Open Specy
Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
Raman and (FT)IR spectral analysis tool for plastic particles and
other environmental samples (Cowger et al. 2021, doi:
10.1021/acs.analchem.1c00123).
Supported features include reading spectral data files (.asp, .csv, .jdx, .spc,
.spa, .0), Savitzky-Golay smoothing of spectral intensities with
smooth_intens()
, correcting background noise with subtr_bg()
in accordance
with Zhao et al. (2007, doi:
10.1366/000370207782597003), and
identifying spectra using an onboard reference library (Cowger et al. 2020, doi: 10.1177/0003702820929064).
Analyzed spectra can be shared with the Open Specy community. A Shiny app is
available via run_app()
or online at
https://openanalysis.org/openspecy/.
Installation
OpenSpecy is available from CRAN and GitHub.
Install from CRAN (stable version)
You can install the latest release of OpenSpecy from CRAN with:
install.packages("OpenSpecy")
Install from GitHub (development version)
To install the development version of this package, paste the following code into your R console (requires devtools):
if (!require(devtools)) install.packages("devtools")
devtools::install_github("wincowgerDEV/OpenSpecy")
Getting started
library(OpenSpecy)
run_app()
See package vignette for a detailed standard operating procedure.
Workflow
library(dplyr)
# Fetch current spectral library from https://osf.io/x7dpz/
get_lib()
# Load library into global environment
spec_lib <- load_lib()
# Read sample spectrum
raman_hdpe <- read_text(read_extdata("raman_hdpe.csv"))
# Share your spectrum with the Open Spey community
share_spec(raman_hdpe,
metadata = c(user_name = "Win Cowger",
contact_info = "wincowger@gmail.com",
spectrum_type = "Raman",
spectrum_identity = "HDPE")
)
# Adjust spectral intensity
raman_adj <- raman_hdpe %>%
adj_intens()
# Smooth and background-correct spectrum
raman_proc <- raman_adj %>%
smooth_intens() %>%
subtr_bg()
# Match spectrum with library and retrieve meta data
match_spec(raman_proc, library = spec_lib, which = "raman")
find_spec(sample_name == 5381, library = spec_lib, which = "raman")
Citations
Cowger W, Steinmetz Z, Gray A, Munno K, Lynch J, Hapich H, Primpke S, De Frond H, Rochman C, Herodotou O (2021). “Microplastic Spectral Classification Needs an Open Source Community: Open Specy to the Rescue!” Analytical Chemistry, 93(21), 7543–7548. doi: 10.1021/acs.analchem.1c00123.
Cowger W, Steinmetz Z (2021). “OpenSpecy: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra.” R package, 0.9.5. https://github.com/wincowgerDEV/OpenSpecy-package.