InSpectoR: InSpectoR

In PannetonB/inspectrar: GWidgets2/RGtk2 GUI for viewing and modeling spectroscopy data

InSpectoR

Description

InSpectoR is a tool for exploring spectroscopic data sets and to develop models. It was developped as a companion to a custom spectrometric data acquisition system for gathering induced fluorescence with up to 6 excitation wavelengths, Raman spectra excited at ~785 nm and transmittance data or reflectance data. It is general enough to accomodate any spectroscopic data sets provided that the format of the required files conformed to the description below. The program is structured around a top level window with tabs giving access to other interfaces dedicated to specialized tasks such as selecting and viewing raw data, performing data normalization, doing some pretreament on the data, performing principal component analysis, developping PLS models... These are referred to as "task interfaces".

Usage

InSpectoR(yfile = NULL, parcomp = TRUE, MainWidth = 1200, MainHeight = 800)

Arguments

yfile	to load data associated with this Y data file. Default is NULL: no data loaded on startup.
parcomp	to set up for parallel computation with caret package (default to TRUE)
MainWidth	width of GUI in pixels (default to 1200)
MainHeight	height of GUI in pixels (default to 800)

Details

The data sets are made of a number of files defined as follows:

• Y_somename.txt : Y data file.

  • This is a tab delimited text file with a header line and decimal symbol is ".".

  • After header, each following lines correspond to samples.

  • Columns contain user defined data such as a sample identification number, some data or factor associated with the sample (e.g. color, pH, concentration of something...).

  • The filename MUST start with "Y_". It is followed by "somename" which is a user defined name (anything will do) and followed by the ".txt" extension.

  • The GUI offers access to a support function that can merge Y data in an other file. This is useful when spectral data and accompanying data are acquired in separate processes that might result in data stored in different files. The only requirement for successfull merging is that both files share a common column.

• *_somename*.txt : Spectral data files. Tab delimiter, header and decimal=".".

  • These are files containing spectroscopic data.

  • The first line contains wavelengths or wavenumbers associated with the spectra.

  • The first column is a sample ID (same as first column of associated Y file).

  • One sample per line.

  • The first cell [1,1] is not used (could be empty).

  • Name: The first star to the left is a placeholder for describing the data. For example, EX350 could be used to indicate fluorescence spectra obtained under excitation at 350 nm. These data type are used throughout the program as labels for options, buttons... Should not start with a number or special character. It is up to the user to define and recognize the names. The * before the extension could be anything. The key is that "somename" matches the "somename" of the associated Y_somename.txt file. This is how Y data are connected to spectral data.

It is mandatory to group Ys and spectral data files in the same directory. There could be as many spectral data files as the user wants.

Value

NOTHING

Examples

dfile <- system.file("foodstuff_powder","Y_foodstuff.txt",package="inspectrar")
InSpectoR(dfile,0,1600,1024)

PannetonB/inspectrar documentation built on Feb. 4, 2023, 1:57 p.m.