Nothing
#' Create a complete ggplot for an irradiation calibration spectrum.
#'
#' This function returns a ggplot object with an annotated plot of a
#' calibration_spct object.
#'
#' @note 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.
#' When \code{spct} has more than one column with spectral data, each of these
#' columns is normalized individually.
#'
#' @param spct a calibration_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 percents instead of fraction of one
#' @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 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. Always skipped for
#' \code{plot.qty == "all"}, which is the default.
#' @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. If \code{idfactor=NA} no aesthetic is mapped
#' to the spectra and the user needs to use 'ggplot2' functions to manually
#' map an aesthetic or use facets for the spectra.
#' @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
#'
cal_plot <- function(spct,
w.band,
range,
pc.out,
label.qty,
span,
wls.target,
annotations,
geom,
norm,
text.size,
idfactor,
facets,
ylim,
na.rm,
...) {
if (!is.calibration_spct(spct)) {
stop("cal_plot() can only plot calibration_spct objects.")
}
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))
}
mult.cols <- names(spct)[grep("^irrad.mult", names(spct))]
num.mult.cols <- length(mult.cols)
# if individual spectra have multiple columns we force facets
if (!as.logical(facets) && num.mult.cols > 1L && getMultipleWl(spct) > 1L) {
message("Usings facets because spectra contain multiple scans.")
facets <- TRUE
}
# other.cols <- setdiff(names(x), mult.cols)
if (is.null(norm)) {
# we will use the original data
scale.factor <- 1
} else {
for (col in mult.cols) {
if (is.character(norm)) {
if (norm %in% c("max", "maximum")) {
idx <- which.max(spct[[col]])
} else {
warning("Invalid character '", norm, "'value in 'norm'")
return(ggplot())
}
scale.factor <- 1 / as.numeric(spct[idx, col])
norm <- as.numeric(spct[idx, "w.length"])
} else if (is.numeric(norm) && norm >= min(spct) && norm <= max(spct)) {
scale.factor <- 1 / interpolate_spct(spct, norm)[[col]]
} else if (is.numeric(norm)) {
warning("'norm = ", norm, "' value outside spectral data range of ",
round(min(spct)), " to ", round(max(spct)), " (nm)")
return(ggplot())
} else {
stop("'norm' should be numeric or character")
}
spct[[col]] <- spct[[col]] * scale.factor
}
}
if (scale.factor != 1) {
if (!pc.out) {
multiplier.label <- "rel."
# scale.factor <- 1 * scale.factor
} else {
multiplier.label <- "%"
scale.factor <- 100 * scale.factor
}
if (is.numeric(norm)) {
norm <- signif(norm, digits = 4)
}
s.counts.label <-
bquote(Coefficients~~k[italic(lambda)]/k( .(norm))~~(.(multiplier.label)))
counts.label <- ""
} else {
s.counts.label <-
expression(Coefficients~~k[italic(lambda)]~~(J~m^{-2}~nm^{-1}~n^{-1}))
counts.label <- ""
}
if (!is.na(ylim[1])) {
y.min <- ylim[1]
spct[["irrad.mult"]] <- ifelse(spct[["irrad.mult"]] < y.min,
NA_real_,
spct[["irrad.mult"]])
} else {
y.min <- min(spct[["irrad.mult"]], 0, na.rm = TRUE)
}
if (!is.na(ylim[2])) {
y.max <- ylim[2]
spct[["irrad.mult"]] <- ifelse(spct[["irrad.mult"]] > y.max,
NA_real_,
spct[["irrad.mult"]])
} else {
y.max <- max(spct[["s.e.irrad"]], 0, y.min, na.rm = TRUE)
}
if (num.mult.cols > 1L) {
spct <- photobiology::spct_wide2long(spct = spct, idfactor = "scan")
plot <- ggplot(spct) + aes(x = .data[["w.length"]], y = .data[["irrad.mult"]], linetype = .data[["scan"]])
temp <- find_idfactor(spct = spct,
idfactor = idfactor,
facets = facets,
annotations = annotations,
num.columns = num.mult.cols)
plot <- plot + temp$ggplot_comp
annotations <- temp$annotations
} else {
plot <- ggplot(spct) + aes(x = .data[["w.length"]], y = .data[["irrad.mult"]])
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
if ("boundaries" %in% annotations) {
if (y.min < -0.01 * y.max) {
plot <- plot + geom_hline(yintercept = 0,
linetype = "dashed", colour = "red")
} else {
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.counts.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 = counts.label,
text.size = text.size,
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)
}
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 an irradiation calibration spectrum.
#'
#' These methods return a ggplot object with an annotated plot of a
#' calibration_spct object or of the spectra contained in a calibration_mspct
#' object.
#'
#' @note 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.
#'
#' @inheritSection decoration Plot Annotations
#' @inheritSection autotitle Title Annotations
#'
#' @param object a calibration_spct object or a calibration_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. Always skipped for
#' \code{plot.qty == "all"}, which is the default.
#' @param unit.out character IGNORED.
#' @param pc.out logical, if TRUE use percents instead of fraction of one.
#' @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 ("summaries" is ignored). 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 "max"
#' for normalization at the wavelength of highest peak.
#' @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. If \code{idfactor=NA} no aesthetic is mapped to the
#' spectra and the user needs to use 'ggplot2' functions to manually map an
#' aesthetic or use facets for the spectra.
#' @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.
#'
#' @seealso \code{\link[photobiology]{normalize}},
#' \code{\link[photobiology]{calibration_spct}},
#' \code{\link[photobiology]{waveband}},
#' \code{\link[photobiologyWavebands]{photobiologyWavebands-package}} and
#' \code{\link[ggplot2]{autoplot}}
#'
#' @export
#'
#' @family autoplot methods
#'
autoplot.calibration_spct <-
function(object, ...,
w.band = getOption("photobiology.plot.bands",
default = list(UVC(), UVB(), UVA(), PhR())),
range = NULL,
unit.out = "ignored",
pc.out = FALSE,
label.qty = "mean",
span = NULL,
wls.target = "HM",
annotations = NULL,
geom = "line",
time.format = "",
tz = "UTC",
norm = NULL,
text.size = 2.5,
idfactor = NULL,
facets = FALSE,
ylim = c(NA, NA),
object.label = deparse(substitute(object)),
na.rm = TRUE) {
force(object.label)
annotations.default <-
getOption("photobiology.plot.annotations",
default = c("boxes", "labels", "colour.guide", "peaks"))
annotations <- decode_annotations(annotations,
annotations.default)
if (length(w.band) == 0) {
if (is.null(range)) {
w.band <- waveband(object)
} else if (is.waveband(range)) {
w.band <- range
} else {
w.band <- waveband(range, wb.name = "Total")
}
}
cal_plot(spct = object,
w.band = w.band,
range = range,
label.qty = label.qty,
span = span,
wls.target = wls.target,
pc.out = pc.out,
annotations = annotations,
geom = geom,
norm = norm,
text.size = text.size,
idfactor = idfactor,
facets = facets,
na.rm = na.rm,
ylim = ylim,
...) +
autotitle(object = object,
time.format = time.format,
tz = tz,
object.label = object.label,
annotations = annotations)
}
#' @rdname autoplot.calibration_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.calibration_mspct <-
function(object,
...,
range = NULL,
unit.out = "ignored",
norm = getOption("ggspectra.normalize",
default = "skip"),
pc.out = FALSE,
plot.data = "as.is",
idfactor = TRUE,
facets = FALSE,
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 <- trim_wl(object, range = range, use.hinges = TRUE, fill = NULL)
}
# 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)
)
if (is.calibration_spct(z) && "irrad.mult" %in% names(z)) {
autoplot(object = z,
range = NULL,
unit.out = unit.out,
norm = norm,
pc.out = pc.out,
idfactor = idfactor,
facets = facets,
object.label = object.label,
na.rm = na.rm,
...)
} else {
z <- as.generic_spct(z)
autoplot(object = z,
y.name = paste("irrad.mult", plot.data, sep = "."),
range = NULL,
unit.out = unit.out,
norm = norm,
pc.out = pc.out,
idfactor = idfactor,
facets = facets,
object.label = object.label,
na.rm = na.rm,
...)
}
}
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