stat_peaks: Find peaks and valleys.
In aphalo/ggspectra: Extensions to 'ggplot2' for Radiation Spectra

stat_peaks

R Documentation

Find peaks and valleys.

Description

stat_peaks finds at which x positions local maxima are located. If you want find local minima, you can use stat_valleys instead. Axis flipping is currently not supported.

Usage

stat_peaks(
  mapping = NULL,
  data = NULL,
  geom = "point",
  position = "identity",
  ...,
  span = 5,
  ignore_threshold = 0.01,
  global.threshold = ignore_threshold,
  local.threshold = NULL,
  strict = is.null(span),
  refine.wl = FALSE,
  method = "spline",
  chroma.type = "CMF",
  label.fmt = "%.3g",
  x.label.fmt = label.fmt,
  y.label.fmt = label.fmt,
  x.label.transform = I,
  y.label.transform = I,
  x.colour.transform = x.label.transform,
  na.rm = FALSE,
  show.legend = FALSE,
  inherit.aes = TRUE
)

stat_valleys(
  mapping = NULL,
  data = NULL,
  geom = "point",
  position = "identity",
  ...,
  span = 5,
  ignore_threshold = 0.01,
  global.threshold = ignore_threshold,
  local.threshold = NULL,
  strict = is.null(span),
  refine.wl = FALSE,
  method = "spline",
  chroma.type = "CMF",
  label.fmt = "%.3g",
  x.label.fmt = label.fmt,
  y.label.fmt = label.fmt,
  x.label.transform = I,
  y.label.transform = I,
  x.colour.transform = x.label.transform,
  na.rm = FALSE,
  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`.
`ignore_threshold`	Deprecated synonym for `global.threshold`.
`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 the range of the data. 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 are returned.
`local.threshold`	numeric A value belonging to class `"AsIs"` is interpreted as an absolute minimum height (depth) expressed in data units relative to the within-window computed minimum (maximum) value. A bare `numeric` value (normally between 0.0 and 1.0), is interpreted as expressed in units relative to the range of the data. In both cases `local.threshold` sets a local height (depth) threshold below which peaks (valleys) are ignored. If `local.threshold = NULL` or if `span` spans the whole of `x`, no threshold is applied.
`strict`	logical flag: if `TRUE`, an element must be strictly greater than all other values in its window to be considered a peak.
`refine.wl`	logical Flag indicating if peak or valleys locations should be refined by fitting a function.
`method`	character String with the name of a method used for peak fitting. Currently only spline interpolation is implemented.
`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.
`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`.

Details

These stats use geom_point by default as it is the geom most likely to work well in almost any situation without need of tweaking. The default aesthetics set by these stats 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.

Value

A data frame with one row for each peak (or valley) found in the data.

Computed variables

x: x-value at the peak (or valley) as numeric
y: y-value at the peak (or valley) as numeric
x.label: x-value at the peak (or valley) formatted as character
y.label: y-value at the peak (or valley) formatted as character
wl.color: color definition calculated by assuming that x-values are wavelengths expressed in nanometres.
BW.color: color definition, either "black" or "white", as needed to ensure high contrast to wl.color.

Default aesthetics

Set by the statistic and available to geoms.

label: stat(x.label)
xintercept: stat(x)
yintercept: stat(y)
fill: 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

Note

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. To discard overlapping labels use check_overlap = TRUE as argument to geom_text. 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.

Examples

# ggplot() methods for spectral objects set a default mapping for x and y.

# PEAKS

ggplot(sun.spct) +
  geom_line() +
  stat_peaks()

# threshold relative to data range [0..1]
ggplot(sun.spct) +
  geom_line() +
  stat_peaks(global.threshold = 0.6) # 0.6 * range of data

# threshold in data units
ggplot(sun.spct) +
  geom_line() +
  stat_peaks(global.threshold = I(0.4))

# threshold in data units
ggplot(sun.spct, unit.out = "photon") +
  geom_line() +
  stat_peaks(global.threshold = I(2e-6)) # Q in mol m-2 s-1

# VALLEYS

ggplot(sun.spct) +
  geom_line() +
  stat_valleys()

# discard multiple maxima or minima
ggplot(sun.spct) +
  geom_line() +
  stat_valleys(strict = TRUE)

# threshold relative to data range [0..1]
ggplot(sun.spct) +
  geom_line() +
  stat_valleys(global.threshold = 0.6)

# reverse threshold relative to data range [-1..0]
ggplot(sun.spct) +
  geom_line() +
  stat_valleys(global.threshold = -0.9)

# threshold in data units using I()
ggplot(sun.spct) +
  geom_line() +
  stat_valleys(global.threshold = I(0.6), strict = TRUE)

# USING OTHER COMPUTED VALUES

# colours matching the wavelength at peaks
ggplot(sun.spct) +
  geom_line() +
  stat_peaks(span = 51, size = 2.7,
             mapping = aes(colour = after_stat(wl.colour))) +
  scale_color_identity()

# labels for local maxima
ggplot(sun.spct) +
  geom_line() +
  stat_peaks(span = 51, geom = "point", colour = "red") +
  stat_peaks(span = 51, geom = "text", colour = "red",
             vjust = -0.4, label.fmt = "%3.2f nm")

# labels for local fitted peaks
ggplot(sun.spct) +
  geom_line() +
  stat_peaks(span = 51, geom = "point", colour = "red", refine.wl = TRUE) +
  stat_peaks(span = 51, geom = "text", colour = "red",
             vjust = -0.4, label.fmt = "%3.2f nm",
             refine.wl = TRUE)

# fitted peaks and valleys
ggplot(sun.spct) +
  geom_line() +
  stat_peaks(span = 31, geom = "point", colour = "red", refine.wl = TRUE) +
  stat_peaks(mapping = aes(fill = after_stat(wl.colour), color = after_stat(BW.colour)),
             span = 31, geom = "label",
             size = 3, vjust = -0.2, label.fmt = "%.4g nm",
             refine.wl = TRUE) +
  stat_valleys(span = 51, geom = "point", colour = "blue", refine.wl = TRUE) +
  stat_valleys(mapping = aes(fill = after_stat(wl.colour), color = after_stat(BW.colour)),
               span = 51, geom = "label",
               size = 3, vjust = 1.2, label.fmt = "%.4g nm",
               refine.wl = TRUE) +
  expand_limits(y = 0.85) + # make room for label
  scale_fill_identity() +
  scale_color_identity()

aphalo/ggspectra documentation built on June 10, 2025, 4:56 p.m.