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What is ChemoSpec?

ChemoSpec is a collection of functions for top-down exploratory data analysis of spectral data including nuclear magnetic resonance (NMR), infrared (IR), Raman, X-ray fluorescence (XRF) and other similar types of spectroscopy. Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA) and model-based clustering. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed for structured experiments, such as metabolomics investigations, where the samples fall into treatment and control groups. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and to help you get usable results quickly. A vignette covering typical operations is available.

Learn more about ChemoSpec

Installing ChemoSpec from CRAN:

chooseCRANmirror() # choose a CRAN mirror
install.packages("ChemoSpec")
library("ChemoSpec")

Installing ChemoSpec from Github:

install.packages("remotes")
library("remotes")
install_github(repo = "bryanhanson/ChemoSpec@main")
library("ChemoSpec")

If you use @some_other_branch you can download other branches that might be available. They may or may not pass CRAN checks and thus may not install automatically using the method above. Check the NEWS file to see what's up.

Also...

ChemoSpec requires ChemoSpecUtils to work. It should install automatically, but if not, you can use a command similar to the above to install it.

To view the Vignettes:

To access the vignettes, use the following, or visit here.

browseVignettes("ChemoSpec")

Code of Conduct

This project is released with a Contributor Code of Conduct. By contributing, you agree to abide by its terms.

Contributing

If you would like to contribute to the project, please see Contributing Guide.

License Information

ChemoSpec is distributed under the GPL-3 license, as stated in the DESCRIPTION file. For more info, see the GPL site.

Questions? hanson@depauw.edu

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Version

Install

install.packages('ChemoSpec')

Monthly Downloads

1,123

Version

6.1.10

License

GPL-3

Maintainer

Bryan Hanson

Last Published

February 3rd, 2024

Functions in ChemoSpec (6.1.10)

hcaSpectra

Plot HCA Results of a Spectra Object
metMUD1

Made Up NMR Data Sets
removeFreq

Remove Frequencies from a Spectra or Spectra2D Object
plotSpectraDist

Plot the Distance Between Spectra and a Reference Spectrum in a Spectra Object
chkGraphicsOpt

Check the Graphics Output Option/Mode
removeGroup

Remove Groups from a Spectra or Spectra2D Object
pcaDiag

Outlier Diagnostic Plots for PCA of a Spectra Object
plotSpectra

Plot Spectra Object
plotScores

Plot Scores from PCA, MIA or PARAFAC Analysis of a Spectra or Spectra2D Object
plot2Loadings

Plot PCA Loadings from a Spectra Object Against Each Other
normSpectra

Normalize a Spectra Object
plotScree

Scree Plots from PCA or MIA Analysis of a Spectra or Spectra2D Object
removeSample

Remove Samples from a Spectra or Spectra2D Object
sampleDist

Compute the Distances Between Samples in a Spectra or Spectra2D Object
s_pcaSpectra

Sparse PCA of Spectra Objects
reviewAllSpectra

Review All the Spectra in a Spectra Object
hmapSpectra

Seriated Heat Map for a Spectra Object
rowDist

Compute Distance Between Rows of a Matrix
updateGroups

Update Group Names in a Spectra or Spectra2D Object
sgfSpectra

Apply Savitzky-Golay filters to a Spectra object
sPlotSpectra

s-Plot of Spectra Data (Post PCA)
surveySpectra

Plot Measures of Central Tendency and Spread for a Spectra Object
plot3dScores

3D PCA Score Plot for a Spectra Object
mclustSpectra

mclust Analysis of a Spectra Object PCA Results
mclust3dSpectra

mclust Analysis of a Spectra Object in 3D
splitSpectraGroups

Create New Groups from an Existing Spectra Object
sumGroups

Summarize the Group Membership of a Spectra or Spectra2D Object
hypTestScores

Conduct MANOVA using PCA Scores and Factors in a Spectra Object
plotLoadings

Plot PCA Loadings for a Spectra Object
sumSpectra

Summarize a Spectra or Spectra2D Object
plotSpectraJS

Plot a Spectra Object Interactively
irlba_pcaSpectra

IRLBA PCA of Spectra Objects
r_pcaSpectra

Robust PCA of a Spectra Object
binSpectra

Bin or Bucket a Spectra Object
SrE.IR

IR and NMR Spectra of Serenoa repens (Saw Palmetto) Oil Extracts and Reference Oils
Spectra

Spectra Objects
c_pcaSpectra

Classical PCA of Spectra Objects
aovPCAloadings

Plot aovPCAscores Loadings of a Spectra Object
baselineSpectra

Baseline Correction of a Spectra Object
chkSpectra

Verify the Integrity of a Spectra or Spectra2D Object
check4Gaps

Check for Discontinuities (Gaps) in a Vector & Optionally Make a Plot
colorSymbol

Color and Symbols in ChemoSpec and ChemoSpec2D
hcaScores

HCA on PCA/MIA/PARAFAC scores from a Spectra or Spectra2D Object
conColScheme

Change the Color Scheme of a Spectra or Spectra2D Object
aov_pcaSpectra

ANOVA-PCA Analysis of Spectra Data
cv_pcaSpectra

Cross-Validation of Classical PCA Results for a Spectra Object
clupaSpectra

Hierarchical Cluster-Based Peak Alignment on a Spectra Object
evalClusters

Evaluate or Compare the Quality of Clusters Quantitatively
aovPCAscores

Plot ANOVA-PCA Scores from a Spectra Object
files2SpectraObject

Import Data into a Spectra Object
ChemoSpec-package

Exploratory Chemometrics for Spectroscopy
averageReplicates

Average Replicates in a Spectra Object