R/SpectrogramFunction.R

In DenaJGibbon/behaviouR: An R Package for Online Teaching of Fundamental Concepts in Behavior and Ecology

#' A function to calculate spectrograms over a set of focal recordings
#'
#' @param input.dir The location of the .wav files
#' @param min.freq The minimum frequency (Hz) of the signal of interest
#' @param max.freq The maximum frequency (Hz) of the signal of interest
#' @param Colors Whether to return a black and white or color spectrogram
#' @param downsample.new <- If downsampling is desired, which frequency (Hz) to use for downsampling
#' @importFrom stringr str_split_fixed
#' @importFrom tuneR readWave
#' @importFrom tuneR downsample
#' @importFrom signal specgram
#' @importFrom graphics plot
#' @importFrom grDevices gray
#' @return multiple spectrogram images
#' @export
#'
#' @examples
#' \donttest{SpectrogramFunction(input.dir = "FocalRecordings",
#' min.freq = 500,max.freq=2500)}

SpectrogramFunction <- function(input.dir, min.freq = 500,max.freq=2500,
                                Colors='BW',downsample.new=16000) {

  call.timing.list <- list.files(input.dir,full.names = T,pattern='.wav')
  call.timing.list.short <- list.files(input.dir,full.names = F,pattern='.wav')
  Class <- str_split_fixed(call.timing.list.short,pattern = '.wav',n=2)[,1]

  subsamps <- lapply(1:length(call.timing.list),
                     function(i) tuneR::readWave(call.timing.list[[i]]))

  for(j in 1:length(subsamps)) {
    short.wav <-subsamps[[j]]
    if(short.wav@samp.rate > downsample.new){
      short.wav <- tuneR::downsample(short.wav,downsample.new)
    }

    short.wav <- tuneR::normalize(short.wav)
    temp.spec <- signal::specgram(short.wav@left, Fs = short.wav@samp.rate,
                                  n = 512, overlap = 95)


    if(Colors=='BW'){
      print(plot(temp.spec, xlab = "Time (s)", ylab = "Frequency (Hz)",
                 ylim = c(min.freq, max.freq), rev(gray(0:255 / 255)),
                 axes=T,useRaster = TRUE, main=Class[j]))
    }

    if(Colors=='Colors'){
      print(plot(temp.spec, xlab = "Time (s)", ylab = "Frequency (Hz)",
                 ylim = c(min.freq, max.freq), matlab::jet.colors(256),
                 axes=T,useRaster = TRUE, main=Class[j]))
    }

  }
}