stat_spikes {ggspectra} | R Documentation |
Find spikes
Description
stat_spikes
finds at which x
positions spikes are located.
Spikes can be either upwards or downwards from the baseline.
Axis flipping is currently not supported.
Usage
stat_spikes(
mapping = NULL,
data = NULL,
geom = "point",
position = "identity",
...,
z.threshold = 9,
max.spike.width = 8,
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
)
Arguments
mapping |
The aesthetic mapping, usually constructed with
|
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 |
z.threshold |
numeric Modified Z values larger than |
max.spike.width |
integer Wider regions with high Z values are not detected as spikes. |
chroma.type |
character one of "CMF" (color matching function) or "CC"
(color coordinates) or a |
label.fmt , x.label.fmt , y.label.fmt |
character strings giving a format
definition for construction of character strings labels with function
|
x.label.transform , y.label.transform , x.colour.transform |
function Applied
to |
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?
|
inherit.aes |
If |
Details
This stat uses 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 this stat allow its 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 of observations found in the data matching the criterion of being part of a spike. That is to say, the returned data frame not only includes the observation at the tip of the spike but also those on its shoulders.
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 of observations in the spike formatted as character
- y.label
y-value of observations in the spike formatted as character
- wl.color
color definition calculated by assuming that x-values are wavelengths expressed in nanometres.
- BW.color
color definition that is either "black" or "white", 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
This stat works 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
argument 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_spikes
, which is used internally,
for a description of the algorithm used.
Other stats functions:
stat_color()
,
stat_find_qtys()
,
stat_find_wls()
,
stat_label_peaks()
,
stat_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
# ggplot() methods for spectral objects set a default mapping for x and y.
# two spurious(?) spikes
ggplot(sun.spct) +
geom_line() +
stat_spikes(colour = "red", alpha = 0.3)
# no spikes detected
ggplot(sun.spct) +
geom_line() +
stat_spikes(colour = "red", alpha = 0.3,
max.spike.width = 3,
z.threshold = 12)
# small noise spikes detected
ggplot(white_led.raw_spct) +
geom_line() +
stat_spikes(colour = "red", alpha = 0.3)
ggplot(white_led.raw_spct) +
geom_line() +
stat_spikes(colour = "red", alpha = 0.3) +
stat_spikes(geom = "text", colour = "red", check_overlap = TRUE,
vjust = -0.5, label.fmt = "%3.0f nm")
ggplot(white_led.raw_spct, aes(w.length, counts_2)) +
geom_line() +
stat_spikes(colour = "red", alpha = 0.3,
max.spike.width = 3,
z.threshold = 12)