stat_labels_peaks
finds at which x positions local maxima are located,
and adds labels and colors to the data without subsetting. To find local
minima, you can use stat_labels_valleys
instead. 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,
ignore_threshold = 0,
strict = TRUE,
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,
label.fill = "",
na.rm = TRUE,
show.legend = FALSE,
inherit.aes = TRUE
)
stat_label_valleys(
mapping = NULL,
data = NULL,
geom = "text",
position = "identity",
...,
span = 5,
ignore_threshold = 0,
strict = TRUE,
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,
label.fill = "",
na.rm = TRUE,
show.legend = FALSE,
inherit.aes = TRUE
)
Arguments
- mapping
The aesthetic mapping, usually constructed with
aes
oraes_
. 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. Seelayer
for more details.- 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.
- 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
fromx
and/ory
values.- x.label.transform, y.label.transform, x.colour.transform
function Applied to
x
ory
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, andTRUE
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 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
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.
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
..x.label..
- xintercept
..x..
- yintercept
..y..
- color
black_or_white(..wl.color..)
- fill
..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
See also
stat_peaks
, stat_valleys
and
find_peaks
, which is used internally.
Other stats functions:
stat_color()
,
stat_find_qtys()
,
stat_find_wls()
,
stat_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.
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 = 3) +
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))
} # }