tutorial_plot_speclib

## Create and parse a speclib object
## LR

library(hsdar)

data(spectral_data) # load sample data

# Extract objects from sample data
# (these should be created/imported by the user, in a standard workflow)
spectra <- spectra(spectral_data)       # spectra (matrix dim n×m)
wavelength <- wavelength(spectral_data) # wavelenghts (vector dim m)
ids <- idSpeclib(spectral_data)         # IDs (character dim n)
SI <- SI(spectral_data)                 # supplemetary info (data.frame dim n×x)

# Create a speclib object
spectra_speclib <- speclib(spectra, wavelength)
idSpeclib(spectra_speclib) <- as.character(ids) # (optional)
SI(spectra_speclib) <- SI # (optional)

# Create a "long" data.table (to be used with ggplot)
library(data.table)
spectra_long <- data.table(
  "spectra" = as.vector(spectra),
  "wavelength" = rep(wavelength, each = length(ids)),
  "id" = rep(as.character(ids), length(wavelength))
)
# Create summary statistics from spectra
spectra_summary <- spectra_long[
  ,list(
    spectra_avg = mean(spectra),
    spectra_sd = sd(spectra),
    spectra_med = median(spectra),
    spectra_q1 = quantile(spectra, .25),
    spectra_q3 = quantile(spectra, .75)
  ),
  by = "wavelength"]


## Examples of ggplot plots (with the equivalent plot.speclib)
library(ggplot2)

# Default plot (average and standard deviation)
plot(spectra_speclib, main = "Default Plot")
ggplot(spectra_summary, aes(x = wavelength)) +
  geom_ribbon(aes(ymin = spectra_avg-spectra_sd, ymax = spectra_avg+spectra_sd), alpha = .2) +
  geom_line(aes(y = spectra_avg)) +
  xlab("Wavelength (nm)") + ylab("Reflectance (%)") + ggtitle("Default plot") +
  theme_light()

# Median (and quartiles)
plot(spectra_speclib, FUN = "median", main = "Median spectrum")
ggplot(spectra_summary, aes(x = wavelength)) +
  geom_ribbon(aes(ymin = spectra_q1, ymax = spectra_q3), alpha = .2) +
  geom_line(aes(y = spectra_med)) +
  xlab("Wavelength (nm)") + ylab("Reflectance (%)") + ggtitle("Median spectrum") +
  theme_light()

# Specific spectrum
plot(spectra_speclib, FUN = 1, main = "First spectrum of Speclib")
ggplot(spectra_long[id==1,], aes(x = wavelength)) +
  geom_ribbon(data = spectra_summary, aes(ymin = spectra_q1, ymax = spectra_q3), alpha = .2) +
  geom_line(aes(y = spectra), colour = "blue", size = .75) +
  xlab("Wavelength (nm)") + ylab("Reflectance (%)") + ggtitle("First spectrum of Speclib") +
  theme_light()

# More spectra
plot(spectra_speclib, FUN = 1, col = "red", main = "Three spectra")
plot(spectra_speclib, FUN = 2, col = "blue", new = FALSE)
plot(spectra_speclib, FUN = 3, col = "orange", new = FALSE)
ggplot(spectra_long[id %in% c(1:3),], aes(x = wavelength)) +
  geom_ribbon(data = spectra_summary, aes(ymin = spectra_q1, ymax = spectra_q3), alpha = .2) +
  geom_line(aes(y = spectra, colour = id)) +
  xlab("Wavelength (nm)") + ylab("Reflectance (%)") + ggtitle("Three spectra") +
  theme_light()

# More spectra with panels
ggplot(spectra_long[id %in% c(1:3),], aes(x = wavelength)) +
  geom_ribbon(data = spectra_summary, aes(ymin = spectra_q1, ymax = spectra_q3), alpha = .2) +
  geom_line(data = spectra_summary, aes(y = spectra_med), alpha = .2) +
  geom_line(aes(y = spectra)) +
  facet_wrap(~id) +
  xlab("Wavelength (nm)") + ylab("Reflectance (%)") + ggtitle("Three spectra") +
  theme_light()