OrgMassSpecR (version 0.5-3)

DrawChromatogram: Plot a Chromatogram

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().

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

Details

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

Examples

# NOT RUN {
## 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"))
# }