| Type: | Package |
| Title: | Binning and Visualizing NMR Spectra in Environmental Samples |
| Version: | 1.0.0 |
| Description: | A reproducible workflow for binning and visualizing NMR (nuclear magnetic resonance) spectra from environmental samples. The 'nmrrr' package is intended for post-processing of NMR data, including importing, merging and, cleaning data from multiple files, visualizing NMR spectra, performing binning/integrations for compound classes, and relative abundance calculations. This package can be easily inserted into existing analysis workflows by users to help with analyzing and interpreting NMR data. |
| URL: | https://github.com/kaizadp/nmrrr |
| BugReports: | https://github.com/kaizadp/nmrrr/issues |
| License: | MIT + file LICENSE |
| Copyright: | Battelle Memorial Institute |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.3 |
| Imports: | DescTools, ggplot2, tidyr, utils |
| Suggests: | covr, knitr, rmarkdown, testthat (≥ 3.0.0), tibble |
| Config/testthat/edition: | 3 |
| Depends: | R (≥ 3.50) |
| LazyData: | true |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2023-05-09 17:27:00 UTC; pate212 |
| Author: | Kaizad Patel 
[aut, cre],
Allison Myers-Pigg
[aut],
Ben Bond-Lamberty
[ctb],
Morgan Barnes
[ctb] |
| Maintainer: | Kaizad Patel <kaizad.patel@pnnl.gov> |
| Repository: | CRAN |
| Date/Publication: | 2023-05-10 16:10:02 UTC |
NMR grouping bins from Cade-Menun (2015).
Description
NMR grouping bins from Cade-Menun (2015), for 31P, using D2O as a solvent. (1) polyphosphate (-20 to -4); (2) diester (-1.5 to 2.0); (3) monoester (3.0 to 5.5); (4) orthophosphate (5.5 to 9.0); (5) phosphate (9.0 to 40.0)
Usage
bins_CadeMenun2015
Format
A data frame with 5 rows and 5 variables:
- number
Bin number
- group
Name of bin group
- start
ppm shift range, lower limit
- stop
ppm shift range, upper limit
- description
Description of the bin group
Note
The NMR spectrum can be split into several bins, based on chemical shift (ppm). Binsets are specific to nuclei and solvents and by definition are open on the left and closed on the right; for example, a bin of (0,1) includes 1 but not 0.
Source
B. Cade-Menun. "Improved peak identification in 31P-NMR spectra of environmental samples with a standardized method and peak library". Geoderma. doi:10.1016/j.geoderma.2014.12.016
See Also
bins_Clemente2012 bins_Lynch2019
bins_Mitchell2018
NMR grouping bins from Clemente et al. (2012).
Description
NMR grouping bins from Clemente et al. (2012), using DMSO-D6 as solvent. (1) aliphatic polymethylene and methyl groups (0.6–1.3 ppm, “aliphatic1”); (2) aliphatic methyl and methylene near O and N (1.3–2.9 ppm, “aliphatic2”); (3) O-alkyl, mainly from carbohydrates and lignin (2.9–4.1 ppm); (4) alpha-proton of peptides (4.1–4.8 ppm); (5) aromatic and phenolic (6.2–7.8 ppm); and (6) amide, from proteins (7.8–8.4 ppm).
Usage
bins_Clemente2012
Format
A data frame with 6 rows and 5 variables:
- number
Bin number
- group
Name of bin group
- start
ppm shift range, lower limit
- stop
ppm shift range, upper limit
- description
Description of the bin group
Note
The NMR spectrum can be split into several bins, based on chemical shift (ppm). Binsets are specific to nuclei and solvents and by definition are open on the left and closed on the right; for example, a bin of (0,1) includes 1 but not 0.
Source
JS Clemente et al. 2012. “Comparison of Nuclear Magnetic Resonance Methods for the Analysis of Organic Matter Composition from Soil Density and Particle Fractions.” Environmental Chemistry doi:10.1071/EN11096
See Also
bins_Lynch2019
bins_Mitchell2018 bins_Hertkorn2013
NMR grouping bins from Hertkorn et al. (2013).
Description
NMR grouping bins from Hertkorn et al. (2013), using MeOD as solvent. (1) aliphatics, HCCC (0.0-1.9); (2) acetate analogs and CRAM (carboxyl-rich alicyclic materials), HCX (1.9-3.1); (3) carbohydrate-like and methoxy, HCO (3.1-4.9); (4) olefinic HC=C (5.3-7.0); (5) aromatic (7.0-10.0).
Usage
bins_Hertkorn2013
Format
A data frame with 5 rows and 5 variables:
- number
Bin number
- group
Name of bin group
- start
ppm shift range, lower limit
- stop
ppm shift range, upper limit
- description
Description of the bin group
Note
The NMR spectrum can be split into several bins, based on chemical shift (ppm). Binsets are specific to nuclei and solvents and by definition are open on the left and closed on the right; for example, a bin of (0,1) includes 1 but not 0.
Source
N. Hertkorn et al. 2013. "High-field NMR spectroscopy and FTICR mass spectrometry: powerful discovery tools for the molecular level characterization of marine dissolved organic matter" Biogeosciences doi:10.5194/bg-10-1583-2013
See Also
bins_Clemente2012 bins_Lynch2019
bins_Mitchell2018
NMR grouping bins from Lynch et al. (2019).
Description
NMR grouping bins from Lynch et al. (2019), using D2O as solvent. (1) methyl, methylene, and methane bearing protons (0.6–1.6 ppm) ; (2) unsaturated functional groups (1.6–3.2 ppm), including ketone, benzylic, and alicyclic-bearing protons; (3) unsaturated, heteroatomic compounds, including O-bearing carbohydrates, ethers, and alcohols (3.2–4.5 ppm); (4) conjugated, double bond functionalities, including aromatic, amide, and phenolic structures (6.5–8.5 ppm).
Usage
bins_Lynch2019
Format
A data frame with 4 rows and 5 variables:
- number
Bin number
- group
Name of bin group
- start
ppm shift range, lower limit
- stop
ppm shift range, upper limit
- description
Description of the bin group
Note
The NMR spectrum can be split into several bins, based on chemical shift (ppm). Binsets are specific to nuclei and solvents and by definition are open on the left and closed on the right; for example, a bin of (0,1) includes 1 but not 0.
Source
LM Lynch et al. 2019. “Dissolved Organic Matter Chemistry and Transport along an Arctic Tundra Hillslope.” Global Biogeochemical Cycles doi:10.1029/2018GB006030
See Also
bins_Clemente2012
bins_Mitchell2018 bins_Hertkorn2013
NMR grouping bins from Mitchell et al. (2018).
Description
NMR grouping bins from Mitchell et al. (2018), using DMSO-D6 as solvent. (1) aliphatic polymethylene and methyl groups (0.6–1.3 ppm); (2) N- and O-substituted aliphatic (1.3–2.9 ppm); (3) O-alkyl (2.9–4.1 ppm); (4) alpha-proton of peptides (4.1–4.8 ppm); (5) anomeric proton of carbohydrates (4.8–5.2 ppm); (6) aromatic and phenolic (6.2–7.8 ppm); (7) amide (7.8–8.4 ppm).
Usage
bins_Mitchell2018
Format
A data frame with 7 rows and 5 variables:
- number
Bin number
- group
Name of bin group
- start
ppm shift range, lower limit
- stop
ppm shift range, upper limit
- description
Description of the bin group
Note
The NMR spectrum can be split into several bins, based on chemical shift (ppm). Binsets are specific to nuclei and solvents and by definition are open on the left and closed on the right; for example, a bin of (0,1) includes 1 but not 0.
Source
P Mitchell et al. 2018. “Nuclear Magnetic Resonance Analysis of Changes in Dissolved Organic Matter Composition with Successive Layering on Clay Mineral Surfaces.” Soil Systems doi:10.3390/soils2010008
See Also
bins_Clemente2012 bins_Lynch2019
bins_Hertkorn2013
NMR grouping bins from Baldock et al. (2004).
Description
NMR grouping bins from Baldock et al. (2004), for solid-state NMR. (1) alkyl C (0-45); (2) methoxyl C and N-alkyl C (45-60); (3) O-alkyl C (60-95); (4) di-O-alkyl C (95-110); (5) aromatic C (110-145); (6) phenolic C (145-165); (7) amide and carboxyl C (165-215)
Usage
bins_ss_Baldock2004
Format
A data frame with 5 rows and 5 variables:
- number
Bin number
- group
Name of bin group
- start
ppm shift range, lower limit
- stop
ppm shift range, upper limit
- description
Description of the bin group
Note
The NMR spectrum can be split into several bins, based on chemical shift (ppm). Binsets are specific to nuclei and solvents and by definition are open on the left and closed on the right; for example, a bin of (0,1) includes 1 but not 0.
Source
J. Baldock et al. "Cycling and composition of organic matter in terrestrial and marine ecosystems". Marine Chemistry. doi:10.1016/j.marchem.2004.06.016
See Also
bins_Clemente2012 bins_Lynch2019
bins_Mitchell2018
NMR grouping bins from Clemente et al. (2012) - ss.
Description
NMR grouping bins from Clemente et al. (2012), for solid-state NMR. (1) alkyl C (0-50); (2) O-alkyl C (60-93); (3) anomeric C (95-110); (4) aromatic C (110-160); (5) carboxyl-carbonyl C (160-200)
Usage
bins_ss_Clemente2012
Format
A data frame with 5 rows and 5 variables:
- number
Bin number
- group
Name of bin group
- start
ppm shift range, lower limit
- stop
ppm shift range, upper limit
- description
Description of the bin group
Note
The NMR spectrum can be split into several bins, based on chemical shift (ppm). Binsets are specific to nuclei and solvents and by definition are open on the left and closed on the right; for example, a bin of (0,1) includes 1 but not 0.
Source
JS Clemente et al. 2012. “Comparison of Nuclear Magnetic Resonance Methods for the Analysis of Organic Matter Composition from Soil Density and Particle Fractions.” Environmental Chemistry doi:10.1071/EN11096
See Also
bins_Clemente2012 bins_ss_Preston2009
bins_Mitchell2018
NMR grouping bins from Preston et al. (2009).
Description
NMR grouping bins from Preston et al. (2009), for solid-state NMR. (1) alkyl C (0-50); (2) methoxyl C (50-60); (3) O-alkyl C (60-93); (4) di-O-alkyl C (93-112); (5) aromatic C (112-140); (6) phenolic C (140-165); (7) carboxyl C (165-190)
Usage
bins_ss_Preston2009
Format
A data frame with 5 rows and 5 variables:
- number
Bin number
- group
Name of bin group
- start
ppm shift range, lower limit
- stop
ppm shift range, upper limit
- description
Description of the bin group
Note
The NMR spectrum can be split into several bins, based on chemical shift (ppm). Binsets are specific to nuclei and solvents and by definition are open on the left and closed on the right; for example, a bin of (0,1) includes 1 but not 0.
Source
C. Preston et al. 2009. "Chemical Changes During 6 Years of Decomposition of 11 Litters in Some Canadian Forest Sites. Part 1. Elemental Composition, Tannins, Phenolics, and Proximate Fractions". Ecosystems. doi:10.1007/s10021-009-9266-0
See Also
bins_Clemente2012 bins_Lynch2019
bins_Mitchell2018
Assign compound classes using the chosen binset
Description
Assign group (bin name) to each row of the data based on
the ppm column.
Usage
nmr_assign_bins(dat, binset)
Arguments
dat |
Input dataframe. This could be spectral data, or peak picked data. Must include a 'ppm' column for compound class assignment |
binset |
A binset; e.g. |
Value
The input data with a new group column whose entries
are drawn from the binset. Entries will be NA if a ppm
value does not fall into any group.
Author(s)
Kaizad Patel
Examples
sdir <- system.file("extdata", "kfp_hysteresis", "spectra_mnova", package = "nmrrr")
spec <- nmr_import_spectra(path = sdir, method = "mnova")
nmr_assign_bins(spec, bins_Clemente2012)
Import and process picked peaks data
Description
Process data of peaks picked with NMR software.
Usage
nmr_import_peaks(path, method, pattern = "*.csv$", quiet = FALSE)
Arguments
path |
Directory where the peaks data are saved |
method |
Format of input data, depending on how the data were exported. "multiple columns": data are in split-column format, obtained by pasting "peaks table" in MNova. "single column": data are in single-column format, exported from MNova as "peaks script". |
pattern |
Filename pattern to search for (by default "*.csv$") |
quiet |
Print diagnostic messages? Logical |
Value
A dataframe with columns describing sample ID, ppm, intensity, area, group name.
Author(s)
Kaizad Patel
Examples
sdir <- system.file("extdata", "kfp_hysteresis", "peaks_mnova_multiple", package = "nmrrr")
nmr_import_peaks(path = sdir, method = "multiple columns")
Import and process NMR spectral data
Description
Imports multiple spectra files and then combines and cleans the data.
Usage
nmr_import_spectra(path, method, pattern = "*.csv$", quiet = FALSE)
Arguments
path |
Directory where the spectra files are saved |
method |
Software used for initial processing of NMR spectra (before using this package). Available options include "mnova" and "topspin". |
pattern |
Filename pattern to search for (by default "*.csv$") |
quiet |
Print diagnostic messages? Logical |
Value
A link{data.frame} with data from all files found,
concatenated and sorted.
Author(s)
Kaizad Patel
Examples
sdir <- system.file("extdata", "kfp_hysteresis", "spectra_mnova", package = "nmrrr")
nmr_import_spectra(path = sdir, method = "mnova")
Plot NMR spectra
Description
Plot NMR spectra, with line-brackets denoting binned regions. Uses spectra data processed in MestreNova or TopSpin.
Usage
nmr_plot_spectra(
dat,
binset,
label_position = 100,
mapping = aes(x = ppm, y = intensity),
stagger = 10
)
Arguments
dat |
Processed spectral data, output from (a) |
binset |
A binset; e.g. |
label_position |
y-axis position for bin labels |
mapping |
An aesthetic mapping generated by |
stagger |
How much to stagger the labels, numeric;
same units as |
Value
A ggplot object.
Author(s)
Kaizad Patel
Examples
sdir <- system.file("extdata", "kfp_hysteresis", "spectra_mnova", package = "nmrrr")
spec <- nmr_import_spectra(path = sdir, method = "mnova")
library(ggplot2)
p_aes <- aes(x = ppm, y = intensity)
p <- nmr_plot_spectra(spec, bins_Clemente2012, 5, p_aes, stagger = 0.5)
p + ylim(0, 6)
Compute relative abundance for each sample
Description
Compute relative abundance of compound classes for each sample.
Usage
nmr_relabund(dat, method)
Arguments
dat |
Processed spectral data, output from (a) |
method |
The method for calculating relative abundance. Options include (a) "AUC", integrating the spectral region within each bin; (b) "peaks", adding areas of peaks if a peak-picked file is provided. |
Value
A data.frame with columns describing relative contributions of
compound classes. Compound classes are determined by selecting the desired
binset.
Author(s)
Kaizad Patel
Examples
sdir <- system.file("extdata", "kfp_hysteresis", "peaks_mnova_multiple", package = "nmrrr")
peaks <- nmr_import_peaks(path = sdir, method = "multiple columns")
peaks <- nmr_assign_bins(peaks, bins_Clemente2012)
nmr_relabund(peaks, "peaks")