drawEEM: Draw contour for EEM data

In EEM: Read and Preprocess Fluorescence Excitation-Emission Matrix (EEM) Data

Description

This function is a wrapper function for filled.contour to draw contour for EEM data.

Usage

drawEEM(x, ...)

## S3 method for class 'EEM'
drawEEM(x, n, exlab = "Excitation wavelength [nm]",
  emlab = "Emission wavelength [nm]", color.palette = matlab.like,
  nlevels = 50, main = NULL, flipaxis = FALSE, ...)

## S3 method for class 'EEMweight'
drawEEM(x, ncomp, exlab = "Excitation wavelength [nm]",
  emlab = "Emission wavelength [nm]", color.palette = matlab.like,
  nlevels = 50, main = NULL, flipaxis = FALSE, ...)

## S3 method for class 'matrix'
drawEEM(x, n, exlab = "Excitation wavelength [nm]",
  emlab = "Emission wavelength [nm]", color.palette = matlab.like,
  nlevels = 50, main = NULL, flipaxis = FALSE, ...)

## S3 method for class 'data.frame'
drawEEM(x, n, exlab = "Excitation wavelength [nm]",
  emlab = "Emission wavelength [nm]", color.palette = matlab.like,
  nlevels = 50, main = NULL, flipaxis = FALSE, ...)

## S3 method for class 'numeric'
drawEEM(x, exlab = "Excitation wavelength [nm]",
  emlab = "Emission wavelength [nm]", color.palette = matlab.like,
  nlevels = 50, main = NULL, flipaxis = FALSE, ...)

Arguments

x	a list of EEM data generated by readEEM function or EEMweight object generated by extract-related functions.
...	(optional) further arguments passed to other methods of filled.contour
n	sample number. The number should not exceed length(EEM)
exlab	(optional) excitation-axis label
emlab	(optional) emission-axis label
color.palette	(optional) contour color palette. See palette for more details
nlevels	(optional) number of levels used to separate range of intensity value
main	(optional) plot title
flipaxis	(optional) flip axis
ncomp	number of components

Value

A figure is returned on the graphic device

Methods (by class)

• EEM: draw contour of EEM data created by readEEM function

• EEMweight: draw contours of the output from getLoading and getReg.

• matrix: draw contour of unfolded matrix which have column names in the format of EX...EM...

• data.frame: draw contour of unfolded data.frame which have column names in the format of EX...EM...

• numeric: draw contour of a vector of numeric values which have names in the format of EX...EM...

See Also

drawEEM

Examples

# method for class "EEM"
data(applejuice)
drawEEM(applejuice, 1) # draw contour of the first sample
drawEEM(applejuice, 1, flipaxis = TRUE) # flip the axis

# method for class "EEMweight"
applejuice_uf <- unfold(applejuice) # unfold list into matrix
result <- prcomp(applejuice_uf) 
drawEEM(getLoading(result), 1) # plot loading of the first PC

EEM documentation built on May 2, 2019, 5:58 a.m.