R/plot_trace_all_1to7.R

In michathoma/flywalkr: Analysis tools for the flywalk behavioral paradigm

#' Plot overview over the experiment within flies.
#'
#' Plot overview over the experiment within flies. Creates a \code{_overview.pdf} per fly in a given experiment containing one line plot including
#' all single tracking events and the fly's mean and median response time-course.
#'
#' @param object object a \code{data.frame} as produced by \code{read.esm}.
#' @return one \code{_overview.pdf} per fly analyzed.
#' @export
plot_trace_all_1to7 <- function(object){

  colnames(object) <- c("fly.nr", "odour", "pulse", seq(-9.95, 9.95, 0.1))
  data.short <- data.frame(cbind(object[, 1:3], object[, 94:173]))

  data.clean <- data.short[!apply(is.na(data.short), 1, any),]

  animals <- levels(as.factor(data.clean$fly.nr))
  i.animals <- 1:length(levels(as.factor(data.clean$fly.nr)))

  for(i in i.animals){

	  animalx <- subset(data.clean, fly.nr == animals[i])
	  animalx$odour <- factor(animalx$odour)


	  pdf(file = paste(animals[i], "_overview.pdf"), paper = "a4", height = 11.69, width = 8.27)

	  k.animal <- 1:dim(animalx)[1]
	  par(mfrow = c(3, 3))

	  odors <- levels(as.factor(animalx$odour))
	  j.odors <- 1:length(odors)

	  for (j in j.odors){

		  odorx <- subset(animalx, odour == odors[j])
		  odorx$odour <- factor(odorx$odour)

		  mediodor <- apply(odorx[, 4:83], 2, median, na.rm = T)
		  meanodor <- apply(odorx[, 4:83], 2, mean, na.rm = T)


		  ylim <- c(-1, 1)
		  x <- seq(-0.95, 6.95, 0.1)
		  xr <- rev(x)

		  plot(seq(-0.95, 6.95, 0.1), -mediodor, type = "n", xlim = c(-1, 7), ylim = ylim,
		       main = paste(animalx[1, 1], odorx$odour[1]), xlab = "time(s)", ylab = "mean speed (cm/s)", bty = "n")

		  for(l in 1:dim(odorx)[1]){
			  lines(x, -odorx[l, 4:83], col = "gray")
		  }

		  lines(x, -mediodor, col = "red")
		  lines(x, -meanodor, col = "green")

		  lines(x = c(0, 0), y = ylim)
		  legend("topright", legend = paste("N =", dim(odorx)[1]), bty = "n")
		}

	  dev.off()
  }
}