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https://github.com/wincowgerDEV/OpenSpecy-package
Analyze, Process, Identify, and Share, Raman and (FT)IR Spectra
https://github.com/wincowgerDEV/OpenSpecy-package
Last synced: 3 months ago
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Analyze, Process, Identify, and Share, Raman and (FT)IR Spectra
- Host: GitHub
- URL: https://github.com/wincowgerDEV/OpenSpecy-package
- Owner: wincowgerDEV
- License: cc-by-4.0
- Created: 2021-01-29T12:52:33.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2024-03-19T13:59:45.000Z (8 months ago)
- Last Synced: 2024-03-22T02:21:51.341Z (8 months ago)
- Language: R
- Homepage: http://wincowger.com/OpenSpecy-package/
- Size: 175 MB
- Stars: 21
- Watchers: 3
- Forks: 9
- Open Issues: 15
-
Metadata Files:
- Readme: README.md
- Funding: .github/FUNDING.yml
- License: LICENSE.md
Awesome Lists containing this project
- open-sustainable-technology - OpenSpecy - Raman and (FT)IR spectral analysis tool for plastic particles and other environmental samples. (Industrial Ecology / Circular Economy and Waste)
README
# Open Specy 1.0
Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
[](https://CRAN.R-project.org/package=OpenSpecy)
[](https://www.repostatus.org/#active)
[](https://github.com/wincowgerDEV/OpenSpecy-package/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/wincowgerDEV/OpenSpecy-package?branch=main)
[](https://creativecommons.org/licenses/by/4.0/)
[](https://doi.org/10.1021/acs.analchem.1c00123)
[](https://openanalysis.org/openspecy/)
[](https://app.gitter.im/#/room/#Open-Specy_community:gitter.im)
Raman and (FT)IR spectral analysis tool for plastic particles and other
environmental samples (Cowger et al. 2021, doi:
[10.1021/acs.analchem.1c00123](https://doi.org/10.1021/acs.analchem.1c00123)).
With `read_any()`, Open Specy provides a single function for reading individual,
batch, or map spectral data files like .asp, .csv, .jdx, .spc, .spa, .0, and
.zip. `process_spec()` simplifies processing spectra, including smoothing,
baseline correction, range restriction and flattening, intensity conversions,
wavenumber alignment, and min-max normalization.
Spectra can be identified in batch using an onboard reference library
(Cowger et al. 2020, doi: [10.1177/0003702820929064](https://doi.org/10.1177/0003702820929064))
using `match_spec()`. A Shiny app is available via `run_app()`
or online at [https://openanalysis.org/openspecy/](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](https://CRAN.R-project.org) with:
```r
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**):
```r
if (!require(devtools)) install.packages("devtools")
devtools::install_github("wincowgerDEV/OpenSpecy-package")
```
## Getting started
```r
library(OpenSpecy)
run_app()
```
## Simple workflow for single spectral identification
See [package vignette](https://wincowger.com/OpenSpecy-package/articles/sop.html)
for a detailed standard operating procedure.
```r
# Fetch current spectral library from https://osf.io/x7dpz/
get_lib("derivative")
# Load library into global environment
spec_lib <- load_lib("derivative")
# Read sample spectrum
raman_hdpe <- read_extdata("raman_hdpe.csv") |>
read_any()
# Look at the spectrum
plotly_spec(raman_hdpe)
# Process the spectra and conform it to the library format
raman_proc <- raman_hdpe |>
process_spec(conform_spec_args = list(range = spec_lib$wavenumbers),
smooth_intens = T, make_rel = T)
# Compare raw and processed spectra
plotly_spec(raman_hdpe, raman_proc)
top_matches <- match_spec(raman_proc, library = spec_lib, na.rm = T, top_n = 5,
add_library_metadata = "sample_name",
add_object_metadata = "col_id")
# Print the top 5 results with relevant metadata
top_matches[, c("object_id", "library_id", "match_val", "SpectrumType",
"SpectrumIdentity")]
# Get all metadata for the matches
get_metadata(spec_lib, logic = top_matches$library_id)
```
## 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](https://doi.org/10.1021/acs.analchem.1c00123).
Cowger W, Steinmetz Z, Leong N, Faltynkova A, Sherrod H (2024). “OpenSpecy: Analyze,
Process, Identify, and Share Raman and (FT)IR Spectra.” *R package*, **1.0.8**.
[https://github.com/wincowgerDEV/OpenSpecy-package](https://github.com/wincowgerDEV/OpenSpecy-package).