Options for package hyperSpec
Functions to access and set hyperSpec's options.
aggregate hyperSpec objects
Barbiturates Spectra from .spc example files
A time series of mass spectra in a list of hyperSpec objects.
dimnames,hyperSpec-method
Dimnames for hyperSpec objects
Arithmetical Operators for hyperSpec objects
qplotmap with colour mixing for multivariate overlay
Calibration- and Timeseries Plots, Depth-Profiles and the like
plotc
plots intensities of a hyperSpec
object over another
dimension such as concentration, time, or a spatial coordinate.
Bind matrices by row, and fill missing columns with NA
Class "hyperSpec"
makeraster
Laser Emission
A time series of an unstable laser emission.
Collapse hyperSpec objects
command line completion for $
cov,hyperSpec,missing-method
Covariance matrices for hyperSpec objects
merge,hyperSpec,hyperSpec-method
Merge hyperSpec objects
Plotting hyperSpec Objects
Mark groups in hclust
dendrograms Comparison of hyperSpec objects
Convert Principal Component Decomposition or the like into a hyperSpec Object
Binding hyperSpec Objects
Two S3 functions cbind.hyperSpec
and rbind.hyperSpec
act as
an interfaces to cbind2
and rbind2
because neither
rBind
and cBind
nor S4 versions
of cbind
and rbind
do work at the moment. Interactively select a polygon (grid graphics) and highlight points
apply
Computes summary statistics for the spectra of a hyperSpec
object.
Polynomial Baseline Fitting
These functions fit polynomal baselines.
Get and Set Labels of a hyperSpec Object
value
may be a list or vector of labels giving the new label for
each of the entries specified by which
.
Quinine Fluorescence Spectra
Fluorescence spectra of different dilutions of quinine forming a
calibration set.
Extract and Replace parts of hyperSpec objects
Spectra plotting with ggplot2
Plotting Spectra
Plot the spectra of a hyperSpec
object, i.e. intensity over
wavelength. Instead of the intensity values of the spectra matrix summary
values calculated from these may be used.
colSums, colMeans, rowSums and rowMeans functions for hyperSpec objects
The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an
hyperSpec Object)
Rubberband baseline correction
Read INI files
Creating a hyperSpec Object
Like other S4 objects, a hyperSpec object can be created by new
. The
hyperSpec object is then initialize
d using the given parameters.
levelplot,hyperSpec,missing-method
Plot a Map and Identify/Select Spectra in the Map
levelplot
functions for hyperSpec objects. An image or map of a summary
value of each spectrum is plotted. Spectra may be identified by mouse click. Math Functions for hyperSpec Objects
Sweep Summary Statistic out of an hyperSpec Object
sweep
for hyperSpec
objects. Matlab-like Palettes
Two palettes going from blue over green to red, approximately as the
standard palette of Matlab does. The second one has darker green values and
is better suited for plotting lines on white background.
Paracetamol Spectrum
A Raman spectrum of a paracetamol tablet.
The functions
Import Horiba Labspec exported ASCII files
Quick data frame.
Experimental version of as.data.frame
that converts a
list to a data frame, but doesn't do any checks to make sure it's a
valid format. Much faster. Evaluate function on wavelengths of hyperSpec object
Spectra plotting with ggplot2
File Import Witec Raman
JCAMP-DX Import for Shimadzu Library Spectra
hyperSpec unit tests
If svUnit
is available, run the unit tests and
display the results. Center and scale hyperSpec object
Import for Thermo Galactic's spc file format
These functions allow to import Thermo Galactic/Grams .spc files.
as.character,hyperSpec-method
Convert a hyerSpec object to character strings for Display
print
, show
, and summary
show the result of
as.character
.
Plot spectra matrix
Import for Cytospec mat files
Wavelength Binning
In order to reduce the spectral resolution and thus gain signal to noise
ratio or to reduce the dimensionality of the spectral data set, the
spectral resolution can be reduced.
Identifying Spectra and Spectral Data Points
This function allows to identify the spectrum and the wavelength of a point
in a plot produced by plotspc
. Color coding legend for factors
Modifies a list of lattice arguments (as for levelplot
, etc.) according to
the factor levels. The colorkey will shows all levels (including unused), and the drawing colors
will be set accordingly. Conversion between Wavelength and Spectra Matrix Column
Index wl2i
returns the column indices for the spectra matrix for the given wavelengths.
i2wl
converts column indices into wavelengths.
wc
word count of ASCII files
read Kaiser .spc files
Reads Shimadzu GCxGC-qMS - Spectra Files (.txt) as exported by Shimadzu Chrome Solution (v. 2.72)
Mass Spectrometer: Shimadzu GCMS-QP 2010 Ultra (www.shimadzu.com)
Random Samples and Permutations
Take a sample of the specified size from the elements of x with or without
replacement.
loess smoothing interpolation for spectra
Spectra can be smoothed and interpolated on a new wavelength axis using
loess
. import Raman measurements from Renishaw ASCII-files
import Raman measurements from Renishaw (possibly compressed) .txt file.
Import and Export of hyperSpec objects
Besides save
and load
, two general
ways to import and export data into hyperSpec
objects exist. subset
Multivariate normal random numbers
Spectra plotting with ggplot2
Split a hyperSpec object according to groups
split
divides the hyperSpec
object into a list of
hyperSpec
objects according to the groups given by f
.
Getting and Setting the Wavelength Axis
wl
returns the wavelength axis, wl<-
sets it.
Conversion of a hyperSpec object into a data.frame or matrix
as.data.frame
returns x@data
(as data.frame) as.matrix
returns the spectra matrix x@data$spc
as matrix
Validation of hyperSpec objects
Raman spectra of 2 Chondrocytes in Cartilage
A Raman-map (laterally resolved Raman spectra) of chondrocytes in
cartilage.
Mean and Standard Deviation
Calculate mean and standard deviation, and mean, mean $+-$ one
standard deviation, respectively.
Package hyperSpec
Sorting the Wavelengths of a hyperSpec Object
Rearranges the hyperSpec
object so that the wavelength vector is in increasing (or
decreasing) order.
Nicolet uses some more keywords in their header file.
They are interpreted as follows:
description
giving the position of the first spectrum
z plot titles
wavelength and intensity axis units, comma separated
These parameters can be overwritten by giving a list with the respective
elements in parameter header
. Sequence generation along spectra or wavelengths
This function generates sequences along the spectra (rows) or wavelengths of hyperSpec objects.
Function evaluation on hyperSpec objects
Impute missing data points
normalization for mixed colors
Empty hyperSpec object
Plot multivariate data into colour channels
Distance based on Pearson's $R squared$
Spectral smoothing by splines