Label peaks and valleys.

stat_labels_peaks finds at which x positions the global maximum or local maxima are located, and adds labels and color definitions to the data without subsetting. stat_labels_valleys finds instead minima. The variable mapped to the x aesthetic is expected to contain wavelength values expressed in nanometres. Axis flipping is currently not supported.

Usage

stat_label_peaks(
  mapping = NULL,
  data = NULL,
  geom = "text",
  position = "identity",
  ...,
  span = 5,
  global.threshold = 0.01,
  strict = FALSE,
  chroma.type = "CMF",
  label.fmt = "%.3g",
  x.label.fmt = label.fmt,
  y.label.fmt = label.fmt,
  x.label.transform = function(x) {
     x
 },
  y.label.transform = function(x) {
     x
 },
  x.colour.transform = x.label.transform,
  label.fill = "",
  na.rm = TRUE,
  show.legend = FALSE,
  inherit.aes = TRUE
)

stat_label_valleys(
  mapping = NULL,
  data = NULL,
  geom = "text",
  position = "identity",
  ...,
  span = 5,
  global.threshold = -0.99,
  strict = FALSE,
  chroma.type = "CMF",
  label.fmt = "%.3g",
  x.label.fmt = label.fmt,
  y.label.fmt = label.fmt,
  x.label.transform = function(x) {
     x
 },
  y.label.transform = function(x) {
     x
 },
  x.colour.transform = x.label.transform,
  label.fill = "",
  na.rm = TRUE,
  show.legend = FALSE,
  inherit.aes = TRUE
)

Arguments

mapping: The aesthetic mapping, usually constructed with aes or aes_. Only needs to be set at the layer level if you are overriding the plot defaults.
data: A layer specific dataset - only needed if you want to override the plot defaults.
geom: The geometric object to use display the data
position: The position adjustment to use for overlapping points on this layer
...: other arguments passed on to layer. This can include aesthetics whose values you want to set, not map. See layer for more details.
span: odd positive integer A peak is defined as an element in a sequence which is greater than all other elements within a moving window of width span centred at that element. The default value is 5, meaning that a peak is taller than its four nearest neighbours. span = NULL extends the span to the whole length of x.
global.threshold: numeric A value belonging to class "AsIs" is interpreted as an absolute minimum height or depth expressed in data units. A bare numeric value (normally between 0.0 and 1.0), is interpreted as relative to threshold.range. In both cases it sets a global height (depth) threshold below which peaks (valleys) are ignored. A bare negative numeric value indicates the global height (depth) threshold below which peaks (valleys) are be ignored. If global.threshold = NULL, no threshold is applied and all peaks returned.
strict: logical flag: if TRUE, an element must be strictly greater than all other values in its window to be considered a peak.
chroma.type: character one of "CMF" (color matching function) or "CC" (color coordinates) or a chroma_spct object.
label.fmt, x.label.fmt, y.label.fmt: character strings giving a format definition for construction of character strings labels with function sprintf from x and/or y values.
x.label.transform, y.label.transform, x.colour.transform: function Applied to x or y values when constructing the character labels or computing matching colours.
label.fill: character string to use for labels not at peaks or valleys being highlighted.
na.rm: a logical value indicating whether NA values should be stripped before the computation proceeds.
show.legend: logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes.
inherit.aes: If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders.

Value

The original data with additional computed variables added.

Details

These statistics assemble text labels for each peak or valley and compute the colour corresponding to the wavelength of the peaks and valleys. Defaults work as long as the variable mapped to the x aesthetic contains wavelengths expressed in nanometres and the plot has an x-scale that does not apply a transformation. The three transform parameters can be used to back-transform the values when scales apply transformations so that peak/valley labels and axis labels match. Of course, x.label.transform and y.label.transform make also possible to scale the values in the labels.

Both statistics use geom_text by default as it is the geom most likely to work well in almost any situation without need of tweaking. These statistics work best with geom_text_repel and geom_label_repel from package 'ggrepel' as they are designed so that peak or valley labels will not overlap any observation in the whole data set. Default aesthetics set by these statistics allow their direct use with geom_text, geom_label, geom_line, geom_rug, geom_hline and geom_vline. The formatting of the labels returned can be controlled by the user.

Note

When using geom_text, to discard overlapping labels pass check_overlap = TRUE in the call to the statistic.

These stats work nicely together with geoms geom_text_repel and geom_label_repel from package ggrepel to solve the problem of overlapping labels by displacing them, without discarding any of them. The difference between stat_peaks and stat_label_peaks, and between stat_valleys and stat_label_valleys, is that while the first only returns the rows in data matching peaks or valleys, the second return all rows, but set the labels to the value passed as argument to label.fill. In the "label" stats the default label.fill = "" ensures that when using repulsive geoms the labels do not overlap any observations, labelled or not.

By default the labels are character values suitable to be plotted as is, but with a suitable label.fmt labels suitable for parsing by the geoms (e.g. into expressions containing greek letters or super or subscripts) can be also easily obtained.

Computed variables

x.label: x-value at a peak (or valley) formatted as character or otherwise the value passed to label.fill which defaults to an empty string ("").
y.label: y-value at the peak (or valley) formatted as character or otherwise the value passed to label.fill which defaults to an empty string ("").
wl.color: At peaks and valleys, color definition calculated by assuming that x-values are wavelengths expressed in nanometres, otherwise, rgb(1, 1, 1, 0) (transparent white).

Default aesthetics

Set by the statistic and available to geoms.

label: after_stat(x.label)
xintercept: after_stat(x)
yintercept: after_stat(y)
color: black_or_white(after_stat(wl.color))
fill: after_stat(wl.color)

Required aesthetics

Required by the statistic and need to be set with aes().

x: numeric, wavelength in nanometres
y: numeric, a spectral quantity

Examples


# ggplot() methods for spectral objects set a default mapping for x and y.
ggplot(sun.spct) +
  geom_line() +
  stat_label_peaks(hjust = "left", span = 31, angle = 90, color = "red")


ggplot(sun.spct) +
  geom_line() +
  stat_label_valleys(hjust = "right", span = 21, angle = 90, color = "blue")


# using transformed scales requires the user to pass functions as arguments
ggplot(sun.spct) +
  geom_line() +
  stat_label_peaks(hjust = "left", span = 31, angle = 90, color = "red",
                   x.label.transform = abs) +
  scale_x_reverse()


ggplot(sun.spct) +
  geom_line() +
  stat_label_peaks(hjust = "left", span = 31, angle = 90, color = "red",
                   x.label.transform = function(x) {10^x}) +
  scale_x_log10()


# geom_label
ggplot(sun.spct) +
  geom_line() +
  stat_peaks(span = 41, shape = 21, size = 3) +
  stat_label_peaks(span = 41, geom = "label", label.fmt = "%3.0f nm") +
  scale_fill_identity() +
  scale_color_identity() +
  expand_limits(y = c(NA, 1))


# using 'ggrepel' to avoid overlaps
# too slow for CRAN checks
if (FALSE) { # \dontrun{
library(ggrepel)

ggplot(sun.spct) + geom_line() +
  stat_peaks(span = 41, shape = 21, size = 2) +
  stat_label_peaks(span = 41, geom = "label_repel", segment.colour = "red",
                   nudge_y = 0.12, label.fmt = "%3.0f nm",
                   max.overlaps = Inf, min.segment.length = 0) +
  scale_fill_identity() +
  scale_color_identity() +
  expand_limits(y = c(NA, 1))
} # }