as.hyperSpec: convenience conversion functions
Barbiturates Spectra from .spc example files
A time series of mass spectra in a list of hyperSpec objects.
droplevels,hyperSpec-method
droplevels for hyperSpec object
Raman spectra of 2 Chondrocytes in Cartilage
A Raman-map (laterally resolved Raman spectra) of chondrocytes in
cartilage.
Polynomial Baseline Fitting
These functions fit polynomal baselines.
Empty hyperSpec object
guess wavelengths from character vector
command line completion for $
colSums, colMeans, rowSums and rowMeans functions for hyperSpec objects
Comparison of hyperSpec objects
Interactively select a polygon (grid graphics) and highlight points
Package hyperSpec
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.
Arithmetical Operators for hyperSpec objects
Collapse hyperSpec objects
Sorting the Wavelengths of a hyperSpec Object
Rearranges the hyperSpec
object so that the wavelength vector is in increasing (or
decreasing) order.
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.
Mark groups in hclust
dendrograms Paracetamol Spectrum
A Raman spectrum of a paracetamol tablet.
Class "hyperSpec"
This class handles hyperspectral data sets, i.e. spatially or time-resolved
spectra, or spectra with any other kind of information associated with the
spectra.
Spectra plotting with ggplot2
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. 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. Binding hyperSpec Objects
Import WinSpec SPE file
Read XML footer from SPE file format version 3.0
Import Horiba Labspec exported ASCII files
Plot spectra matrix
Read INI files
Bind matrices by row, and fill missing columns with NA
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
cov,hyperSpec,missing-method
Covariance matrices for hyperSpec objects
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
. 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.
Validation of hyperSpec objects
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.
Convert Principal Component Decomposition or the like into a hyperSpec
Object
Rubberband baseline correction
Distance based on Pearson's \(R^2\)
Convert different wavelength units
Spectral smoothing by splines
Quinine Fluorescence Spectra
Fluorescence spectra of different dilutions of quinine forming a
calibration set.
Mark peak
Marks location of the first spectrum at the data point closes to the
specified position on the current plot.
The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an
hyperSpec Object)
normalization for mixed colors
Extract and Replace parts of hyperSpec objects
Function evaluation on hyperSpec objects
Options for package hyperSpec
Functions to access and set hyperSpec's options.
makeraster
wc
word count of ASCII files
Mean and Standard Deviation
Calculate mean and standard deviation, and mean, mean \(\pm\) one
standard deviation, respectively.
Math Functions for hyperSpec Objects
merge,hyperSpec,hyperSpec-method
Merge hyperSpec objects
Spectra plotting with ggplot2
Plot multivariate data into colour channels
Spectra plotting with ggplot2
Import for Cytospec mat files
JCAMP-DX Import for Shimadzu Library Spectra
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)
Plotting hyperSpec Objects
File Import Witec Raman
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.
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.
Sweep Summary Statistic out of an hyperSpec Object
sweep
for hyperSpec
objects. as.character,hyperSpec-method
Convert a hyperSpec object to character strings for Display
print
, show
, and summary
show the result of
as.character
.
read Kaiser .spc files
Multivariate normal random numbers
qplotmap with colour mixing for multivariate overlay
Import for Thermo Galactic's spc file format
These functions allow to import Thermo Galactic/Grams .spc files.
Import of ENVI data as hyperSpec object
Import and Export of hyperSpec objects
Besides save
and load
, two general
ways to import and export data into hyperSpec
objects exist. Random Samples and Permutations
Take a sample of the specified size from the elements of x with or without
replacement.
File Import Andor Solis
Center and scale hyperSpec object
Sequence generation along spectra or wavelengths
This function generates sequences along the spectra (rows) or wavelengths of hyperSpec objects.
Impute missing data points
subset
Getting and Setting the Wavelength Axis
wl
returns the wavelength axis, wl<-
sets it.
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
.
The functions
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. Evaluate function on wavelengths of hyperSpec object
hyperSpec unit tests
aggregate hyperSpec objects
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
dimnames,hyperSpec-method
dimnames for hyperSpec objects
apply
Computes summary statistics for the spectra of a hyperSpec
object.
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
.
Laser Emission
A time series of an unstable laser emission.