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ChemoSpec (version 4.0.1)

Exploratory Chemometrics for Spectroscopy

Description

A collection of functions for plotting spectra (NMR, IR, Raman) and carrying out various forms of top-down exploratory data analysis, such as HCA, PCA, model-based clustering and 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 illustrating typical operations is available.

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Version

Install

install.packages('ChemoSpec')

Monthly Downloads

957

Version

4.0.1

License

GPL-3

Issues

2

Pull Requests

0

Stars

63

Forks

20

Maintainer

Bryan Hanson

Last Published

March 16th, 2015

Functions in ChemoSpec (4.0.1)

labelExtremes3d

Identify Extreme Values in 3D
groupNcolor

Assign Group Membership and Colors for a Spectra Object
pcaDiag

Outlier Diagnostic Plots for PCA of a Spectra Object
coordProjCS

Modified Version of coordProj from mclust
c_pcaSpectra

Classical PCA of Spectra Objects
seXy

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

Order Rows of a Covariance Matrix by Absolute Value
sumSpectra

Summarize a Spectra Object
normVec

Normalize a Vector to range -1 to +1
binSpectra

Bin or Bucket a Spectra Object
plotScores3D

3D PCA Score Plot for a Spectra Object
r_pcaSpectra

Robust PCA of a Spectra Object
mclust3D

mclust Analysis in 3D
colLeaf

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

Determine if a Number is a Whole Number
sumGroups

Summarize the Group Parameters of a Spectra Object
plotScoresRGL

Interactive 3D Score Plot of a Spectra Object
removeSample

Remove Samples or Groups from a Spectra Object
removeFreq

Remove Frequencies from a Spectra Object
plotHCA

Plot Dendrogram for Spectra Object
plotLoadings

Plot PCA Loadings for a Spectra Object
aovPCAscores

Plot ANOVA-PCA Scores from a Spectra Object
clupaSpectra

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

Verify the Integrity of a Spectra Object
aov_pcaSpectra

ANOVA-PCA Analysis of Spectra Data
chooseLvls

Select Levels for Contour and Image Type Plots
plotScree

Scree Plots of PCA Results for a Spectra Object
cv_pcaSpectra

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

Create Ellipsoid
metMUD1

Made Up NMR Data Sets
plotSpectraJS

Plot a Spectra Object Interactively
plotScoresDecoration

Decorate PCA Score Plot of a Spectra Object
baselineSpectra

Baseline Correction of a Spectra Object
q2rPCA

Conversion Between PCA Classes
plot2Loadings

Plot PCA Loadings from a Spectra Object Against Each Other
splitSpectraGroups

Create New Groups from an Existing Spectra Object
plotScoresCor

Compute Confidence Ellipses
Spectra

Spectra Objects
hcaScores

HCA on PCA scores from a Spectra Object
loopThruSpectra

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

Plot HCA Results of a Spectra Object
binData

Bin or Bucket Data
mclustSpectra

mclust Analysis of a Spectra Object PCA Results
rowDist

Compute Distance Between Rows of a Matrix
avgFacLvls

Average Levels of a Factor in a Data Matrix
check4Gaps

Check for Missing Values (Gaps)
plotSpectra

Plot Spectra Object
readJDX

Read and process a JCAMP-DX file.
ChemoSpec-package

Exploratory Chemometrics for Spectroscopy
sPlotSpectra

s-Plot of Spectra Data Post PCA
mclust3dSpectra

mclust Analysis of a Spectra Object in 3D
colorSymbol

Colors and Symbols in ChemoSpec and Spectra Objects
conColScheme

Change the Color Scheme of a Spectra Object
hypTestScores

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

Label Extreme Values in a 2D Data Set
plotScores

Plot PCA Scores of a Spectra Object
shrinkLeaf

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

Plot aovPCAscores Loadings of a Spectra Object
evalClusters

Evaluate or Compare the Quality of Clusters Quantitatively
sampleDistSpectra

Compute the Distance Between Samples in a Spectra Object
SrE.IR

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

Tools for STOCSY Analysis of a Spectra Object
hmapSpectra

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

Normalize a Spectra Object
surveySpectra

Plot Measures of Central Tendency and Spread for a Spectra Object
files2SpectraObject

Merge Files in a Directory into a Spectra Object