Visualize spectra

01_visualize-spectra.R

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## Task: Example script to visualize spectra in simplerspec framework
################################################################################

# Remove all R objects from memory
rm(list = ls())

# Load packages
pkgs <- c("tidyverse", "simplerspec")
lapply(pkgs, library, character.only = TRUE)

## Read spectra from OPUS files ================================================

# Create vector with list of OPUS files to be read
lf <- dir(path = "data/spectra", full.names = TRUE)

# Read into list
spc_l <- read_opus_univ(fnames = lf, parallel = FALSE)
# Possible to read in parallel to increase speed; see 

## Gather and process spectra ==================================================

# Spectral processing pipe
spc_tbl <- spc_l %>%
  # Gather list of spectra data into tibble data frame
  gather_spc()

# Investigate spectral tibble (data.frame)
# Get raw spectrum from first sample
dim(spc_tbl$spc[[1]])


spc_tbl <- spc_tbl %>%
  # Resample spectra to new wavenumber interval
  resample_spc(wn_lower = 500, wn_upper = 3996, wn_interval = 2) %>%
  # Average replicate scans per sample_id
  average_spc() %>%
  # Preprocess spectra using Savitzky-Golay first derivative with a window size
  # of 21 points
  preprocess_spc(select = "sg_1_w21")
  

# Print preprocessed spectral tibble (data.frame)
spc_tbl

## Exploratory data analysis ===================================================

spc_tbl %>% 
  plot_spc_ext(group_panel = FALSE, group_color = FALSE)

# Check which sample has absorbance above 2
spc_m <- do.call(rbind, spc_tbl$spc)
# -> manually remove; check in OPUS software