DrawChromatogram: Plot a Chromatogram

In OrgMassSpecR: Organic Mass Spectrometry

Description

Plot a chromatogram, color the area under specified peak(s), and calculate the peak area(s).

Usage

DrawChromatogram(time, intensity, range = list(start, stop), color = "blue", 
                 xlab = "retention time", ylab = "intensity", 
                 ylim = c(0, max(intensity) * 1.1), las = 1, ...)

Arguments

time	numeric vector containing the time points (the x-axis).
intensity	numeric vector containing the respective signal intensities at each time point (the y-axis).
range	list describing the start and stop time points for each peak, defined as range = list(start, stop), where start is the numeric vector of starting time points and stop is the numeric vector of the respective ending time points.
color	vector of character strings specifying the color for each peak given in range. If a single color is specified, it is applied to all peaks.
xlab	character string specifying the x-axis label.
ylab	character string specifying the y-axis label.
ylim	numeric vector of length 2 specifying the range of the y axis.
las	numeric value specifying the rotation of the axis labels, see par for options.
...	additional parameters to be passed to plot().

Details

The area under the peak(s) is rendered using the polygon function. The area calculation assumes that the polygon does not self-intersect.

Value

A data frame with the following column names.

retention.time	retention times of the peaks specified in range
area	the respective peak areas
apex.intensity	the respective intensities at each peak apex

Author(s)

Nathan G. Dodder

Examples

## single peak
x <- DrawChromatogram(example.chromatogram.single$time,  
                      example.chromatogram.single$intensity/100, 
                      range = list(start = 25.4, stop = 26.1), 
                      main = "example chromatogram 1",
                      ylab = "intensity x 100")
# label peak with retention time and area
text(x$retentionTime, x$apexIntensity + 1500, 
     labels = paste("RT = ", round(x$retentionTime, digits = 1),
                    ", Area = ", round(x$peakArea), sep = ""), cex = 0.9) 

## multiple peaks 
y <- DrawChromatogram(example.chromatogram.multiple$time, 
                      example.chromatogram.multiple$intensity / 1000, 
                      range = list(start = c(21.5, 21.925, 23.1, 25.5, 27.35), 
                        stop = c(21.925, 22.4, 23.6, 26.2, 28.0)),
                      color = c("blue", "red", "green", "yellow", "orange"), 
                      xlab = "retention time (min)", 
                      ylab = "intensity x 1000 (cps)", 
                      main = "Example Chromatogram")
## label peaks
text(y$retentionTime, y$apexIntensity + 50, labels = c("a", "b", "c", "d", "e"))

Example output

OrgMassSpecR documentation built on May 2, 2019, 11:04 a.m.