monitoR (version 1.2)

plot-methods: Methods for the plot Function

Description

Plotting acoustic templates and template scores

Usage

# S4 method for 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 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

Sasha D. Hafner

See Also

makeCorTemplate, makeBinTemplate

Examples

if (FALSE) {
# 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)
}