Nothing
#' Create a complete ggplot for response spectra.
#'
#' This function returns a ggplot object with an annotated plot of a
#' response_spct object.
#'
#' @note Note that scales are expanded so as to make space for the annotations.
#' The object returned is a ggplot objects, and can be further manipulated.
#'
#' @param spct a response_spct object.
#' @param w.band list of waveband objects.
#' @param range an R object on which range() returns a vector of length 2, with
#' min annd max wavelengths (nm).
#' @param pc.out logical, if TRUE use percent instead of fraction of one for
#' normalized spectral data.
#' @param label.qty character string giving the type of summary quantity to use
#' for labels, one of "mean", "total", "contribution", and "relative".
#' @param span a peak is defined as an element in a sequence which is greater
#' than all other elements within a window of width span centered at that
#' element.
#' @param wls.target numeric vector indicating the spectral quantity values for
#' which wavelengths are to be searched and interpolated if need. The
#' \code{character} strings "half.maximum" and "half.range" are also accepted
#' as arguments. A list with \code{numeric} and/or \code{character} values is
#' also accepted.
#' @param annotations a character vector.
#' @param geom character The name of a ggplot geometry, currently only
#' \code{"area"}, \code{"spct"} and \code{"line"}. The default \code{NULL}
#' selects between them based on \code{stacked}.
#' @param text.size numeric size of text in the plot decorations.
#' @param idfactor character Name of an index column in data holding a
#' \code{factor} with each spectrum in a long-form multispectrum object
#' corresponding to a distinct spectrum. If \code{idfactor=NULL} the name of
#' the factor is retrieved from metadata or if no metadata found, the
#' default "spct.idx" is tried.
#' @param facets logical or integer Indicating if facets are to be created for
#' the levels of \code{idfactor} when \code{spct} contain multiple spectra in
#' long form.
#' @param na.rm logical.
#' @param ylim numeric y axis limits,
#' @param ... currently ignored.
#'
#' @return a \code{ggplot} object.
#'
#' @keywords internal
#'
e_rsp_plot <- function(spct,
w.band,
range,
pc.out,
label.qty,
span,
wls.target,
annotations,
geom,
text.size,
idfactor,
facets,
ylim,
na.rm,
...) {
if (!is.response_spct(spct)) {
stop("e_Rsp_plot() can only plot response_spct objects.")
}
spct[["s.q.response"]] <- NULL
if (!is.null(geom) && !geom %in% c("area", "line", "spct")) {
warning("'geom = ", geom, "' not supported, using default instead.")
geom <- NULL
}
if (is.null(ylim) || !is.numeric(ylim)) {
ylim <- rep(NA_real_, 2L)
}
if (!is.null(range)) {
spct <- trim_wl(spct, range = range)
}
if (!is.null(w.band)) {
w.band <- trim_wl(w.band, range = range(spct))
}
exposure.label <- NA
if (is_scaled(spct)) {
if (pc.out) {
warning("Percent scale supported only for normalized cps_spct objects.")
pc.out <- FALSE
}
s.rsp.label <- expression(Spectral~~energy~~response~~k %*% R[E~lambda]~~("rel."))
rsp.label.total <- "atop(k %*% R[E], (\"rel.\"))"
rsp.label.avg <- "atop(bar(k %*% R[E~lambda]), (\"rel.\"))"
} else if (is_normalized(spct)) {
if (!pc.out) {
multiplier.label <- "rel."
} else {
multiplier.label <- "%"
}
norm.ls <- photobiology::getNormalization(spct)
norm.wl <- round(norm.ls[["norm.wl"]], digits = 1)
s.rsp.label <-
bquote(Spectral~~energy~~response~~R[E~lambda]/R[E~lambda==.(norm.wl)]~~(.(multiplier.label)))
rsp.label.total <- bquote(atop(integral(R[E]/R[E~lambda==.(norm.wl)], min, max), (.(multiplier.label))))
rsp.label.avg <- bquote(atop(bar(R[E~lambda]/R[E](lambda==.(norm.wl))), (.(multiplier.label))))
} else {
if (pc.out) {
warning("Percent scale supported only for normalized cps_spct objects.")
pc.out <- FALSE
}
time.unit <- getTimeUnit(spct)
if (!length(time.unit)) {
time.unit <- "unkonwn"
}
time.unit.char <- duration2character(time.unit)
if (time.unit.char=="second") {
s.rsp.label <- expression(Spectral~~energy~~response~~R[E~lambda]~~(resp.~~unit~~s^{-1}~nm^{-1}))
rsp.label.total <- "atop(R[E], (resp.~~unit~~s^{-1}))"
rsp.label.avg <- "atop(bar(R[E~lambda]), (resp.~~unit~~s^{-1}~nm^{-1}))"
} else if (time.unit.char=="day") {
s.rsp.label <- expression(Spectral~~energy~~response~~R[E~lambda]~~(resp.~~unit~~d^{-1}~nm^{-1}))
rsp.label.total <- "atop(R[E], (resp.~~unit~~d^{-1}))"
rsp.label.avg <- "atop(bar(R[E~lambda]), (resp.~~unit~~d^{-1}~nm^{-1}))"
} else if (time.unit.char=="hour") {
s.rsp.label <- expression(Spectral~~energy~~response~~R[E~lambda]~~(resp.~~unit~~h^{-1}~nm^{-1}))
rsp.label.total <- "atop(R[E], (resp.~~unit~~h^{-1}))"
rsp.label.avg <- "atop(bar(R[E~lambda]), (resp.~~unit~~h^{-1}~nm^{-1}))"
} else if (time.unit.char=="duration") {
s.rsp.label <- expression(Spectral~~energy~~response~~R[E~lambda]~~(resp.~~unit~nm^{-1}))
rsp.label.total <- "atop(R[E], (resp.~~unit))"
rsp.label.avg <- "atop(bar(R[E~lambda]), (resp.~~unit~nm^{-1}))"
exposure.label <- paste("Length of time:",
ifelse(lubridate::is.duration(time.unit),
as.character(time.unit), "unknown"))
} else if (time.unit.char=="exposure") {
s.rsp.label <- expression(Spectral~~energy~~response~~R[E~lambda]~~(resp.~~unit~nm^{-1}))
rsp.label.total <- "atop(R[E], (resp.~~unit))"
rsp.label.avg <- "atop(bar(R[E~lambda]), (resp.~~unit~nm^{-1}))"
} else {
s.rsp.label <- expression(Spectral~~energy~~response~~R[E~lambda]~~(arbitrary~~units))
rsp.label.total <- "atop(R[E], (arbitrary~~units))"
rsp.label.avg <- "atop(bar(R[E~lambda]), (arbitrary~~units))"
}
}
if (!is.na(ylim[1])) {
y.min <- ylim[1]
spct[["s.e.response"]] <- ifelse(spct[["s.e.response"]] < y.min,
NA_real_,
spct[["s.e.response"]])
} else {
y.min <- min(spct[["s.e.response"]], 0, na.rm = TRUE)
}
if (!is.na(ylim[2])) {
y.max <- ylim[2]
spct[["s.e.response"]] <- ifelse(spct[["s.e.response"]] > y.max,
NA_real_,
spct[["s.e.response"]])
} else {
y.max <- max(spct[["s.e.response"]], y.min, 0, na.rm = TRUE)
}
if (label.qty == "total") {
rsp.label <- "integral(R[E](lambda))"
} else if (label.qty %in% c("average", "mean")) {
rsp.label <- "bar(R[E](lambda))"
} else if (label.qty == "contribution") {
rsp.label <- "atop(Contribution~~to~~total, R[E]~~(\"/1\"))"
} else if (label.qty == "contribution.pc") {
rsp.label <- "atop(Contribution~~to~~total, R[E]~~(\"%\"))"
} else if (label.qty == "relative") {
rsp.label <- "atop(Relative~~to~~sum, R[E]~~(\"/1\"))"
} else if (label.qty == "relative.pc") {
rsp.label <- "atop(Relative~~to~~sum, R[E]~~(\"%\"))"
} else {
rsp.label <- ""
}
plot <- ggplot(spct, aes(x = .data[["w.length"]], y = .data[["s.e.response"]]))
temp <- find_idfactor(spct = spct,
idfactor = idfactor,
facets = facets,
annotations = annotations)
plot <- plot + temp$ggplot_comp
annotations <- temp$annotations
# We want data plotted on top of the boundary lines
# Negative response is valid!
if ("boundaries" %in% annotations) {
plot <- plot + geom_hline(yintercept = 0, linetype = "dashed", colour = "black")
}
if (!is.null(geom) && geom %in% c("area", "spct")) {
plot <- plot + geom_spct(fill = "black", colour = NA, alpha = 0.2)
}
plot <- plot + geom_line(na.rm = na.rm)
plot <- plot + labs(x = "Wavelength (nm)", y = s.rsp.label)
if (length(annotations) == 1 && annotations == "") {
return(plot)
}
plot <- plot + scale_fill_identity() + scale_color_identity()
plot <- plot + decoration(w.band = w.band,
y.max = y.max,
y.min = y.min,
x.max = max(spct),
x.min = min(spct),
annotations = annotations,
label.qty = label.qty,
span = span,
wls.target = wls.target,
summary.label = rsp.label,
text.size = text.size,
na.rm = TRUE)
if (!is.na(exposure.label)) {
plot <- plot + annotate("text",
x = min(spct),
y = y.max,
label = exposure.label,
vjust = -0.5,
hjust = 0,
size = rel(3),
na.rm = TRUE )
}
if (!is.null(annotations) &&
length(intersect(c("boxes", "segments", "labels", "summaries",
"colour.guide", "reserve.space"), annotations)) > 0L) {
y.limits <- c(y.min, y.min + (y.max - y.min) * 1.25)
x.limits <- c(min(spct) - wl_expanse(spct) * 0.025, NA) # NA needed because of rounding errors
} else {
y.limits <- c(y.min, y.max)
x.limits <- range(spct)
}
if (abs(y.min) < 5e-2 && (abs(y.max - 1) < 5.e-2)) {
plot <- plot +
scale_y_continuous(breaks = c(0, 0.25, 0.5, 0.75, 1), limits = y.limits)
} else {
plot <- plot + scale_y_continuous(limits = y.limits)
}
plot + scale_x_continuous(limits = x.limits, breaks = scales::pretty_breaks(n = 7))
}
#' Create a complete ggplot for response spectra.
#'
#' This function returns a ggplot object with an annotated plot of a
#' response_spct object.
#'
#' @note Note that scales are expanded so as to make space for the annotations.
#' The object returned is a ggplot objects, and can be further manipulated.
#'
#' @param spct a response_spct object.
#' @param w.band list of waveband objects.
#' @param range an R object on which range() returns a vector of length 2, with
#' min annd max wavelengths (nm).
#' @param pc.out logical, if TRUE use percent instead of fraction of one for
#' normalized spectral data.
#' @param label.qty character string giving the type of summary quantity to use
#' for labels, one of "mean", "total", "contribution", and "relative".
#' @param span a peak is defined as an element in a sequence which is greater
#' than all other elements within a window of width span centered at that
#' element.
#' @param wls.target numeric vector indicating the spectral quantity values for
#' which wavelengths are to be searched and interpolated if need. The
#' \code{character} strings "half.maximum" and "half.range" are also accepted
#' as arguments. A list with \code{numeric} and/or \code{character} values is
#' also accepted.
#' @param annotations a character vector.
#' @param geom character The name of a ggplot geometry, currently only
#' \code{"area"}, \code{"spct"} and \code{"line"}. The default \code{NULL}
#' selects between them based on \code{stacked}.
#' @param text.size numeric size of text in the plot decorations.
#' @param idfactor character Name of an index column in data holding a
#' \code{factor} with each spectrum in a long-form multispectrum object
#' corresponding to a distinct spectrum. If \code{idfactor=NULL} the name of
#' the factor is retrieved from metadata or if no metadata found, the
#' default "spct.idx" is tried.
#' @param facets logical or integer Indicating if facets are to be created for
#' the levels of \code{idfactor} when \code{spct} contain multiple spectra in
#' long form.
#' @param ylim numeric y axis limits,
#' @param na.rm logical.
#' @param ... currently ignored.
#'
#' @return a \code{ggplot} object.
#'
#' @keywords internal
#'
q_rsp_plot <- function(spct,
w.band,
range,
pc.out,
label.qty,
span,
wls.target,
annotations,
geom,
text.size,
idfactor,
facets,
ylim,
na.rm,
...) {
if (!is.response_spct(spct)) {
stop("q_Rsp_plot() can only plot response_spct objects.")
}
spct[["s.e.response"]] <- NULL
if (!is.null(geom) && !geom %in% c("area", "line", "spct")) {
warning("'geom = ", geom, "' not supported, using default instead.")
geom <- NULL
}
if (is.null(ylim) || !is.numeric(ylim)) {
ylim <- rep(NA_real_, 2L)
}
if (!is.null(range)) {
spct <- trim_wl(spct, range = range)
}
if (!is.null(w.band)) {
w.band <- trim_wl(w.band, range = range(spct))
}
exposure.label <- NA
if (is_scaled(spct)) {
if (pc.out) {
warning("Percent scale supported only for normalized response_spct objects.")
pc.out <- FALSE
}
s.rsp.label <- expression(Spectral~~photon~~response~~k %*% R[Q~lambda]~~("rel."))
rsp.label.total <- "atop(k %*% R[Q], (\"rel.\"))"
rsp.label.avg <- "atop(bar(k %*% R[Q~lambda]), (\"rel.\"))"
} else if (is_normalized(spct)) {
if (!pc.out) {
multiplier.label <- "rel."
} else {
multiplier.label <- "%"
}
norm.ls <- photobiology::getNormalization(spct)
norm.wl <- round(norm.ls[["norm.wl"]], digits = 1)
s.rsp.label <-
bquote(Spectral~~photon~~response~~R[Q~lambda]/R[Q~lambda==.(norm.wl)]~~(.(multiplier.label)))
rsp.label.total <- bquote(atop(integral(R[Q~lambda], min, max), (.(multiplier.label))))
rsp.label.avg <- bquote(atop(bar(R[Q~lambda]/R[Q~lambda==.(norm.wl)]), (.(multiplier.label))))
} else {
if (pc.out) {
warning("Percent scale supported only for normalized cps_spct objects.")
pc.out <- FALSE
}
time.unit <- getTimeUnit(spct)
if (!length(time.unit)) {
time.unit <- "unkonwn"
}
time.unit.char <- duration2character(time.unit)
if (time.unit.char=="second") {
s.rsp.label <- expression(Spectral~~photon~~response~~R[Q~lambda]~~(resp.~~unit~~s^{-1}~nm^{-1}))
rsp.label.total <- "atop(R[Q], (resp.~~unit~~s^{-1}))"
rsp.label.avg <- "atop(bar(R[Q~lambda]), (resp.~~unit~~s^{-1}~nm^{-1}))"
} else if (time.unit.char=="day") {
s.rsp.label <- expression(Spectral~~photon~~response~~R[Q~lambda]~~(resp.~~unit~~d^{-1}~nm^{-1}))
rsp.label.total <- "atop(R[Q], (resp.~~unit~~d^{-1}))"
rsp.label.avg <- "atop(bar(R[Q~lambda]), (resp.~~unit~~d^{-1}~nm^{-1}))"
} else if (time.unit.char=="hour") {
s.rsp.label <- expression(Spectral~~photon~~response~~R[Q~lambda]~~(resp.~~unit~~h^{-1}~nm^{-1}))
rsp.label.total <- "atop(R[Q], (resp.~~unit~~h^{-1}))"
rsp.label.avg <- "atop(bar(R[Q~lambda]), (resp.~~unit~~h^{-1}~nm^{-1}))"
} else if (time.unit.char=="duration") {
s.rsp.label <- expression(Spectral~~photon~~response~~R[Q~lambda]~~(resp.~~unit~nm^{-1}))
rsp.label.total <- "atop(R[Q], (resp.~~unit))"
rsp.label.avg <- "atop(bar(R[Q~lambda]), (resp.~~unit~nm^{-1}))"
exposure.label <- paste("Length of time:",
ifelse(lubridate::is.duration(time.unit),
as.character(time.unit), "unknown"))
} else if (time.unit.char=="exposure") {
s.rsp.label <- expression(Spectral~~photon~~response~~R[Q~lambda]~~(resp.~~unit~nm^{-1}))
rsp.label.total <- "atop(R[Q], (resp.~~unit))"
rsp.label.avg <- "atop(bar(R[Q~lambda]), (resp.~~unit~nm^{-1}))"
} else {
s.rsp.label <- expression(Spectral~~photon~~response~~R[Q~lambda]~~(arbitrary~~units))
rsp.label.total <- "atop(R[Q], (arbitrary~~units))"
rsp.label.avg <- "atop(bar(R[Q~lambda]), (arbitrary~~units))"
}
}
if (!is.na(ylim[1])) {
y.min <- ylim[1]
spct[["s.q.response"]] <- ifelse(spct[["s.q.response"]] < y.min,
NA_real_,
spct[["s.q.response"]])
} else {
y.min <- min(spct[["s.q.response"]], 0, na.rm = TRUE)
}
if (!is.na(ylim[2])) {
y.max <- ylim[2]
spct[["s.q.response"]] <- ifelse(spct[["s.q.response"]] > y.max,
NA_real_,
spct[["s.q.response"]])
} else {
y.max <- max(spct[["s.q.response"]], y.min, 0, na.rm = TRUE)
}
if (label.qty == "total") {
rsp.label <- "integral(R[Q](lambda))"
} else if (label.qty %in% c("average", "mean")) {
rsp.label <- "bar(R[Q](lambda))"
} else if (label.qty == "contribution") {
rsp.label <- "atop(Contribution~~to~~total, R[Q]~~(\"/1\"))"
} else if (label.qty == "contribution.pc") {
rsp.label <- "atop(Contribution~~to~~total, R[Q]~~(\"%\"))"
} else if (label.qty == "relative") {
rsp.label <- "atop(Relative~~to~~sum, R[Q]~~(\"/1\"))"
} else if (label.qty == "relative.pc") {
rsp.label <- "atop(Relative~~to~~sum, R[Q]~~(\"%\"))"
} else {
rsp.label <- ""
}
plot <- ggplot(spct, aes(x = .data[["w.length"]], y = .data[["s.q.response"]]))
temp <- find_idfactor(spct = spct,
idfactor = idfactor,
facets = facets,
annotations = annotations)
plot <- plot + temp$ggplot_comp
annotations <- temp$annotations
# We want data plotted on top of the boundary lines
# Negative response is valid!
if ("boundaries" %in% annotations) {
plot <- plot + geom_hline(yintercept = 0, linetype = "dashed", colour = "black")
}
if (!is.null(geom) && geom %in% c("area", "spct")) {
plot <- plot + geom_spct(fill = "black", colour = NA, alpha = 0.2)
}
plot <- plot + geom_line(na.rm = na.rm)
plot <- plot + labs(x = "Wavelength (nm)", y = s.rsp.label)
if (length(annotations) == 1 && annotations == "") {
return(plot)
}
plot <- plot + scale_fill_identity() + scale_color_identity()
plot <- plot + decoration(w.band = w.band,
y.max = y.max,
y.min = y.min,
x.max = max(spct),
x.min = min(spct),
annotations = annotations,
label.qty = label.qty,
span = span,
wls.target = wls.target,
summary.label = rsp.label,
text.size = text.size,
na.rm = TRUE)
if (!is.na(exposure.label)) {
plot <- plot + annotate("text",
x = min(spct),
y = y.max,
label = exposure.label,
vjust = -0.5,
hjust = 0,
size = rel(3),
na.rm = TRUE )
}
if (abs(y.max - 1) < 0.02 && abs(y.min) < 0.02) {
y.breaks <- c(0, 0.25, 0.5, 0.75, 1)
} else {
y.breaks <- scales::pretty_breaks(n = 5)
}
if (!is.null(annotations) &&
length(intersect(c("boxes", "segments", "labels", "summaries",
"colour.guide", "reserve.space"), annotations)) > 0L) {
y.limits <- c(y.min, y.min + (y.max - y.min) * 1.25)
x.limits <- c(min(spct) - wl_expanse(spct) * 0.025, NA) # NA needed because of rounding errors
} else {
y.limits <- c(y.min, y.max)
x.limits <- range(spct)
}
if (pc.out) {
plot <- plot +
scale_y_continuous(labels = scales::percent,
breaks = y.breaks,
limits = y.limits)
} else {
plot <-
plot + scale_y_continuous(breaks = y.breaks,
limits = y.limits)
}
plot + scale_x_continuous(limits = x.limits, breaks = scales::pretty_breaks(n = 7))
}
#' Create a complete ggplot for a response spectrum.
#'
#' These methods return a ggplot object with an annotated plot of a
#' response_spct object or of the spectra contained in a response_mspct object.
#'
#' Note that scales are expanded so as to make space for the annotations. The
#' object returned is a ggplot object, and can be further manipulated and added
#' to.
#'
#' @inheritSection decoration Plot Annotations
#' @inheritSection autotitle Title Annotations
#'
#' @param object a response_spct object or a response_mspct object.
#' @param ... in the case of collections of spectra, additional arguments passed
#' to the plot methods for individual spectra, otherwise currently ignored.
#' @param w.band a single waveband object or a list of waveband objects.
#' @param range an R object on which range() returns a vector of length 2, with
#' min annd max wavelengths (nm).
#' @param norm numeric Normalization wavelength (nm) or character string "max",
#' or "min" for normalization at the corresponding wavelength, "update" to
#' update the normalization after modifying units of expression, quantity
#' or range but respecting the previously used criterion, or "skip" to force
#' return of \code{object} unchanged.
#' @param unit.out character string indicating type of radiation units to use
#' for plotting: "photon" or its synomin "quantum", or "energy".
#' @param pc.out logical, if TRUE use percent instead of fraction of one for
#' normalized spectral data.
#' @param label.qty character string giving the type of summary quantity to use
#' for labels, one of "mean", "total", "contribution", and "relative".
#' @param span a peak is defined as an element in a sequence which is greater
#' than all other elements within a window of width span centered at that
#' element.
#' @param wls.target numeric vector indicating the spectral quantity values for
#' which wavelengths are to be searched and interpolated if need. The
#' \code{character} strings "half.maximum" and "half.range" are also accepted
#' as arguments. A list with \code{numeric} and/or \code{character} values is
#' also accepted.
#' @param annotations a character vector. For details please see sections Plot
#' Annotations and Title Annotations.
#' @param geom character The name of a ggplot geometry, currently only
#' \code{"area"}, \code{"spct"} and \code{"line"}. The default \code{NULL}
#' selects between them based on \code{stacked}.
#' @param time.format character Format as accepted by
#' \code{\link[base]{strptime}}.
#' @param tz character Time zone to use for title and/or subtitle.
#' @param norm numeric normalization wavelength (nm) or character string \code{"max"}
#' for normalization at the wavelength of highest peak, or \code{NULL} for
#' plotting the spectrum as is.
#' @param text.size numeric size of text in the plot decorations.
#' @param idfactor character Name of an index column in data holding a
#' \code{factor} with each spectrum in a long-form multispectrum object
#' corresponding to a distinct spectrum. If \code{idfactor=NULL} the name of
#' the factor is retrieved from metadata or if no metadata found, the
#' default "spct.idx" is tried.
#' @param facets logical or integer Indicating if facets are to be created for
#' the levels of \code{idfactor} when \code{spct} contain multiple spectra in
#' long form.
#' @param ylim numeric y axis limits,
#' @param object.label character The name of the object being plotted.
#' @param na.rm logical.
#'
#' @return a \code{ggplot} object.
#'
#' @export
#'
#' @seealso \code{\link[photobiology]{normalize}},
#' \code{\link[photobiology]{response_spct}},
#' \code{\link[photobiology]{waveband}},
#' \code{\link[photobiologyWavebands]{photobiologyWavebands-package}} and
#' \code{\link[ggplot2]{autoplot}}
#'
#' @examples
#'
#' autoplot(photodiode.spct)
#' autoplot(photodiode.spct, geom = "spct")
#' autoplot(photodiode.spct, unit.out = "photon")
#' autoplot(photodiode.spct, annotations = "")
#' autoplot(photodiode.spct, norm = "skip")
#' autoplot(photodiode.spct, norm = 400)
#'
#' two_sensors.mspct <-
#' response_mspct(list("Photodiode" = photodiode.spct,
#' "Coupled charge device" = ccd.spct))
#' autoplot(two_sensors.mspct, normalize = TRUE, unit.out = "photon")
#' autoplot(two_sensors.mspct, normalize = TRUE, idfactor = "Spectra")
#' autoplot(two_sensors.mspct, normalize = TRUE, facets = 2)
#' autoplot(two_sensors.mspct, normalize = TRUE, geom = "spct")
#'
#' @family autoplot methods
#'
autoplot.response_spct <-
function(object, ...,
w.band = getOption("photobiology.plot.bands",
default = list(UVC(), UVB(), UVA(), PhR())),
range = NULL,
norm = getOption("ggspectra.norm", default = "max"),
unit.out = getOption("photobiology.radiation.unit",
default = "energy"),
pc.out = FALSE,
label.qty = NULL,
span = NULL,
wls.target = "HM",
annotations = NULL,
geom = "line",
time.format = "",
tz = "UTC",
text.size = 2.5,
idfactor = NULL,
facets = FALSE,
ylim = c(NA, NA),
object.label = deparse(substitute(object)),
na.rm = TRUE) {
force(object.label)
force(norm)
annotations.default <-
getOption("photobiology.plot.annotations",
default = c("boxes", "labels", "summaries", "colour.guide", "peaks"))
annotations <- decode_annotations(annotations,
annotations.default)
# avoid warning in 'photobiology' (== 0.10.10)
if (is.character(norm) && norm == "update" && !is_normalized(object)) {
norm <- "skip"
}
# normalization needs to be redone if unit.out has changed
object <- photobiology::normalize(x = object,
range = range,
norm = norm,
unit.out = unit.out,
na.rm = na.rm)
if (is.null(label.qty)) {
if (photobiology::is_normalized(object) ||
photobiology::is_scaled(object)) {
label.qty = "contribution"
} else {
label.qty = "total"
}
}
if (length(w.band) == 0) {
if (is.null(range)) {
w.band <- photobiology::waveband(object)
} else if (photobiology::is.waveband(range)) {
w.band <- range
} else {
w.band <- photobiology::waveband(range, wb.name = "Total")
}
}
if (is.waveband(w.band)) {
w.band <- list(w.band)
}
labels <- sapply(w.band, labels)[1, ]
if (unit.out %in% c("photon", "quantum")) {
# change "PhR" label into "PAR" because we compute photon irradiance
wb.PAR <- grep("^PhR$", labels)
if (length(wb.PAR)) {
w.band[[wb.PAR]] <-
photobiology::waveband(x = c(400, 700), wb.name = "PAR")
}
}
if (unit.out=="photon" || unit.out == "quantum") {
out.ggplot <- q_rsp_plot(spct = object,
w.band = w.band,
range = range,
pc.out = pc.out,
label.qty = label.qty,
span = span,
wls.target = wls.target,
annotations = annotations,
geom = geom,
norm = norm, # read from object
text.size = text.size,
idfactor = idfactor,
facets = facets,
ylim = ylim,
na.rm = na.rm,
...)
} else if (unit.out=="energy") {
out.ggplot <- e_rsp_plot(spct = object,
w.band = w.band,
range = range,
pc.out = pc.out,
label.qty = label.qty,
span = span,
wls.target = wls.target,
annotations = annotations,
geom = geom,
norm = norm,
text.size = text.size,
idfactor = idfactor,
facets = facets,
ylim = ylim,
na.rm = na.rm,
...)
} else {
stop("Invalid 'unit.out' argument: '", unit.out, "'")
}
out.ggplot +
autotitle(object = object,
time.format = time.format,
tz = tz,
object.label = object.label,
annotations = annotations)
}
#' @rdname autoplot.response_spct
#'
#' @param plot.data character Data to plot. Default is "as.is" plotting one line
#' per spectrum. When passing "mean", "median", "sum", "prod", "var", "sd",
#' "se" as argument all the spectra must contain data at the same wavelength
#' values.
#'
#' @export
#'
autoplot.response_mspct <-
function(object,
...,
range = NULL,
norm = getOption("ggspectra.norm",
default = "max"),
unit.out = getOption("photobiology.radiation.unit", default="energy"),
pc.out = FALSE,
plot.data = "as.is",
facets = FALSE,
idfactor = TRUE,
object.label = deparse(substitute(object)),
na.rm = TRUE) {
force(object.label)
idfactor <- validate_idfactor(idfactor = idfactor)
# We trim the spectra to avoid unnecessary computations later
if (!is.null(range)) {
object <- photobiology::trim_wl(object,
range = range,
use.hinges = TRUE,
fill = NULL)
}
# We apply the normalization to the collection if it is to be bound
# otherwise normalization is applied to the "parallel-summary" spectrum
if (plot.data == "as.is") {
object <- photobiology::normalize(object,
norm = norm,
unit.out = unit.out,
na.rm = na.rm)
norm <- "skip"
}
# we ensure the units are correct
object <- switch(unit.out,
photon = e2q(object, action = "replace"),
energy = q2e(object, action = "replace"))
# we convert the collection of spectra into a single spectrum object
# containing a summary spectrum or multiple spectra in long form.
z <- switch(plot.data,
as.is = photobiology::rbindspct(object, idfactor = idfactor),
mean = photobiology::s_mean(object),
median = photobiology::s_median(object),
sum = photobiology::s_sum(object),
prod = photobiology::s_prod(object),
var = photobiology::s_var(object),
sd = photobiology::s_sd(object),
se = photobiology::s_se(object)
)
col.name <- c(photon = "s.q.response", energy = "s.e.response")
if (is.response_spct(z) && any(col.name %in% names(z))) {
autoplot(object = z,
range = NULL,
norm = norm,
unit.out = unit.out,
pc.out = pc.out,
facets = facets,
idfactor = idfactor,
object.label = object.label,
na.rm = na.rm,
...)
} else {
z <- as.generic_spct(z)
autoplot(object = z,
y.name = paste(col.name[unit.out], plot.data, sep = "."),
range = NULL,
norm = norm,
pc.out = pc.out,
facets = facets,
idfactor = idfactor,
object.label = object.label,
na.rm = na.rm,
...)
}
}
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