directly as arguments, but this defeats the purpose of these wrappers.
Currently one x-scale function suitable for wavelengths in nanometres is exported by package 'ggspectra', as well as scales for wave number, frequency and energy, expecting the respective data quantities expressed in SI units with no scale factor.
These scale functions can be also used when plots are based on ordinary data frames or tibbles. However, in this case users must ensure that the data are expressed as expected as otherwise the axis labels and the power of ten multipliers plotted are wrong.
ggplot(sun.spct) + geom_line() + scale_x_wl_continuous()
Except scale_x_wl_continuous()
the x scales if used with source_spct()
objects as data
require the wavelength values to be converted to the expected quantity using aes()
to map variables to both x and y aesthetics.
ggplot(sun.spct, aes(x = wl2frequency(w.length), y = s.e.irrad)) + geom_line() + scale_x_frequency_continuous()
Functions automating the addition of secondary axes are available. They expect wavelength in nanometres in data and convert it into other equivalent physical quantities: wave number, frequency and energy per photon.
ggplot(sun.spct) + geom_line() + scale_x_wl_continuous(sec.axis = sec_axis_w_frequency())
ggplot(sun.spct) + geom_line() + scale_x_wl_continuous(sec.axis = sec_axis_energy_eV())
As shown above for the main axis, it is possible to set a different SI scaling factor for the units in secondary scales.
ggplot(sun.spct) + geom_line() + scale_x_wl_continuous(sec.axis = sec_axis_w_frequency(15))
Raw counts from array detectors are expressed in counts, as "counts" is a whole word rather than a unit a power of ten multiplier is used.
ggplot(white_led.raw_spct) + geom_line() + scale_x_wl_continuous() + scale_y_counts_continuous()
The tg
for tag version adds a suffix to the tick labels, as is common
in engineering.
ggplot(white_led.raw_spct) + geom_line() + scale_x_wl_continuous() + scale_y_counts_tg_continuous()
Raw counts from array detectors are expressed as a rate, as "counts" is a whole word rather than a unit a power of ten multiplier is used.
ggplot(white_led.cps_spct) + geom_line() + scale_x_wl_continuous() + scale_y_cps_continuous(unit.exponent = 3)
Four scales are available, one for energy irradiance and one for photon
irradiance. We show those for energy irradiance. There are equivalent
scales scale_y_s.q.irrad_continuous()
and scale_y_s.e.irrad_log10()
for photon irradiance.
ggplot(sun.spct) + geom_line() + scale_x_wl_continuous() + scale_y_s.e.irrad_continuous()
ggplot(sun.spct, unit.out = "photon", range = c(293, NA)) + geom_line() + scale_x_wl_continuous() + scale_y_s.e.irrad_log10(unit.exponent = -6)
Four scales are available, for energy response and action and for photon
response and action. We show those for energy irradiance. There are
equivalent scales scale_y_q.e.resoponse_continuous()
and
scale_y_s.q.action_continuous()
for photon irradiance.
The difference between response and action spectra stems from the measurement procedure. We will wrongly use here response data for both examples.
ggplot(ccd.spct) + geom_line() + scale_x_wl_continuous() + scale_y_s.e.response_continuous(unit.exponent = 6)
The figures are identical, but the text and symbol on the y-axis label are different.
ggplot(ccd.spct) + geom_line() + scale_x_wl_continuous() + scale_y_s.e.action_continuous(unit.exponent = 6)
Two definitions of transmittance exist, total and internal. To obtain
the correct labels we query the object containing the data. If we plot
data from a data frame or tibble, then we can manualy pass one of
"total"
or "internal"
as argument.
ggplot(yellow_gel.spct) + geom_line() + scale_x_wl_continuous() + scale_y_Tfr_continuous(Tfr.type = getTfrType(yellow_gel.spct))
ggplot(yellow_gel.spct) + geom_line() + scale_x_wl_continuous() + scale_y_Tfr_continuous(Tfr.type = getTfrType(yellow_gel.spct), labels = percent)
gel_internal.spct <- convertTfrType(yellow_gel.spct, Tfr.type = "internal") ggplot(gel_internal.spct) + geom_line() + scale_x_wl_continuous() + scale_y_Tfr_continuous(Tfr.type = getTfrType(gel_internal.spct))
Two definitions of absorbance exist, total and internal. To obtain the
correct labels we query the object containing the data. If we plot data
from a data frame or tibble, then we can manualy pass one of "total"
or "internal"
as argument. This package only supports absorbance as
defined using logs on base 10.
ggplot(gel_internal.spct, plot.qty = "absorbance") + geom_line() + scale_x_wl_continuous() + scale_y_A_continuous(Tfr.type = getTfrType(gel_internal.spct))
Absorptance has only one definition, at least within this package.
ggplot(yellow_gel.spct, plot.qty = "absorptance") + geom_line() + scale_x_wl_continuous() + scale_y_Afr_continuous()
Two definitions of reflectance exist, total and specular. To obtain the
correct labels we query the object containing the data. If we plot data
from a data frame or tibble, then we can manualy pass one of "total"
or "specular"
as argument.
ggplot(green_leaf.spct) + geom_line() + scale_x_wl_continuous() + scale_y_Rfr_continuous(Rfr.type = getRfrType(green_leaf.spct))
Several ggplot
stats are defined by this package. All of them target
light spectra, as they expect $x$ to represent wavelengths expressed in
nanometres. However, they should behave correctly as long as this is
true, with any ggplot
object, based on any data format acceptable to
ggplot
. The name of the original variable is irrelevant, and it is the
user responsibility to supply the correct variables through aes()
. Of
course, when using the spectral classes defined in package
photobiology
the defaults easy this task.
Four stats are available for peaks and valleys, with the same formal
parameters. These stats do not fit peaks, simply search for local maxima
and local minima in the data as supplied. Stats stat_peaks()
and
stat_valleys()
subset the original data while stat_label_peaks()
and
stat_label_valleys()
only set a boolean flag to mark the local
extremes. Two stats are available for highlighting arbitrary locations
in spectra, one of them, stat_find_wls()
accepts a target for the
spectral quantity and locates the corresponding wavelength values while
the other, stat_find_qtys()
accepts a target wavelength value and
locates the corresponding spectral quantity value. Stats
stat_find_wls()
and stat_find_qtys()
subset the original data or
generate new data by interpolation.
All six stats set the same default aesthetics based on calculated
values. Not all of these default aesthetics are used by the default
geom, but they make using other geoms easier. Furthermore generated text
labels are formatted with sptintf()
and these six stats accept format
definitions through parameters label.fmt
, x.label.fmt
, and
y.label.fmt
. Please see the documentation for a list of all the
computed varaibles returned in data
. These stats use internally
functions photobiology::find_peaks()
and photobiology::find_wls()
and arguments are passed down to them.
The examples that follow, apply with minimal changes to stat_peaks()
,
stat_valleys()
, stat_find_wls()
and stat_find_qtys()
.
ggplot(sun.spct) + geom_line() + stat_peaks(color = "red")
Because of the conversion, the location of maxima and minima when an irradiance or response spectrum is expressed in photon- vs. energy-based units may differ. This is expected and not a bug.
ggplot(sun.spct, unit.out = "photon") + geom_line() + stat_peaks(color = "red")
The complement to stat_peaks()
is stat_valleys
.
ggplot(sun.spct) + geom_line() + stat_valleys(color = "blue")
Stats stat_find_wls()
and stat_find_qtys()
are another complementary
pair. The default target, used in this example, is the half maximum.
ggplot(yellow_gel.spct) + geom_line() + stat_find_wls(color = "orange")
One of the values calculated and mapped is colour as seen by humans
corresponding to the wavelength at the location of peaks and valleys.
The colour is mapped to the fill
aesthetic, so using a 'filled' shape
results in a colourful plot. The identity scale is needed so that the
correct colours are displayed using the colour definitions in the
calculated data instead of a palette.
ggplot(sun.spct) + geom_line() + stat_peaks(shape = 21, color = "black") + scale_fill_identity()
We can use any of the aesthetics affecting the default geom,
"point"
, and also with other _geom_s.
ggplot(sun.spct) + geom_line() + stat_peaks(span = 35, shape = 4, color = "red", size = 2) + stat_peaks(span = 35, color = "red", geom = "rug", sides = "b")
We can use several other geoms as needed, demonstrated here with
geom "text"
. To displace the text we can use nudging, justification
or both. If we want to have the bottom edge of the label 0.01 y-data
units above its natural position we can use.
ggplot(sun.spct) + geom_line() + stat_peaks(geom = "text", span = 35, color = "red", vjust = "bottom", position = position_nudge(y = 0.01))
The same stat can be included more than once in the same plot, using
different geoms. We here in addition demonstrate the use of several
different parameters. The span
argument determines the number of
consecutive observations tested when searching for a local extreme, and
it should be an odd integer number. In addition we here demonstrate the
use of a geom new to ggplot2
2.0.0 called "label"
which again
results in colourful labels by default. Here we make use of the computed
variable BW.color
which is set to "white"
or "white"
for maximum
contrast with the computed variable fill
.
ggplot(sun.spct) + geom_line() + stat_peaks(shape = 21, span = 35, size = 2) + stat_label_peaks(geom = "label", span = 35, vjust = "bottom", size = 3, position = position_nudge(y = 0.01)) + scale_fill_identity() + scale_color_identity() + expand_limits(y = 0.9)
Using a larger number as argument to span reduces the number of peaks detected.
ggplot(sun.spct) + geom_line() + stat_peaks(shape = 21, span = 35, size = 2) + stat_label_peaks(geom = "label", span = 35, size = 3, na.rm = TRUE, vjust = "bottom", position = position_nudge(y = 0.01)) + scale_fill_identity() + scale_color_identity() + expand_limits(y = 0.9)
Setting span
to NULL
results in the span set to the range of the
data, and so in this case the stat returns the global extreme, instead
of a local one. In this case we use geoms "vline"
and "hline"
taking
advantage that suitable aesthetics are set by the stats.
ggplot(sun.spct) + geom_line() + stat_peaks(span = NULL, geom = "vline", linetype = "dotted", color = "red") + stat_peaks(span = NULL, geom = "hline", linetype = "dotted", color = "red")
By default the label
aesthetic is mapped to a calculated label
x.label
giving the wavelength in nanometres. This mapping can be
changed to give to a label giving the y-value at the peak. We cannot
pass nudge_y
directly, we need to the nudge as a position
.
ggplot(sun.spct) + geom_line() + stat_peaks(shape = 21, span = 35, size = 2) + stat_label_peaks(aes(label = after_stat(y.label)), span = 35, geom = "label", size = 3, position = position_nudge(y = 0.04), label.fmt = "%1.2f") + expand_limits(y = 1) + scale_fill_identity() + scale_color_identity()
ggplot(sun.spct) + geom_line() + stat_valleys(shape = 21, span = 35, size = 2) + stat_label_valleys(geom = "label", span = 35, size = 3, na.rm = TRUE, vjust = "top", position = position_nudge(y = -0.01)) + scale_fill_identity() + scale_color_identity()
Above, using geom_label()
there is some overlap. We can use
geom_label_repel()
from package 'ggrepel' to avoid it. These geometry
has additional parameters to which we need to pass arguments to get a
satisfactory positioning of labels.
ggplot(sun.spct) + geom_line() + stat_peaks(shape = 21, span = 35, size = 2) + stat_label_peaks(segment.colour = "black", span = 35, geom = "label_repel", size = 3, max.overlaps = Inf, position = position_nudge_repel(y = 0.12), min.segment.length = 0, box.padding = 0.5, force_pull = 0) + expand_limits(y = 1) + scale_fill_identity() + scale_color_identity()
ggplot(sun.spct) + geom_line() + stat_valleys(shape = 21, span = 35, size = 2) + stat_label_valleys(segment.colour = "black", span = 35, geom = "label_repel", size = 3, max.overlaps = Inf, position = position_nudge_repel(y = -0.12), min.segment.length = 0, box.padding = 0.53, force = 0.5, force_pull = 1) + scale_fill_identity() + scale_color_identity()
As aesthetics can use values computed on-the-fly we can even use
paste()
to map a label that combines both values and adds additional
text.
ggplot(sun.spct) + geom_line() + stat_peaks(span = NULL, color = "red") + stat_peaks(span = NULL, geom = "text", vjust = -0.5, color = "red", aes(label = paste(after_stat(y.label), "at", after_stat(x.label), "nm"))) + expand_limits(y = c(NA, 0.9))
Finally we demonstrate that both stats can be simultaneously used. One can also choose to use different spans as demonstrated here, resulting in more maxima being marked by points than labelled with text.
ggplot(sun.spct) + geom_line() + stat_peaks(span = 21, geom = "point", colour = "red") + stat_valleys(span = 21, geom = "point", colour = "blue") + stat_peaks(span = 51, geom = "text", colour = "red", vjust = -0.3, label.fmt = "%3.0f nm") + stat_valleys(span = 51, geom = "text", colour = "blue", vjust = 1.2, label.fmt = "%3.0f nm")
This final example shows a few additional tricks used in this case to mark and label the maximum of the spectrum. This example also demonstrates why it is important that these are stats. The peaks are searched and labels generated once for each group, in this case each facet.
ggplot(two_suns.spct) + aes(color = spct.idx) + geom_line() + ylim(NA, 0.9) + stat_peaks(span = NULL, color = "black") + stat_peaks(span = NULL, geom = "text", vjust = -0.5, size = 3, color = "black", aes(label = paste(stat(y.label), "at", after_stat(x.label), "nm"))) + facet_grid(rows = vars(spct.idx))
An additional statistics, stat_spikes()
, returns the same computed
variables as stat_peaks()
and stat_valleys()
but detects only very
narrow peaks and valleys, usually called spikes. They are common in
Raman spectra but can also appear occasionally in any measurement with
array spectrometers when integration times are long or if some pixels in
an array detector are defective (e.g., hot pixels and dead pixels).
Usually spikes are considered "noise" to be removed, but occasionally we
may want to highlight in a plot the spikes. (Spikes can be replaced by values
interpolated from neighbours with function despike()
from package
'photobiology'.)
ggplot(white_led.raw_spct, aes(w.length, counts_3)) + geom_line() + stat_spikes(color = "red", z.threshold = 8, max.spike.width = 7)
ggplot(despike(white_led.raw_spct, z.threshold = 8, max.spike.width = 7), aes(w.length, counts_3)) + geom_line() + stat_spikes(color = "red", z.threshold = 8, max.spike.width = 7)
This stat calculates the colour corresponding to each $x$-value (assumed
expressed in nanometres) and adds it to the data. It does not summarize
the data like stat_summary()
nor does it subset the data like
stat_peaks
, consequently the plot does not require any additional
geom to have all observations plotted. It sets both color and fill
aesthetics to a suitable default.
ggplot(sun.spct) + stat_color() + scale_color_identity()
All statistics that generate color definitions from wavelengths or
wavebands have a parameter, chroma.type
to which can be used to select
the color matching function or color coordinates to be used. If we use
chromaticity coordinates, "CC"
, instead of the default color matching
fucntion, "CMF"
, the apparent luminance is not taken into account,
only the hue.
ggplot(sun.spct) + stat_color(chroma.type = "CC") + scale_color_identity()
We here show pseudo honey-bee vision colors. Bees have trichromic vision, but see green, blue and ultraviolet (GBU) instead of red, green and blue (RGB). The luminance is matched to wavelengths, but the colors shifted so that green becomes red, blue becomes green, and ultraviolet becomes blue.
ggplot(clip_wl(sun.spct)) + stat_color(chroma.type = beesxyzCMF.spct) + scale_color_identity()
By use of a filled shape and adding a black border by overriding the default color aesthetic and over-plotting these points on top of a line, we obtain a better separation from the background.
ggplot(sun.spct) + geom_line() + stat_color(shape = 21, color = "black") + scale_fill_identity()
With a trick using many narrow bars we can fill the area under the line with a the calculated colours. This works satisfactorily as the data set has a small wavelength step, as in this case we are using a bar of uniform colour for each wavelength value in the data set.
ggplot(sun.spct) + stat_color(geom = "bar") + geom_line(color = "black") + geom_point(shape = 21, color = "black", stroke = 1.2, fill = "white") + scale_fill_identity() + scale_color_identity() + theme_bw()
ggplot(sun.spct) + stat_color(geom = "bar", chroma.type = beesxyzCMF.spct) + geom_line(color = "black") + geom_point(shape = 21, color = "black", stroke = 1.2, fill = "white") + scale_fill_identity() + scale_color_identity() + theme_bw()
As final example we demonstrate a plot with facets and shape based groups.
ggplot(two_suns.spct) + aes(shape = spct.idx) + stat_color() + scale_color_identity() + geom_line() + facet_grid(cols = vars(spct.idx), scales = "free_y")
Our summary statistics are quite different to ggplot2
s
stat_summary()
. One could criticize that they calculates summaries
using a grouping that is not based on a ggplot aesthetic. This is a
deviation from the grammar of graphics but allows the calculation of
summaries for an arbitrary region of the range of $x$-values in the
spectral data.
Three statistics generate only graphic output. First we demonstrate
stat_wb_box()
that produces a filled box for each waveband, filled
with the color corresponding to the waveband.
ggplot(sun.spct) + geom_line() + stat_wb_box(w.band = VIS_bands(), color = "white") + scale_fill_identity()
The statistics stat_wb_column
outputs a column for each waveband,
with an area equal to the integral for the corresponding region of the
spectrum.
ggplot(sun.spct) + stat_wb_column(w.band = VIS_bands()) + geom_line() + scale_fill_identity()
The statistic stat_wd_hbar
outputs a horizontal bar showing the mean
spectral y-value for each waveband.
ggplot(sun.spct) + geom_line() + stat_wb_hbar(w.band = VIS_bands(), size = 1.2) + scale_color_identity()
These graphical summaries are frequently used together with text and label elements with names or numerical summaries.
ggplot(sun.spct) + geom_line() + stat_wb_box(w.band = PAR(), color = "white", ypos.fixed = 0.85) + stat_wb_label(w.band = PAR(), ypos.fixed = 0.85) + scale_fill_identity() + scale_color_identity()
The summary is calculated for a range of wavelengths, and the range
argument defaults to the range of wavelengths in each group defined by
other aesthetics. The default geom is "text"
.
ggplot(sun.spct) + geom_line() + stat_wl_summary()
We can optionally supply an argument for range
to limit the summary to
a certain part of the spectrum, in which case the use of the default
"text"
geom is misleading. We add the line last so that it is drawn
on top of the rectangle.
ggplot(sun.spct) + stat_wl_summary(range = c(300,350), geom = "rect") + geom_line()
Here we show how to add horizontal line and label for the overall mean,
by adding the same stat twice, using different values for geom
.
ggplot(sun.spct) + geom_line() + stat_wl_summary(geom = "hline", color = "red") + stat_wl_summary(label.fmt = "Mean = %.3g", color = "red", vjust = -0.3)
Or we can add the aesthetic twice with two different geoms to get the
value plotted as a rectangular area and the value as formatted text. We
use vjust
to move the text above the end of the bar, instead of it
being centred on the value itself.
ggplot(sun.spct) + stat_wl_summary(range = c(400,500), geom = "rect", alpha = 0.2, fill = color_of(450)) + stat_wl_summary(range = c(400,500), label.fmt = "Mean = %.3g", vjust = -0.3, geom = "text") + geom_line()
An example using the color
aesthetic for grouping and moving the
text label down. Setting
ggplot(two_suns.spct) + aes(color = spct.idx) + geom_line() + stat_wl_summary(geom = "hline") + stat_wl_summary(label.fmt = "Mean = %.3g", vjust = 1.2, show.legend = FALSE) + facet_grid(cols = vars(spct.idx))
Same example as above but using a free scale for $y$, still working as expected.
ggplot(two_suns.spct) + aes(color = spct.idx) + geom_line() + stat_wl_summary(geom = "hline") + stat_wl_summary(label.fmt = "Mean = %.3g", vjust = 1.2, show.legend = FALSE) + facet_grid(cols = vars(spct.idx), scales = "free_y")
Our stat_wb_mean()
is quite different to ggplot2
s stat_summary()
.
One could criticize that it calculates summaries using a grouping that
is not based on a ggplot aesthetic. This is a deviation from the
grammar of graphics but allows the calculation of summaries for an
arbitrary waveband of the spectrum based on photobiology::waveband
objects, or lists of such objects. In contrast to stat_wl_summary()
this allows the use of several ranges, and also of different weighting
functions. This function returns both mean and total values for each
waveband. It differs from stat_wb_total()
only in the default
aesthetics set.
The first example uses a waveband
object created on-the-fly and
defining a range of wavelengths.
ggplot(sun.spct) + geom_line() + stat_wb_hbar(w.band = PAR(), size = 1.3) + stat_wb_mean(aes(color = ..wb.color..), w.band = PAR(), ypos.mult = 0.95) + scale_color_identity() + scale_fill_identity() + theme_bw()
If a numeric vector or a spectrum is supplied as argument to waveband
,
its range is calculated and used to construct a temporary waveband
object.
ggplot(sun.spct) + stat_wb_hbar(w.band = c(400,500), size = 1.2) + stat_wb_mean(aes(color = ..wb.color..), w.band = c(400,500), ypos.mult = 0.95) + geom_line() + scale_color_identity() + scale_fill_identity() + theme_bw()
Lists of wavebands, either user-defined or as in this case using a list constructor can be also used.
ggplot(sun.spct) + geom_line() + stat_wb_hbar(w.band = list(Blue(), Red()), size = 1.2) + stat_wb_mean(aes(color = ..wb.color..), w.band = list(Blue(), Red()), ypos.mult = 0.95, hjust = 1, angle = 90) + scale_color_identity() + scale_fill_identity() + theme_bw()
Our stat_wb_total()
is quite different to ggplot2
s stat_summary()
.
One could criticize that it calculates summaries using a grouping that
is not based on a ggplot aesthetic. This is a deviation from the
grammar of graphics but allows the calculation of summaries for an
arbitrary waveband of the spectrum based on photobiology::waveband
objects, or lists of such objects. In contrast to stat_wl_summary()
this allows the use of several ranges, and also of different weighting
functions. This function returns both mean and total values for each
waveband. It differs from stat_wb_mean()
only in the default
aesthetics set.
The first example uses a waveband
object created on-the-fly and
defining a range of wavelengths.
ggplot(sun.spct) + stat_wb_box(w.band = PAR()) + stat_wb_total(w.band = PAR()) + geom_line() + scale_color_identity() + scale_fill_identity() + theme_bw()
If a numeric vector or a spectrum is supplied as argument to waveband
,
its range is calculated and used to construct a temporary waveband
object.
ggplot(sun.spct) + stat_wb_box(w.band = c(400,500)) + stat_wb_total(w.band = c(400,500)) + geom_line() + scale_color_identity() + scale_fill_identity() + theme_bw()
Lists of wavebands, either user-defined or as in this case using
constructor defined in package photobiologyWavebands
can be also used.
In the case of totals, areas represent them graphically in a very useful
way.
ggplot(sun.spct * yellow_gel.spct) + stat_wb_box(w.band = Plant_bands(), color = "white", ypos.fixed = 0.7) + stat_wb_column(w.band = Plant_bands(), color = "white", alpha = 0.5) + stat_wb_mean(w.band = Plant_bands(), label.fmt = "%1.2f", ypos.fixed = 0.7, size = 2) + geom_line() + scale_fill_identity() + scale_color_identity() + theme_bw()
The _stat_s in previous sections can be used for non-weighed
irradiances, but not for BSWFs. These irrad
_stat_s have additional
formal parameters for passing metadata, and use method
photobiology::irrad()
internally on a photobiology::source_spct
object constructed from the data for $x$ and $y$ aesthetics. Function
stat_wb_sirrad()
is equivalent to stat_wb_mean()
and function
stat_wb_irrad()
is equivalent to stat_wb_total()
following the same
naming convention as in package photobiology
.
ggplot(sun.spct) + stat_wb_box(w.band = PAR()) + stat_wb_irrad(w.band = PAR(), unit.in = "energy", time.unit = "second") + geom_line() + scale_color_identity() + scale_fill_identity() + theme_bw()
ggplot(sun.spct, unit.out = "photon") + stat_wb_box(w.band = PAR()) + stat_wb_irrad(w.band = PAR(), unit.in = "photon", time.unit = "second", aes(label = sprintf("%s = %.3g", ..wb.name.., ..wb.yint.. * 1e6))) + geom_line() + scale_color_identity() + scale_fill_identity() + theme_bw()
Also following the same naming convention as in package photobiology
,
e
and q
versions of these functions default to energy and photon
based quantities to "seconds"
for time unit.
ggplot(sun.spct) + stat_wb_box(w.band = PAR()) + stat_wb_e_irrad(w.band = PAR()) + geom_line() + scale_color_identity() + scale_fill_identity() + theme_bw()
We can also use waveband
objects describing biological spectral
weighting functions (BSWFs), such as CIE's erythema function.
ggplot(sun.spct) + stat_wb_box(w.band = CIE()) + stat_wb_e_irrad(w.band = CIE()) + geom_line() + scale_color_identity() + scale_fill_identity() + theme_bw()
For daily data we need to override the default time unit.
ggplot(sun.daily.spct) + stat_wb_box(w.band = CIE()) + stat_wb_e_irrad(w.band = CIE(), time.unit = "day", label.mult = 1e-3) + geom_line() + scale_color_identity() + scale_fill_identity() + theme_bw()
Here we pass a list of waveband
objects. And add areas to facilitate
comparisons as irradiances are integral over wavelengths.
ggplot(sun.spct, unit.out = "photon") + stat_wb_box(w.band = VIS_bands(), color = "black") + stat_wb_column(w.band = VIS_bands(), color = NA, alpha = 0.5) + stat_wb_q_irrad(w.band = VIS_bands(), label.mult = 1e6, size = 2) + geom_line() + scale_color_identity() + scale_fill_identity() + theme_bw()
Spectral irradiances are equivalent to means, and can be best represented graphically as horizontal bars.
ggplot(sun.spct) + geom_line() + stat_wb_hbar(w.band = PAR(), size = 1.4) + stat_wb_e_sirrad(aes(color = ..wb.color..), w.band = PAR(), ypos.mult = 0.95) + scale_color_identity() + scale_fill_identity() + theme_bw()
ggplot(sun.spct, unit.out = "photon") + stat_wb_column(w.band = PAR(), alpha = 0.8) + stat_wb_q_sirrad(w.band = PAR(), mapping = aes(label = sprintf("Total %s = %.3g", ..wb.name.., ..wb.yint.. * 1e6)), ypos.mult = 0.55) + stat_wb_q_sirrad(w.band = PAR(), mapping = aes(label = sprintf("Mean %s = %.3g", ..wb.name.., ..wb.ymean.. * 1e6)), ypos.mult = 0.45) + geom_line() + scale_color_identity() + scale_fill_identity() + theme_bw()
ggplot(sun.spct) + stat_wb_box(w.band = waveband(CIE()), ypos.fixed = 0.85) + stat_wb_e_sirrad(w.band = CIE(), ypos.fixed = 0.85) + geom_line() + scale_color_identity() + scale_fill_identity() + theme_bw()
ggplot(sun.daily.spct) + stat_wb_box(w.band = waveband(CIE()), ypos.fixed = 34e3) + stat_wb_e_sirrad(w.band = CIE(), label.fmt = "%.2g kj / day", time.unit = "day", ypos.fixed = 34e3) + geom_line() + scale_color_identity() + scale_fill_identity() + theme_bw()
my.bands <- split_bands(c(300,800), length.out = 10) ggplot(sun.spct, unit.out = "photon") + stat_wb_hbar(w.band = my.bands, size = 1.4) + stat_wb_q_sirrad(geom = "label", w.band = my.bands, size = 2.5, ypos.fixed = 3.5e-6) + geom_line() + scale_color_identity() + scale_fill_identity() + theme_bw()
ggplot(sun.spct) + stat_wb_column(w.band = VIS_bands(), alpha = 0.5) + stat_wb_e_irrad(w.band = VIS_bands(), angle = 90, ypos.fixed = 0.05, hjust = 0, aes(label = paste(..wb.name.., ..y.label.., sep = " = "))) + geom_line() + scale_color_identity() + scale_fill_identity() + theme_bw()
ggplot(sun.spct, unit.out = "photon") + stat_wb_column(w.band = VIS_bands(), alpha = 0.5) + stat_wb_q_irrad(w.band = VIS_bands(), angle = 90, label.mult = 1e6, ypos.fixed = 1e-7, hjust = 0, aes(label = paste(..wb.name.., ..y.label.., sep = " = "))) + geom_line() + scale_color_identity() + scale_fill_identity() + theme_bw()
my.bands <- split_bands(c(300,800), length.out = 10) ggplot(sun.spct) + stat_wb_column(w.band = my.bands, alpha = 0.5) + stat_wb_e_irrad(w.band = my.bands, angle = 90, ypos.fixed = 0.05, hjust = 0) + geom_line() + scale_color_identity() + scale_fill_identity() + theme_bw()
Sometimes we may want to only annotate a plot with waveband names and
regions without calculating any summary quantity. stat_wb_label()
fills this role. Although the same result can be achieved with some of
the summary statistics, if no summary is needed this statistic can avoid
unnecessary computations, and more importantly used in plots where the
$y$ is not mapped, as only the $x$ aesthetic is required.
ggplot(data.frame(w.length = 300:800), aes(w.length)) + stat_wl_strip(w.band = VIS_bands(), ymax = Inf, ymin = -Inf) + stat_wb_label(w.band = VIS_bands(), angle = 90) + scale_fill_identity() + scale_color_identity() + scale_y_continuous(labels = NULL) + scale_x_continuous(breaks = seq(from = 300, to = 800, by = 25)) + labs(x = "Wavelength (nm)", title = "Colours according to ISO standard") + theme_minimal()
We can also in a similar way make a plot comparing different sets of wavebands, in the next example we compare the VIS and NIR bands of the different imagers used in Landsat missions 1 to 8.
ggplot(data.frame(w.length = 300:1100), aes(w.length)) + stat_wl_strip(w.band = RBV_bands(), ymax = 1, ymin = 3) + stat_wb_label(w.band = RBV_bands(), ypos.fixed = 2, angle = 90, vjust = 0.3, size = 3) + stat_wl_strip(w.band = MSS_bands(), ymax = 4, ymin = 6, na.rm = TRUE) + stat_wb_label(w.band = MSS_bands(), ypos.fixed = 5, angle = 90, vjust = 0.3, size = 3) + stat_wl_strip(w.band = ETM_bands(), ymax = 7, ymin = 9, na.rm = TRUE) + stat_wb_label(w.band = ETM_bands(), ypos.fixed = 8, angle = 90, vjust = 0.3, size = 3) + stat_wl_strip(w.band = OLI_bands(), ymax = 10, ymin = 12, na.rm = TRUE) + stat_wb_label(w.band = OLI_bands(), ypos.fixed = 11, angle = 90, vjust = 0.3, size = 3) + scale_fill_identity() + scale_color_identity() + scale_y_continuous(labels = c("RBV", "MSS", "TM/ETM", "OLI"), breaks = c(2,5,8,11), limits = c(0, 13), name = "Imager", sec.axis = dup_axis(labels = c("L1-L2", "L1-L5", "L4-L7", "L8"), name = "Landsat mission")) + scale_x_continuous(breaks = seq(from = 300, to = 1200, by = 100), limits = c(400, 1100), sec.axis = dup_axis()) + labs(x = "Wavelength (nm)", title = "Landsat imagers: VIS and NIR bands") + theme_classic()
The different definitions of the ultraviolet regions.
ggplot(data.frame(w.length = 100:400), aes(w.length)) + stat_wl_strip(w.band = UV_bands("ISO"), ymax = 1, ymin = 3, color = "white") + stat_wb_label(w.band = UV_bands("ISO"), ypos.fixed = 2, size = 3) + stat_wl_strip(w.band = UV_bands("CIE"), ymax = 4, ymin = 6, color = "white") + stat_wb_label(w.band = UV_bands("CIE"), ypos.fixed = 5, size = 3) + stat_wl_strip(w.band = UV_bands("plants"), ymax = 7, ymin = 9, color = "white") + stat_wb_label(w.band = UV_bands("plants"), ypos.fixed = 8, size = 3) + stat_wl_strip(w.band = UV_bands("none"), ymax = 10, ymin = 12, color = "white") + stat_wb_label(w.band = UV_bands("none"), ypos.fixed = 11, size = 3) + stat_wl_strip(w.band = UV_bands("medical"), ymax = 13, ymin = 15, color = "white") + stat_wb_label(w.band = UV_bands("medical"), ypos.fixed = 14, size = 3) + scale_fill_identity() + scale_color_identity() + scale_y_continuous(labels = c("ISO", "CIE", "plants", "none", "medical"), breaks = c(2,5,8,11,14), limits = c(0, 16), name = "Definition", sec.axis = dup_axis(labels = c("use", "use", "use?", "avoid!", "avoid!"), name = "Recommendation")) + scale_x_continuous(breaks = c(seq(from = 100, to = 400, by = 50), 280, 315), limits = c(100, 400), sec.axis = dup_axis(breaks = c(100, 150, 200, 220, 250, 290, 320, 340, 400))) + labs(x = "Wavelength (nm)", title = "UV bands", subtitle = "According to ISO standard, CIE recommendations, and non-standard use") + theme_classic()
It should be noted that this approach is rather different from the way one would normally plot a horizontal bar plot with the grammar of graphics of 'ggplot2', but for plottings existing waveband definitions it is convenient and ensures that the waveband definitions agree with those used for computing summary quantities elsewhere.
The stat_wl_summary()
and stat_wb_mean()
return a reduced data set
with fewer rows than the original data. stat_wl_strip()
depending on
the input, can also return a data set with more rows than the input
data. This is the default behaviour, with w.band
with argument NULL
.
This stat operates only on the variable mapped to the x aesthetic,
a y-mapping is not required as input.
my.data <- data.frame(x = 300:800) ggplot(my.data, aes(x)) + stat_wl_strip(ymin = -1, ymax = 1, color = NA) + scale_fill_identity()
The default geom is "rect"
which with suitable mappings of ymin
and ymax
aesthetics can be used to add a colour guide to the
x-axis (if its scale maps wavelengths in nanometres). When w.band
is
NULL
a long series of contiguous wavebands is generated to create the
illusion of a continuous colour gradient.
ggplot(sun.spct) + geom_line() + stat_wl_strip(ymin = -Inf, ymax = -0.025) + scale_fill_identity() + theme_bw()
When a list of wavebands is supplied, it is used for the calculation of colours. These calculations do not use the spectral irradiance, they simply assume a flat spectrum, so the represent the colours of the wavelengths, rather than the colour of the light described by the spectral irradiance.
ggplot(sun.spct) + geom_line() + stat_wl_strip(w.band = VIS_bands(), ymin = -Inf, ymax = -0.025) + scale_fill_identity() + theme_bw()
stat_wl_strip()
can also used to produce a background layer with
colours corresponding to wavebands. Here we use alpha = 0.5
to add
transparency.
ggplot(sun.spct) + stat_wl_strip(w.band = VIS_bands(), ymin = -Inf, ymax = Inf, alpha = 0.4) + scale_fill_identity() + geom_line() + theme_bw()
By default an almost continuous colour gradient can be generated for the background.
ggplot(sun.spct) + stat_wl_strip(alpha = 0.4, ymin = -Inf, ymax = Inf) + scale_fill_identity() + geom_line() + theme_bw()
The stats described above can be used together to produce more complex
plots. This is just one possibility out of a vast range. Be aware that
when adding many layers to the same plot, the order of the layers and
adjusting their transparency using the alpha
aesthetic is very
important, and best tuned by trial and error.
ggplot(sun.spct, unit.out = "photon") + stat_wl_strip(alpha = 0.4, ymin = -Inf, ymax = Inf) + stat_wb_box(w.band = PAR()) + stat_wb_total(w.band = PAR(), label.mult = 1e6, aes(label = paste(..wb.name.., " = ", ..y.label.., sep = ""))) + geom_line() + scale_fill_identity() + scale_color_identity() + theme_bw()
A simple geom called "spct"
is defined. It differs from geom
"area"
only in the default position
which is "stacked"
for geom
"area"
and "identity"
for geom "spct"
which is usually better
for spectra.
ggplot(sun.spct) + geom_spct()
Using as fill the color calculated from the spectral data is different to earlier examples in that the spectral irradiance is actually taken into account in the calculation of the colour, instead of just the wavelength range.
ggplot(sun.spct) + geom_spct(fill = color_of(sun.spct))
ggplot(sun.spct * yellow_gel.spct) + geom_spct(fill = color_of(sun.spct * yellow_gel.spct))
Some of the examples in previous sections can be simplified by use of
wl_guide()
and wb_guide()
which add both the statistics and the
scale, and provide a default mapping for both ymin
and ymax
. This
is handy for simple plots, but it can generate spurious warnings due to
the replacement of existing scales with identical ones. In general only
one of wl_guide()
or wb_guide()
should be used in a plot, and each
one, only once. They just save some typing for the simplest uses, but
are not suitable for complex decorations.
The examples for stat_wl_strip
can be simplified by use of
wl_guide()
which adds both the statistics and the scale, and provides
default mappings for both ymin
(-Inf
) and ymax
(Inf
). Another
important difference is that the "rect"
geom used cannot be set to a
different one by the user.
ggplot(sun.spct) + wl_guide(alpha = 0.4) + geom_line()
ggplot(sun.spct) + wl_guide(ymax = -0.025) + geom_line()
This example produces a plot with a very different look than earlier ones, but can also be achieved with a very succinct statement.
ggplot(sun.spct) + wl_guide() + geom_spct(alpha = 0.75, colour = "white", size = 1)
In the next example we demonstrate a trick achieved by over-plotting two
lines of different width (size
) to make the spectrum visible on a
background of variable luminosity and colour.
ggplot(sun.spct) + wl_guide() + geom_line(size = 2, colour = "white") + geom_line(size = 1, colour = "black") + geom_hline(yintercept = 0, colour = "grey92") + theme_bw()
color_chart(colors())
color_chart(grep("blue", colors(), value = TRUE), ncol = 5, text.size = 4)
color_chart(w_length2rgb(570:689, color.name = as.character(570:689)), use.names = TRUE, text.size = 4) + ggtitle("Reddish colors", subtitle = "Labels: wavelength (nm)")
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