% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/chondro.R
\docType{data}
\name{chondro}
\alias{chondro}
\title{Raman spectra of 2 Chondrocytes in Cartilage
A Raman-map (laterally resolved Raman spectra) of chondrocytes in
cartilage.}
\format{The data set has 875 Raman spectra measured on a 25 \eqn{\times}{x}
  35 grid with 1 micron step size. Spatial information is in
  \code{chondro$x} and \code{chondro$y}. Each spectrum has 300 data points
  in the range of ca. 600 - 1800 cm\eqn{^{-1}}{^-1}.}
\description{
See the vignette \code{vignette ("chondro", package = "hyperSpec")}.
}
\examples{


chondro

## do baseline correction
baselines <- spc.fit.poly.below (chondro)
chondro <- chondro - baselines

## area normalization
chondro <- chondro / colMeans (chondro)

## substact common composition
chondro <- chondro - quantile (chondro, 0.05)

cols <- c ("dark blue", "orange", "#C02020")
plotmap (chondro, clusters ~ x * y, col.regions = cols)

cluster.means <- aggregate (chondro, chondro$clusters, mean_pm_sd)
plot (cluster.means, stacked = ".aggregate", fill = ".aggregate", col = cols)

## plot nucleic acid bands
plotmap (chondro[, , c( 728, 782, 1098, 1240, 1482, 1577)],
       col.regions = colorRampPalette (c ("white", "gold", "dark green"), space = "Lab") (20))

}
\references{
The raw data is available at \url{http://hyperspec.r-forge.r-project.org/blob/chondro.zip}
}
\author{
A. Bonifacio and C. Beleites
}
\keyword{datasets}
