plotabif2: plotabif2

In LazyMLVA: LazyMLVA

Description

This function draws a simple plot of the chromatogram file similar to seqinr::plotabif, yet additionally allows overplotting of several channels.

Usage

plotabif2(abifdata, 
          channels = 1:5, 
          ch.plotcolors = c("blue", "green", "black", "red", "orange"), 
          main = paste("Channels", paste(channels, collapse = ", "), "of", deparse(substitute(abifdata))),
          ylab = "Relative Fluorescent Units (RFU)", 
          xlab = "Time", 
          tmin = 1, 
          tmax = abifdata$Data[["SCAN.1"]], 
          ylim, 
          add.legend = TRUE, 
          ...)

Arguments

abifdata	result returned by seqinr::read.abif
channels	the channel numbers (default is 1:5)
ch.plotcolors	colors for channels 1:5
main	main title, see plot
ylab	label of y-axis, see plot
xlab	label of x-axis, see plot
tmin	unscaled starting time
tmax	unscaled ending time
ylim	see plot
add.legend	logical variable stating whether a legend is to be added
...	arguments passed to plot

Author(s)

Johannes Elias

References

package seqinr by Charif, D. and Lobry, J.R. (2007)

See Also

seqinr::plotabif

Examples

# plot channels of reference abif file r_abif
plotabif2(r_abif)

LazyMLVA documentation built on May 2, 2019, 5:33 p.m.