plot-methods: Methods for the 'plot' Function

In monitoR: Acoustic Template Detection in R

Description

Plotting acoustic templates and template scores

Usage

## S4 method for signature 'TemplateList,ANY'
plot(x, which.one = names(x@templates), click = FALSE, 
ask = if(length(which.one)>1) TRUE else FALSE, spec.col = gray.3(), on.col = '#FFA50075', 
off.col = '#0000FF75', pt.col = '#FFA50075', line.col = 'black')

## S4 method for signature 'detectionList,ANY'
plot(x, flim = c(0, 12), scorelim, 
which.one = names(x@templates), box = TRUE, spec.col = gray.2(), t.each = 30, 
hit.marker = 'lines', 
color = c('red', 'blue', 'green', 'orange', 'purple', 'pink', 'darkgreen', 'turquoise', 
'royalblue', 'orchid4', 'brown', 'salmon2'), legend = TRUE, all.peaks = FALSE, 
ask = if(dev.list() == 2) TRUE else FALSE)

Arguments

x	A template list (TemplateList object) or detection list (detectionList object).
which.one	Names of templates to be plotted.
click	Set to TRUE to see values of locations on plot by mouse clicks.
ask	Set to FALSE to eliminate pause between plots.
spec.col	Color ramp for spectrogram.
on.col	Color for “on” points (binary templates only).
off.col	Color for “off” points (binary templates only).
pt.col	Color for template points (correlation templates only).
line.col	Color for lines if click = TRUE.
flim	Frequency limits for plot.
scorelim	Score limits for plot.
box	If TRUE boxes are plotted in spectrogram for each detection.
t.each	Duration shown in each individual plot (s).
hit.marker	Type of marker used to show detections in score plot. Can be "lines" or "points".
color	Colors used for individual templates.
legend	Show legend?
all.peaks	Indicate location of all peaks?

Author(s)

Sasha D. Hafner

See Also

makeCorTemplate, makeBinTemplate

Examples

## Not run: 
# Not run because of the time required (maybe 5-10 seconds)
# Also some plot calls require user input by default
# Load data
data(btnw)
data(survey)

# Write Wave objects to file (temporary directory used here)
btnw.fp <- file.path(tempdir(), "btnw.wav")
oven.fp <- file.path(tempdir(), "oven.wav")
survey.fp <- file.path(tempdir(), "survey2010-12-31_120000_EST.wav")
writeWave(btnw, btnw.fp)
writeWave(survey, survey.fp)

# Create a template list
ctemp1 <- makeCorTemplate(btnw.fp, name = "w1")
ctemp2 <- makeCorTemplate(btnw.fp, t.lim = c(0.5, 2.5), frq.lim = c(1, 10), dens = 0.1, name = "w2")
ctemps <- combineCorTemplates(ctemp1, ctemp2)

# Then it can be plotted like this
plot(ctemps)

# Next call is not useful for template w1 but good for w2:
plot(ctemps, pt.col = "red")

# Can plot just one template
plot(ctemps, which.one = 2, pt.col = "red")
plot(ctemps, which.one = "w2", pt.col = "red")

# And to check values
plot(ctemps, which.one = 1, click = TRUE)

# To plot detections, let's create some
cscores <- corMatch(survey.fp, ctemps)
cdetects <- findPeaks(cscores)

# And to plot them:
plot(cdetects)

# Clean up (only because these files were created in these examples)
file.remove(btnw.fp)
file.remove(survey.fp)

## End(Not run)

monitoR documentation built on May 1, 2019, 6:28 p.m.