R: Find peaks and valleys.

stat_peaks {ggspectra} | 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.

### Usage

    stat_peaks(mapping = NULL, data = NULL, geom = "point", span = 5,
      ignore_threshold = 0, strict = FALSE, label.fmt = "%.3g",
      x.label.fmt = label.fmt, y.label.fmt = label.fmt, position = "identity",
      na.rm = FALSE, show.legend = FALSE, inherit.aes = TRUE, ...)

    stat_valleys(mapping = NULL, data = NULL, geom = "point", span = 5,
      ignore_threshold = 0, strict = FALSE, label.fmt = "%.3g",
      x.label.fmt = label.fmt, y.label.fmt = label.fmt, position = "identity",
      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
`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. The default value is 5, meaning that a peak is bigger than two consequtive neighbors on each side. Default: 5.
`ignore_threshold` | numeric value between 0.0 and 1.0 indicating the size threshold below which peaks will be ignored.
`strict` | logical flag: if TRUE, an element must be strictly greater than all other values in its window to be considered a peak. Default: FALSE.
`label.fmt` | character string giving a format definition for converting values into character strings by means of function `sprintf`.
`x.label.fmt` | character string giving a format definition for converting $x$-values into character strings by means of function `sprintf`.
`y.label.fmt` | character string giving a format definition for converting $y$-values into character strings by means of function `sprintf`.
`position` | The position adjustment to use for overlapping points on this layer
`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`.
`...` | other arguments passed on to `layer`. This can include aesthetics whose values you want to set, not map. See `layer` for more details.

### 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

color

  color definition calculated by assuming that x-values are wavelengths expressed in nanometres.

### Default aesthetics

Set by the statistic and available to geoms.

label

  ..x.label..

xintercept

  ..x..

yintercept

  ..y..

fill

  ..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.

### See Also

`find_peaks`, which is used internally.

Other stats functions: `stat_color`, `stat_label_peaks`, `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

    library(photobiology)
    library(ggplot2)
    # ggplot() methods for spectral objects set a default mapping for x and y.
    ggplot(sun.spct) + geom_line() + stat_peaks()
    ggplot(sun.spct) + geom_line() + stat_valleys()
    ggplot(sun.spct) + geom_line() +
      stat_peaks(span = 21, geom = "point", colour = "red") +
      stat_peaks(span = 51, geom = "text", colour = "red",
                 vjust = -0.3, label.fmt = "%3.0f nm")
    ggplot(sun.spct, unit.out = "photon") + geom_point() +
      stat_peaks(span = 5, geom = "line", colour = "red")

[Package ggspectra version 0.2.3 Index]