Data analysis for phenolics in R

Introduction

The purpose of this document is to illustrate the functions for data analysis that can be applied to our data sets.
The main steps have been summarized in convenient functions, in order to keep the analysis quick and clean.
Functions are provided to load and print chromatogram traces, and to load and visualize peak areas quantitated from
chromatograms. All the input is done through simple CSV files.

Chromatograms

Chromatograms must be exported from Chemstation through the command “Export 3-D data” in the “tools” menu.
After loading it with the read.csv() function, the result is a data frame in which the first column contains
the scan number and the following columns the intensities for each ion. The chromatogram in this way is not ready
for use yet, and we want to convert the scan number to the time elapsed. To do so, we have the ChromFix()
function. It accepts as input the data.frame of the chromatogram and the time of the first and last scan. It
automatically calculates TIC, and rescales it to an arbitrary factor in order to achieve a better visualization.
As an example we'll use a full scan chromatogram from a chicory sample.

threeD <- read.csv("3D.csv")
chrom.fixed <- ChromFix(threeD)
print(chrom.fixed[1:10, c(1:4, ncol(chrom.fixed))])

##     time  X50  X51  X52    TIC
## 1  6.009 1186 1685 2600  625.0
## 2  6.017 1376 2107 2447  728.0
## 3  6.026 1541 1678 2557  953.8
## 4  6.034 1353 2313 2653 1489.1
## 5  6.043 1639 2968 3338 2304.7
## 6  6.051 1518 3873 3336 3470.8
## 7  6.060 1571 4356 3779 4514.4
## 8  6.068 1738 4660 3206 5107.5
## 9  6.077 1915 3855 3303 4580.8
## 10 6.085 1458 2884 2857 3074.6

After fixing the chromatogram, we want to melt it in long format to be able to graph it with ggplot2. The
function \emph{ChromMelt()} does this and also removes the annoying X's in front of the ion m/z.

chrom.melted <- ChromMelt(chrom.fixed)
head(chrom.melted)

##    time ion value
## 1 6.009  50  1186
## 2 6.017  50  1376
## 3 6.026  50  1541
## 4 6.034  50  1353
## 5 6.043  50  1639
## 6 6.051  50  1518

Finally we can plot the chromatogram with the ChromPlot function. By default it plots TIC in black.
However it is very easy to extract individual ion chromatograms, change colors and zoom.

ions: accepts a vector of ions to be plotted (either 'TIC' or a number between quotes)
ions.color: specifies which color should the ions track have (a valid R color, between quotes). These parameters must be in the same order, that is the first color will be assigned to the first ion in the list. Also the correct numbr of colors (the same as ions) must be specified, or the the function will return an error.
ions.rescale: rescales each individual ion track to a common scale where 0 is minimum and 1 is maximum. The rescaling is calculated before any other subsequent eleboration
ions.zoom : a vector of the same lenght as the number of ions, specifying a factor by which each ion track should be multiplied on the abundance axis
ions.offset : a a vector of the same lenght as the number of ions, specifying a factor by which each ion track should be offset on the abundance axis
x.zoom : a vector of two specifying the start and end time of plotting
y.zoom : the zoom on vertical axis (abundance)

ChromPlot(chrom.fixed)