waterabs: Light absorption by the water column

In seqinr: Biological Sequences Retrieval and Analysis

Light absorption by the water column

Description

The absorption of light by water is highly dependent on the wavelength, this dataset gives the absorption coefficients from 200 to 700 nm.

Usage

data(waterabs)

Format

A data.frame with 2 columns:

lambda

wavelength in nm

abs

absorption coefficient in 1/cm

Source

Data were compiled by Palmeira (2007) from the cited references.

The example section allows to reproduce the left part of figure 2.7 from Palmeira (2007):

References

Palmeira, L. (2007) Analyse et modélisation des dépendances entre sites voisins dans l'évolution des séquences d'ADN, PhD thesis, Université Claude Bernard - Lyon I.

Litjens R. A., Quickenden T. I. and Freeman C. G. (1999). Visible and near-ultraviolet absorption spectrum of liquid water. Applied Optics, 38:1216-1223.

Quickenden T. I. & Irvin J. A. (1980). The ultraviolet absorption spectrum of liquid water. The Journal of Chemical Physics, 72:4416-4428.

citation("seqinr")

Examples

data(waterabs)

d <- 100*seq(from = 0, to = 150, by = 1) # depth in cm
lambda <- waterabs$lambda                # wavelength in nm
abs <- waterabs$absorption               # absorption coefficient cm-1
#
# Smooth signal with cubic splines
#
  tmp <- spline(lambda, abs, n = 255)
  lambda <- tmp$x
  abs <- tmp$y

  zun <- sapply(abs,function(x) 10^(-x*d))
  z <- sapply(nrow(zun):1, function(x) zun[x,])
#
# Set up world coordinates:
#
  plot.new()
  plot.window(xlim = range(lambda), ylim = range(d), xaxs = "i",  yaxs = "i")
#
# Annotate:
#
  title(ylab = 'Depth under water surface (m)', xlab = "Wavelength (nm)",
  main = "Light absorption by the water column")
  axis(2 , at = seq(0, 15000, l = 7),
      labels = rev(c("0","25","50","75","100","125","150")), las = 1)
  axis(1,at=(3:6)*100,labels= TRUE)
#
# Show me rainbow colors:
#
  alpha <- 1
  coul=c(rep(rgb(1,1,1, alpha = alpha), 181),
    rev(hsv(h=seq(0,5/6,l=320),alpha = alpha)))
  rect(seq(200,699), 0, seq(201,700), 15000 , col = coul, border = coul)
#
# Grey scale:
#
  ngris <- 5
  image(x = lambda, y = d, z = z, col = rgb(1:ngris, 1:ngris, 1:ngris, alpha = 0.7*(ngris:1),
  max = ngris),
  axes = F, add = TRUE,
  breaks = seq(from = min(z), to = max(z), length = ngris + 1))

#
# Contour lines:
#
  contour(x = lambda, y = d, z = z, add = TRUE, drawlabels = TRUE,labcex= 0.75,
  col='black',
  levels = seq(from = min(z), to = max(z), length = ngris + 1))
  box()

seqinr documentation built on March 31, 2023, 3:05 p.m.