Raman spectra of 2 Chondrocytes in Cartilage A Raman-map (laterally resolved Raman spectra) of chondrocytes in cartilage.
See the vignette vignette ("chondro", package = "hyperSpec").
chondro
The data set has 875 Raman spectra measured on a 25 x
35 grid with 1 micron step size. Spatial information is in
chondro$x and chondro$y. Each spectrum has 300 data points
in the range of ca. 600 - 1800 cm^-1.
A. Bonifacio and C. Beleites
The raw data is available at http://hyperspec.r-forge.r-project.org/blob/chondro.zip
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))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.