vignettes/plot.R

In jsta/adv: Process Acoustic Doppler Velocimeter Data

## ---- eval=TRUE, echo=FALSE, fig.align='center',fig.width=7, fig.height=4, warning=FALSE----
library(adv)

flist <- list.files("../inst/extdata", include.dirs = TRUE, full.names = TRUE, "*.csv")[3:6]
#flist <- list.files("inst/extdata", include.dirs = TRUE, full.names = TRUE, "*.csv")[3:6]

dt <- lapply(flist, function(x) read.csv(x, header = TRUE, stringsAsFactors = FALSE))

dtnames <- lapply(flist, function(x) rep(strsplit(strsplit(basename(x), "\\.")[[1]][1], "_")[[1]][4]
 , nrow(read.csv(x))))

dtnames <- do.call(c, dtnames)
dt <- do.call(rbind, dt)
dt$site <- dtnames
dt$datetime <- as.POSIXct(dt$datetime)

dt$spikes <- as.POSIXct(dt$spikes, origin = "1970-01-01")
dt[!is.na(dt$spikes),"spikes"] <- as.POSIXct(dt[!is.na(dt$spikes),"datetime"])

dt$speed_highsnr <- dt$speed
dt[dt$snr_mean < 5, "speed_highsnr"] <- NA

library(ggplot2)
theme_opts <- list(ggplot2::theme(
	panel.grid.minor = ggplot2::element_blank(),
	panel.grid.major = ggplot2::element_blank(),
	panel.background = ggplot2::element_blank(),
	plot.background = ggplot2::element_rect(fill="white"),
	panel.border = ggplot2::element_blank(),
	axis.line = ggplot2::element_line(),
	axis.text.x = ggplot2::element_text(angle=90),
	axis.text.y = ggplot2::element_text(size=12),
	axis.ticks = ggplot2::element_line(),
	axis.title.x = ggplot2::element_blank(),
	axis.title.y = ggplot2::element_text(size=14),
	plot.title = ggplot2::element_text(size=22),
	legend.position = "none",
	strip.background = ggplot2::element_rect(fill = 'white')))

gg <- ggplot(dt, aes(x = datetime, y = speed, colour = site))
gg <- gg + geom_line(alpha = 0.8)
gg <- gg + geom_point(aes(x = spikes, y = 35))
gg <- gg + theme_opts + ggplot2::ylab("Speed Low SNR \n Points Indicate Spike Positions") + viridis::scale_color_viridis(discrete = TRUE) + scale_x_datetime(date_breaks = "1 week", date_labels = "%m-%d")
gg + facet_grid(site~.)

gg <- ggplot(dt, aes(x = datetime, y = speed_highsnr, colour = site))
gg <- gg + geom_line(alpha = 0.8)
gg <- gg + theme_opts + ggplot2::ylab("Speed High SNR") + viridis::scale_color_viridis(discrete = TRUE) + scale_x_datetime(date_breaks = "1 week", date_labels = "%m-%d")
gg + facet_grid(site~.)

gg <- ggplot(dt, aes(x = datetime, y = speed_raw, colour = site))
gg <- gg + geom_line(alpha = 0.8)
gg <- gg + theme_opts + ggplot2::ylab("Speed Raw") + viridis::scale_color_viridis(discrete = TRUE) + scale_x_datetime(date_breaks = "1 week", date_labels = "%m-%d")
gg + facet_grid(site~.)

gg <- ggplot(dt, aes(x = datetime, y = snr_mean, colour = site))
gg <- gg + geom_line(alpha = 0.8)
gg <- gg + theme_opts + ggplot2::ylab("3-probe average SNR") + viridis::scale_color_viridis(discrete = TRUE) + scale_x_datetime(date_breaks = "1 week", date_labels = "%m-%d")
gg + facet_grid(site~.)