plot-Spectra: Plots an object inheriting from the Spectra class

In spectacles: Storing, Manipulating and Analysis Spectroscopy and Associated Data

Plots an object inheriting from the Spectra class

Description

The philosophy of this plotting routine is to provide a "quick'n'dirty" way to plot your spectra collection. For advanced visualisations, the use of melt_spectra alongside with ggplot2 or lattice is encouraged.

Usage

## S3 method for class 'Spectra'
plot(x,gg,gaps,attr,...)

## S3 method for class 'Spectra'
plot(x, gg = FALSE, gaps = TRUE, attr = NULL, ...)

Arguments

x	an object of class "Spectra" or inheriting from this class
gg	if TRUE, uses the ggplot2 package to plot the data, if FALSE uses matplot from base graphics (much faster)
gaps	if TRUE, gaps in the spectra are not plotted
attr	attribute against which lines are coloured (only for gg = TRUE
...	additional parameters passed to matplot

Author(s)

Pierre Roudier [e-mail]

Examples

# Loading example data
data(australia)
spectra(australia) <- sr_no ~ ... ~ 350:2500

# Default plotting method
plot(australia[1:5,])

# Default plot using ggplot2
plot(australia[1:5,], gg = TRUE)

## Not run: 

# Managing gaps in the spectra
s <- cut(australia, wl =c(-1*450:500, -1*1800:2050))
plot(s, gaps = TRUE)
plot(s, gaps = FALSE)

# passing various options to matplot
plot(
  australia, 
  lty = 1:5, 
  col = 'blue', 
  xlab = 'foo', ylab = 'bar', 
  ylim = c(0.4,0.6), 
  main = 'my plot'
)

# Using colour ramps
plot(
  australia, 
  lty = 1, 
  col = rainbow(10), 
  main = "It is possible to create really ugly visualisations"
)

# Example using colours given by ColorBrewer (http://colorbrewer2.org/)
library(RColorBrewer)
plot(australia, lty = 1, col = brewer.pal(n = 8, name = "Set2"))

# Using an attribute to group spectra

# Generate some kind of factor
australia$fact <- sample(
  LETTERS[1:3], 
  size = nrow(australia), 
  replace = TRUE
) 

s <- aggregate_spectra(australia, fun = mean, id = 'fact')
plot(s, gg = TRUE, attr = 'fact')

## End(Not run)

spectacles documentation built on July 10, 2023, 1:59 a.m.