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ChemoSpec (version 4.0.6)

Exploratory Chemometrics for Spectroscopy

Description

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), model-based clustering and statistical total correlation spectroscopy (STOCSY) analysis. 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.

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Version

Install

install.packages('ChemoSpec')

Monthly Downloads

957

Version

4.0.6

License

GPL-3

Issues

2

Pull Requests

0

Stars

63

Forks

20

Maintainer

Bryan Hanson

Last Published

June 19th, 2015

Functions in ChemoSpec (4.0.6)

pcaDiag

Outlier Diagnostic Plots for PCA of a Spectra Object
removeFreq

Remove Frequencies from a Spectra Object
colLeaf

Color the Leaves of a Dendrogram Based on a Spectra Object
mclustSpectra

mclust Analysis of a Spectra Object PCA Results
colorSymbol

Colors and Symbols in ChemoSpec and Spectra Objects
q2rPCA

Conversion Between PCA Classes
clupaSpectra

Conduct Hierarchical Cluster-Based Peak Alignment on a Spectra Object
plotScoresCor

Compute Confidence Ellipses
loopThruSpectra

Display the Spectra in a Spectra Object One at a Time
mclust3D

mclust Analysis in 3D
hypTestScores

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

Average Levels of a Factor in a Data Matrix
plotSpectraJS

Plot a Spectra Object Interactively
plot2Loadings

Plot PCA Loadings from a Spectra Object Against Each Other
r_pcaSpectra

Robust PCA of a Spectra Object
aovPCAloadings

Plot aovPCAscores Loadings of a Spectra Object
sumSpectra

Summarize a Spectra Object
Spectra

Spectra Objects
coordProjCS

Modified Version of coordProj from mclust
isWholeNo

Determine if a Number is a Whole Number
labelExtremes

Label Extreme Values in a 2D Data Set
check4Gaps

Check for Missing Values (Gaps)
conColScheme

Change the Color Scheme of a Spectra Object
hcaScores

HCA on PCA scores from a Spectra Object
normSpectra

Normalize a Spectra Object
normVec

Normalize a Vector to range -1 to +1
ChemoSpec-package

Exploratory Chemometrics for Spectroscopy
metMUD1

Made Up NMR Data Sets
hmapSpectra

Create a Seriated Heat Map Comparing Samples and Spectral Data for a Spectra Object
plotHCA

Plot Dendrogram for Spectra Object
sPlotSpectra

s-Plot of Spectra Data Post PCA
baselineSpectra

Baseline Correction of a Spectra Object
aov_pcaSpectra

ANOVA-PCA Analysis of Spectra Data
corSpectra

Tools for STOCSY Analysis of a Spectra Object
plotScores

Plot PCA Scores of a Spectra Object
removeSample

Remove Samples or Groups from a Spectra Object
plotScoresRGL

Interactive 3D Score Plot of a Spectra Object
SrE.IR

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

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

Bin or Bucket a Spectra Object
groupNcolor

Assign Group Membership and Colors for a Spectra Object
shrinkLeaf

Shrink the Leaves of a Dendrogram Based on a Spectra Object
chkSpectra

Verify the Integrity of a Spectra Object
evalClusters

Evaluate or Compare the Quality of Clusters Quantitatively
splitSpectraGroups

Create New Groups from an Existing Spectra Object
binData

Bin or Bucket Data
c_pcaSpectra

Classical PCA of Spectra Objects
makeEllipsoid

Create Ellipsoid
mclust3dSpectra

mclust Analysis of a Spectra Object in 3D
plotScoresDecoration

Decorate PCA Score Plot of a Spectra Object
rowDist

Compute Distance Between Rows of a Matrix
sumGroups

Summarize the Group Parameters of a Spectra Object
getMaxCovByFreq

Order Rows of a Covariance Matrix by Absolute Value
plotLoadings

Plot PCA Loadings for a Spectra Object
files2SpectraObject

Merge Files in a Directory into a Spectra Object
plotSpectra

Plot Spectra Object
readJDX

Read and process a JCAMP-DX file.
sampleDistSpectra

Compute the Distance Between Samples in a Spectra Object
plotScree

Scree Plots of PCA Results for a Spectra Object
chooseLvls

Select Levels for Contour and Image Type Plots
aovPCAscores

Plot ANOVA-PCA Scores from a Spectra Object
hcaSpectra

Plot HCA Results of a Spectra Object
labelExtremes3d

Identify Extreme Values in 3D
plotScores3D

3D PCA Score Plot for a Spectra Object
surveySpectra

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

Functions to Compute Measures of Central Tendency and Spread. seX!