chondro: Raman spectra of 2 Chondrocytes in Cartilage A Raman-map...

In GegznaV/hyperSpec2: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

Description

See the vignette vignette ("chondro", package = "hyperSpec").

Format

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.

Author(s)

A. Bonifacio and C. Beleites

References

The raw data is available at http://hyperspec.r-forge.r-project.org/blob/chondro.zip

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))

GegznaV/hyperSpec2 documentation built on Dec. 27, 2019, 9:43 a.m.