ChemoSpec: Exploratory Chemometrics for Spectroscopy

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A collection of functions for top-down exploratory data analysis of spectral data obtained via nuclear magnetic resonance (NMR), infrared (IR) or Raman 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 with metabolomics data sets in mind, where the samples fall into groups such as treatment and control. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and help you get usable results quickly. A vignette covering typical operations is available.

Author
Bryan A. Hanson DePauw University, Greencastle Indiana USA
Date of publication
2016-07-15 17:12:22
Maintainer
Bryan A. Hanson <hanson@depauw.edu>
License
GPL-3
Version
4.3.34
URLs

View on CRAN

Man pages

aovPCAloadings
Plot aovPCAscores Loadings of a Spectra Object
aovPCAscores
Plot ANOVA-PCA Scores from a Spectra Object
aov_pcaSpectra
ANOVA-PCA Analysis of Spectra Data
avgFacLvls
Average Levels of a Factor in a Data Matrix
baselineSpectra
Baseline Correction of a Spectra Object
binData
Bin or Bucket Data
binSpectra
Bin or Bucket a Spectra Object
check4Gaps
Check for Missing Values (Gaps)
ChemoSpec-package
Exploratory Chemometrics for Spectroscopy
chkSpectra
Verify the Integrity of a Spectra Object
clupaSpectra
Conduct Hierarchical Cluster-Based Peak Alignment on a...
colLeaf
Color the Leaves of a Dendrogram Based on a Spectra Object
colorSymbol
Colors and Symbols in ChemoSpec and Spectra Objects
conColScheme
Change the Color Scheme of a Spectra Object
coordProjCS
Modified Version of coordProj from mclust
c_pcaSpectra
Classical PCA of Spectra Objects
cv_pcaSpectra
Cross-Validation of Classical PCA Results for a Spectra...
evalClusters
Evaluate or Compare the Quality of Clusters Quantitatively
files2SpectraObject
Merge Files in a Directory into a Spectra Object
groupNcolor
Assign Group Membership and Colors for a Spectra Object
hcaScores
HCA on PCA scores from a Spectra Object
hcaSpectra
Plot HCA Results of a Spectra Object
hmapSpectra
Create a Seriated Heat Map Comparing Samples and Spectral...
hypTestScores
Conduct MANOVA using PCA Scores and Factors in a Spectra...
isWholeNo
Determine if a Number is a Whole Number
labelExtremes
Label Extreme Values in a 2D Data Set
labelExtremes3d
Identify Extreme Values in 3D
LoopThruSpectra
Display the Spectra in a Spectra Object One at a Time
makeEllipsoid
Create Ellipsoid
matrix2SpectraObject
Process a Data Matrix in a csv File into a Spectra Object
mclust3D
mclust Analysis in 3D
mclust3dSpectra
mclust Analysis of a Spectra Object in 3D
mclustSpectra
mclust Analysis of a Spectra Object PCA Results
MUD
Made Up NMR Data Sets
normSpectra
Normalize a Spectra Object
normVec
Normalize a Vector to range -1 to +1
pcaDiag
Outlier Diagnostic Plots for PCA of a Spectra Object
plot2Loadings
Plot PCA Loadings from a Spectra Object Against Each Other
plotHCA
Plot Dendrogram for Spectra Object
plotLoadings
Plot PCA Loadings for a Spectra Object
plotScores
Plot PCA Scores of a Spectra Object
plotScores3D
3D PCA Score Plot for a Spectra Object
plotScoresCor
Compute Confidence Ellipses
plotScoresDecoration
Decorate PCA Score Plot of a Spectra Object
plotScoresRGL
Interactive 3D Score Plot of a Spectra Object
plotScree
Scree Plots of PCA Results for a Spectra Object
plotSpectra
Plot Spectra Object
plotSpectraDist
Plot the Distance Between Spectra in a Spectra Object
plotSpectraJS
Plot a Spectra Object Interactively
q2rPCA
Conversion Between PCA Classes
readJDX
Read and process a JCAMP-DX file.
removeFreq
Remove Frequencies from a Spectra Object
removeSample
Remove Samples or Groups from a Spectra Object
rowDist
Compute Distance Between Rows of a Matrix
r_pcaSpectra
Robust PCA of a Spectra Object
sampleDistSpectra
Compute the Distance Between Samples in a Spectra Object
seXy
Functions to Compute Measures of Central Tendency and Spread....
sgfSpectra
Apply Savitzky-Golay filters to a Spectra object
shrinkLeaf
Shrink the Leaves of a Dendrogram Based on a Spectra Object
Spectra
Spectra Objects
splitSpectraGroups
Create New Groups from an Existing Spectra Object
sPlotSpectra
s-Plot of Spectra Data Post PCA
SrE.IR
IR and NMR Spectra of Serenoa repens (Saw Palmetto) Oil...
sumGroups
Summarize the Group Parameters of a Spectra Object
sumSpectra
Summarize a Spectra Object
surveySpectra
Plot Measures of Central Tendency and Spread for a Spectra...

Files in this package

ChemoSpec
ChemoSpec/inst
ChemoSpec/inst/CITATION
ChemoSpec/inst/extdata
ChemoSpec/inst/extdata/pS_brushNguides.js
ChemoSpec/inst/extdata/plotSpectraJS.html
ChemoSpec/inst/extdata/pS.css
ChemoSpec/inst/extdata/pS_main.js
ChemoSpec/inst/extdata/pS_spectra.js
ChemoSpec/inst/extdata/pS_globals.js
ChemoSpec/inst/extdata/pS_controls.js
ChemoSpec/inst/doc
ChemoSpec/inst/doc/ChemoSpec.R
ChemoSpec/inst/doc/ChemoSpec.Rnw
ChemoSpec/inst/doc/ChemoSpec.pdf
ChemoSpec/NAMESPACE
ChemoSpec/NEWS
ChemoSpec/data
ChemoSpec/data/SrE.IR.RData
ChemoSpec/data/alignMUD.RData
ChemoSpec/data/datalist
ChemoSpec/data/SrE.NMR.RData
ChemoSpec/data/metMUD2.RData
ChemoSpec/data/metMUD1.RData
ChemoSpec/R
ChemoSpec/R/sumGroups.R
ChemoSpec/R/surveySpectra.R
ChemoSpec/R/removeFreq.R
ChemoSpec/R/readJEOLascii.R
ChemoSpec/R/conColScheme.R
ChemoSpec/R/LoopThruSpectra.R
ChemoSpec/R/hcaSpectra.R
ChemoSpec/R/removeSample.R
ChemoSpec/R/aov_pcaSpectra.R
ChemoSpec/R/matrix2SpectraObject.R
ChemoSpec/R/chkSpectra.R
ChemoSpec/R/isWholeNo.R
ChemoSpec/R/mclustSpectra.R
ChemoSpec/R/cv_pcaSpectra.R
ChemoSpec/R/pcaDiag.R
ChemoSpec/R/plotScores3D.R
ChemoSpec/R/baselineSpectra.R
ChemoSpec/R/plotScree2.R
ChemoSpec/R/labelExtremes.R
ChemoSpec/R/seXy.R
ChemoSpec/R/hypTestScores.R
ChemoSpec/R/files2SpectraObject.R
ChemoSpec/R/plotScoresDecoration.R
ChemoSpec/R/seXyIqr.R
ChemoSpec/R/aovPCAscores.R
ChemoSpec/R/sPlotSpectra.R
ChemoSpec/R/seXyMad.R
ChemoSpec/R/mclust3D.R
ChemoSpec/R/hmapSpectra.R
ChemoSpec/R/groupNcolor.R
ChemoSpec/R/seX.R
ChemoSpec/R/colLeaf.R
ChemoSpec/R/r_pcaSpectra.R
ChemoSpec/R/plotScoresCor.R
ChemoSpec/R/plot2Loadings.R
ChemoSpec/R/hcaScores.R
ChemoSpec/R/r2qPCA.R
ChemoSpec/R/plotScores.R
ChemoSpec/R/seXy95.R
ChemoSpec/R/mclust3dSpectra.R
ChemoSpec/R/evalClusters.R
ChemoSpec/R/binData.R
ChemoSpec/R/plotScree.R
ChemoSpec/R/removeGroup.R
ChemoSpec/R/coordProjCS.R
ChemoSpec/R/plotSpectra.R
ChemoSpec/R/c_pcaSpectra.R
ChemoSpec/R/aovPCAloadings.R
ChemoSpec/R/splitSpectraGroups.R
ChemoSpec/R/sumSpectra.R
ChemoSpec/R/makeEllipsoid.R
ChemoSpec/R/shrinkLeaf.R
ChemoSpec/R/surveySpectra2.R
ChemoSpec/R/avgFacLvls.R
ChemoSpec/R/plotLoadings.R
ChemoSpec/R/plotScoresRGL.R
ChemoSpec/R/q2rPCA.R
ChemoSpec/R/normSpectra.R
ChemoSpec/R/binSpectra.R
ChemoSpec/R/plotSpectraJS.R
ChemoSpec/R/readJDX.R
ChemoSpec/R/clupaSpectra.R
ChemoSpec/R/check4Gaps.R
ChemoSpec/R/plotSpectraDist.R
ChemoSpec/R/sgfSpectra.R
ChemoSpec/R/normVec.R
ChemoSpec/R/rowDist.R
ChemoSpec/R/plotHCA.R
ChemoSpec/R/sampleDistSpectra.R
ChemoSpec/R/labelExtremes3d.R
ChemoSpec/vignettes
ChemoSpec/vignettes/ChemoSpec.Rnw
ChemoSpec/vignettes/aovPCA2.pdf
ChemoSpec/vignettes/aovPCA1.pdf
ChemoSpec/vignettes/MetabPreProcess.pdf
ChemoSpec/vignettes/chemometrics.bib
ChemoSpec/MD5
ChemoSpec/build
ChemoSpec/build/vignette.rds
ChemoSpec/DESCRIPTION
ChemoSpec/man
ChemoSpec/man/MUD.Rd
ChemoSpec/man/sumGroups.Rd
ChemoSpec/man/avgFacLvls.Rd
ChemoSpec/man/rowDist.Rd
ChemoSpec/man/cv_pcaSpectra.Rd
ChemoSpec/man/conColScheme.Rd
ChemoSpec/man/colorSymbol.Rd
ChemoSpec/man/seXy.Rd
ChemoSpec/man/removeFreq.Rd
ChemoSpec/man/q2rPCA.Rd
ChemoSpec/man/hmapSpectra.Rd
ChemoSpec/man/plotSpectraDist.Rd
ChemoSpec/man/binData.Rd
ChemoSpec/man/plotLoadings.Rd
ChemoSpec/man/labelExtremes3d.Rd
ChemoSpec/man/readJDX.Rd
ChemoSpec/man/matrix2SpectraObject.Rd
ChemoSpec/man/sPlotSpectra.Rd
ChemoSpec/man/aovPCAscores.Rd
ChemoSpec/man/mclustSpectra.Rd
ChemoSpec/man/plotSpectraJS.Rd
ChemoSpec/man/chkSpectra.Rd
ChemoSpec/man/check4Gaps.Rd
ChemoSpec/man/clupaSpectra.Rd
ChemoSpec/man/sampleDistSpectra.Rd
ChemoSpec/man/removeSample.Rd
ChemoSpec/man/makeEllipsoid.Rd
ChemoSpec/man/plot2Loadings.Rd
ChemoSpec/man/plotScoresDecoration.Rd
ChemoSpec/man/evalClusters.Rd
ChemoSpec/man/sgfSpectra.Rd
ChemoSpec/man/aov_pcaSpectra.Rd
ChemoSpec/man/mclust3dSpectra.Rd
ChemoSpec/man/LoopThruSpectra.Rd
ChemoSpec/man/surveySpectra.Rd
ChemoSpec/man/sumSpectra.Rd
ChemoSpec/man/aovPCAloadings.Rd
ChemoSpec/man/plotScoresCor.Rd
ChemoSpec/man/SrE.IR.Rd
ChemoSpec/man/plotScores3D.Rd
ChemoSpec/man/colLeaf.Rd
ChemoSpec/man/plotHCA.Rd
ChemoSpec/man/binSpectra.Rd
ChemoSpec/man/baselineSpectra.Rd
ChemoSpec/man/hcaSpectra.Rd
ChemoSpec/man/normSpectra.Rd
ChemoSpec/man/Spectra.Rd
ChemoSpec/man/hcaScores.Rd
ChemoSpec/man/mclust3D.Rd
ChemoSpec/man/files2SpectraObject.Rd
ChemoSpec/man/ChemoSpec-package.Rd
ChemoSpec/man/groupNcolor.Rd
ChemoSpec/man/isWholeNo.Rd
ChemoSpec/man/c_pcaSpectra.Rd
ChemoSpec/man/pcaDiag.Rd
ChemoSpec/man/plotSpectra.Rd
ChemoSpec/man/coordProjCS.Rd
ChemoSpec/man/normVec.Rd
ChemoSpec/man/labelExtremes.Rd
ChemoSpec/man/plotScoresRGL.Rd
ChemoSpec/man/hypTestScores.Rd
ChemoSpec/man/splitSpectraGroups.Rd
ChemoSpec/man/plotScores.Rd
ChemoSpec/man/plotScree.Rd
ChemoSpec/man/r_pcaSpectra.Rd
ChemoSpec/man/shrinkLeaf.Rd