plotter <- function(dir, sample, intensity, speed, error, objsize, quant, flydist, elapsedtime, elapsedtimefvflash, elapsedtimeavflash, exposure, binning, fpsfl, starttimefl, type="all", stim, stimlen){
# Plot speed, fluorescence, and tracking error
pdf(file=paste0(dir, sample, "_intensity_speed_error_", type, ".pdf"), width=8, height=6)
par(mar=c(5,4,3,4))
plot(elapsedtime, intensity, type="l", xlim=c(min(elapsedtime, na.rm=T), max(elapsedtime, na.rm=T)),
ylim=c(0, median(intensity, na.rm=T)*1.5), xlab=paste("Elapsed time (ms) from", starttimefl),
ylab=paste("Fluorescence intensity (A.U.)"), col='blue')
par(new=T)
plot(elapsedtimeavflash, flydist, type="l", xlim=c(min(elapsedtime, na.rm=T), max(elapsedtime, na.rm=T)), ylim=c(0, 10),
axes=F, xlab=NA, ylab=NA, col='black')
par(new=T)
plot(elapsedtimefvflash[1:length(speed)], speed, xlim=c(min(elapsedtime, na.rm=T), max(elapsedtime, na.rm=T)),
axes=F, type='l', xlab=NA, ylab=NA, col="red", ylim=c(0, 40))
rect(elapsedtime[stim], 0, elapsedtime[stim + stimlen], 60, col=rgb(red=0.2, green=0.2, blue=0.2, alpha=0.2), border = NA)
axis(4)
mtext(paste("Fly speed (mm/s), Tracking error (px)"), side = 4, line=3)
#legend("topright", inset=.05, c("Fluorescence","Speed", "Error", "Distance"), col=c("blue", "red", "green", "black"), lty = 1)
#title(main=paste0("Exposure: ", exposure, " ms, ", "Binning: ", binning, ", ", "fps: ", fpsfl))
dev.off()
# Plot fluorescence and tracking error
png(file=paste0(dir, sample, "_intensity_error_", type, ".png"), width=800, height=600)
par(mar=c(5,4,3,4))
plot(elapsedtime, intensity, type="l", xlim=c(min(elapsedtime, na.rm=T), max(elapsedtime, na.rm=T)),
ylim=c(0, median(intensity, na.rm=T)*3), xlab=paste("Elapsed time (ms) from", starttimefl),
ylab=paste("Fluorescence intensity (A.U.)"), col='blue')
par(new=T)
plot(elapsedtimefvflash[1:length(error)], error, xlim=c(min(elapsedtime, na.rm=T), max(elapsedtime, na.rm=T)),
axes=F, type='p', xlab=NA, ylab=NA, col="green", ylim=c(0, 100))
rect(elapsedtime[stim[1]], 0, elapsedtime[stim[2]], 100, col=rgb(red=0.2, green=0.2, blue=0.2, alpha=0.2), border = NA)
axis(4)
mtext(paste("Tracking error (px)"), side = 4, line=3)
legend("topright", inset=.05, c("Fluorescence", "Error"), col=c("blue", "green"), lty = 1)
title(main=paste0("Exposure: ", exposure, " ms, ", "Binning: ", binning, ", ", "fps: ", fpsfl))
dev.off()
# Plot speed and tracking error
png(file=paste0(dir, sample, "_speed_error_", type, ".png"), width=800, height=600)
par(mar=c(5,4,3,4))
plot(elapsedtimefvflash[1:length(error)], error, xlim=c(min(elapsedtime, na.rm=T), max(elapsedtime, na.rm=T)),
type='p', xlab=NA, ylab="Tracking error (px)", col="green", ylim=c(0, 100))
par(new=T)
plot(elapsedtimefvflash[1:length(speed)], speed, xlim=c(min(elapsedtime, na.rm=T), max(elapsedtime, na.rm=T)),
axes=F, type='p', xlab=NA, ylab=NA, col="red", ylim=c(0, 60))
rect(elapsedtime[stim[1]], 0, elapsedtime[stim[2]], 60, col=rgb(red=0.2, green=0.2, blue=0.2, alpha=0.2), border = NA)
axis(4)
mtext(paste("Fly speed (mm/s)"), side = 4, line=3)
legend("topright", inset=.05, c("Speed", "Error"), col=c("red", "green"), lty = 1)
title(main=paste0("Exposure: ", exposure, " ms, ", "Binning: ", binning, ", ", "fps: ", fpsfl))
dev.off()
# Plot speed, fluorescence, and window size
png(file=paste0(dir, sample, "_speed_intensity_window_", type, ".png"), width=800, height=600)
par(mar=c(5,4,3,4))
plot(elapsedtime, objsize, xlim=c(min(elapsedtime, na.rm=T), max(elapsedtime, na.rm=T)),
axes=F, type='l', xlab=NA, ylab=NA, col="green", ylim=c(0, median(objsize, na.rm=T)*1.5))
par(new=T)
plot(elapsedtime, intensity, type="l", xlim=c(min(elapsedtime, na.rm=T), max(elapsedtime, na.rm=T)),
ylim=c(0, median(intensity, na.rm=T)*3), xlab=paste("Elapsed time (ms) from", starttimefl),
ylab=paste("Fluorescence intensity (A.U.)"), col='blue')
par(new=T)
plot(elapsedtimefvflash[1:length(speed)], speed, xlim=c(min(elapsedtime, na.rm=T), max(elapsedtime, na.rm=T)),
axes=F, type='p', xlab=NA, ylab=NA, col="red", ylim=c(0, 60))
rect(elapsedtime[stim[1]], 0, elapsedtime[stim[2]], 60, col=rgb(red=0.2, green=0.2, blue=0.2, alpha=0.2), border = NA)
axis(4)
mtext(paste("Fly speed (mm/s), Window size (px)"), side = 4, line=3)
legend("topright", inset=.05, c("Fluorescence","Speed", "Window size"), col=c("blue", "red", "green"), lty = 1)
title(main=paste0("Exposure: ", exposure, " ms, ", "Binning: ", binning, ", ", "fps: ", fpsfl))
dev.off()
# Plot speed and window size
png(file=paste0(dir, sample, "_speed_window_", type, ".png"), width=800, height=600)
par(mar=c(5,4,3,4))
plot(elapsedtimefvflash[1:length(speed)], speed, xlim=c(min(elapsedtime, na.rm=T), max(elapsedtime, na.rm=T)),
type='l', xlab=NA, ylab="Fly speed (mm/s)", col="red", ylim=c(0, 60))
rect(elapsedtime[stim[1]], 0, elapsedtime[stim[2]], 60, col=rgb(red=0.2, green=0.2, blue=0.2, alpha=0.2), border = NA)
par(new=T)
plot(elapsedtime, objsize, xlim=c(min(elapsedtime, na.rm=T), max(elapsedtime, na.rm=T)),
axes=F, type='l', xlab=NA, ylab=NA, col="green", ylim=c(0, median(objsize, na.rm=T)*1.5))
axis(4)
mtext(paste("Window size (px)"), side = 4, line=3)
legend("topright", inset=.05, c("Speed", "Window size"), col=c("red", "green"), lty = 1)
title(main=paste0("Exposure: ", exposure, " ms, ", "Binning: ", binning, ", ", "fps: ", fpsfl))
dev.off()
# Plot fluorescence and window size
png(file=paste0(dir, sample, "_intensity_window_", type, ".png"), width=800, height=600)
par(mar=c(5,4,3,4))
plot(elapsedtime, intensity, type="l", xlim=c(min(elapsedtime, na.rm=T), max(elapsedtime, na.rm=T)),
ylim=c(0, median(intensity, na.rm=T)*3), xlab=paste("Elapsed time (ms) from", starttimefl),
ylab=paste("Fluorescence intensity (A.U.)"), col='blue')
par(new=T)
plot(elapsedtime, objsize, xlim=c(min(elapsedtime, na.rm=T), max(elapsedtime, na.rm=T)),
axes=F, type='l', xlab=NA, ylab=NA, col="green", ylim=c(0, median(objsize, na.rm=T)*1.5))
rect(elapsedtime[stim[1]], 0, elapsedtime[stim[2]], median(objsize, na.rm=T)*1.5, col=rgb(red=0.2, green=0.2, blue=0.2, alpha=0.2), border = NA)
axis(4)
mtext(paste("Window size (px)"), side = 4, line=3)
legend("topright", inset=.05, c("Fluorescence", "Window size"), col=c("blue", "green"), lty = 1)
title(main=paste0("Exposure: ", exposure, " ms, ", "Binning: ", binning, ", ", "fps: ", fpsfl))
dev.off()
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.