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

In hyperSpec: 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))

Example output

Loading required package: lattice
Loading required package: grid
Loading required package: ggplot2
Package hyperSpec, version 0.99-20180627

To get started, try
   vignette ("hyperspec")
   package?hyperSpec 
   vignette (package = "hyperSpec")

If you use this package please cite it appropriately.
   citation("hyperSpec")
will give you the correct reference.

The project homepage is http://hyperspec.r-forge.r-project.org


hyperSpec object
   875 spectra
   5 data columns
   300 data points / spectrum
wavelength: Delta * tilde(nu)/cm^-1 [numeric] 602 606 ... 1798 
data:  (875 rows x 5 columns)
   1. y: y [numeric] -4.77 -4.77 ... 19.23 
   2. x: x [numeric] -11.55 -10.55 ... 22.45 
   3. filename: filename [character] rawdata/chondro.txt rawdata/chondro.txt ... rawdata/chondro.txt 
   4. clusters: clusters [factor] matrix matrix ... lacuna + NA
   5. spc: I / a.u. [matrix300] 501.8194 500.4552 ... 169.2942 

hyperSpec documentation built on May 2, 2019, 5:45 p.m.