ggspectra (version 0.3.16)

stat_peaks: 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,
  local.reference = "median",
  strict = FALSE,
  refine.wl = FALSE,
  method = "spline",
  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,
  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,
  local.reference = "median",
  strict = FALSE,
  refine.wl = FALSE,
  method = "spline",
  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,
  na.rm = FALSE,
  show.legend = FALSE,
  inherit.aes = TRUE
)

Value

A data frame with one row for each peak (or valley) found in the data. If refine.wl = FALSE, the returned rows have x and

y matching those in a row in the input data. If

refine.wl = TRUE, interpolation based on a fitted spline is used to compute new x and y values.

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.

local.reference

character One of "minimum"/maximum or "median". The reference used to assess the height of the peak, either the minimum value within the window or the median of all values in the window.

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.

Computed and copied variables in the returned data frame

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

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.

Two tests make it possible to ignore irrelevant peaks or valleys. One test controlled by (global.threshold) is based on the absolute height/depth of peaks/valleys and can be used in all cases to ignore globally low peaks and shallow valleys. A second test controlled by (local.threshold) is available when the window defined by `span` does not include all observations and can be used to ignore peaks/valleys that are not locally prominent. In this second approach the height/depth of each peak/valley is compared to a summary computed from other values within the window where it was found. In this second case, the reference value used is the summary indicated by local.reference. The values global.threshold and local.threshold if bare numeric are relative to the range of y. Thresholds for ignoring too small peaks are applied after peaks are searched for, and threshold values can in some cases result in no peaks being displayed.

See Also

find_peaks, which is used internally.

Other stats functions: stat_color(), stat_find_qtys(), stat_find_wls(), stat_label_peaks(), stat_spikes(), stat_wb_box(), stat_wb_column(), stat_wb_contribution(), stat_wb_hbar(), stat_wb_irrad(), stat_wb_label(), stat_wb_mean(), stat_wb_relative(), stat_wb_sirrad(), stat_wb_total(), stat_wl_strip(), stat_wl_summary()

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()