RFLPrefplot: Function for a visual comparison of RFLP samples with...

In RFLPtools: Tools to Analyse RFLP Data

Description

Given RFLP samples are plotted together with reference samples and sorted by their distance to the reference sample.

Usage

RFLPrefplot(x, ref, distfun = dist, nrBands, mar.bottom = 5, 
            cex.main = 1.2, cex.axis = 0.5, devNew = FALSE, 
            colBands, xlab = "", ylab = "molecular weight", 
            ylim, ...)

Arguments

x	data.frame with RFLP data; e.g. RFLPdata.
ref	data.frame with RFLP reference data; e.g. RFLPref.
distfun	function computing the distance with default dist; see dist.
nrBands	if not missing, then only samples with the specified number of bands are considered.
mar.bottom	bottom margin of the plot; see par.
cex.main	size of the plot title.
cex.axis	size of the x-axis annotation.
devNew	logical. Open new graphics device for each plot.
colBands	color for the bands. Has to be of length 1 or number of samples. If missing, "Set1" of RColorBrewer is used; see ColorBrewer.
xlab	passed to function plot.
ylab	passed to function plot.
ylim	passed to function plot. If missing an appropriate range of y-values is computed.
...	additional arguments passed to function plot except xlim which is defined inside of RFLPplot.

Details

Given RFLP samples are plotted together with reference samples and sorted by their distance to the reference sample.

Value

invisible

Author(s)

Fabienne Flessa [e-mail],
Alexandra Kehl [e-mail],
Matthias Kohl [e-mail]

References

Flessa, F., Kehl, A., Kohl, M. Analysing diversity and community structures using PCR-RFLP: a new software application. Molecular Ecology Resources 2013 Jul; 13(4):726-33.

See Also

RFLPplot

Examples

data(RFLPdata)
data(RFLPref)
dev.new(width = 12)
RFLPrefplot(RFLPdata, RFLPref, nrBands = 4, cex.axis = 0.5)

dev.new()
RFLPrefplot(RFLPdata, RFLPref, nrBands = 6, cex.axis = 0.8)
RFLPrefplot(RFLPdata, RFLPref, nrBands = 9, cex.axis = 0.8)

RFLPrefplot(RFLPdata, RFLPref[RFLPref$Sample == "Ni_29_A3",], nrBands = 4, cex.axis = 0.7)

Dir <- system.file("extdata", package = "RFLPtools") # input directory 
filename <- file.path(Dir, "AZ091016_report.txt")
RFLP1 <- read.rflp(file = filename)
RFLP2 <- RFLPqc(RFLP1)

dev.new(width = 12)
RFLPrefplot(RFLP1, RFLPref, nrBands = 4, cex.axis = 0.8)

dev.new()
RFLPrefplot(RFLP1, RFLPref, nrBands = 5, cex.axis = 0.8)

RFLPtools documentation built on Feb. 8, 2022, 5:06 p.m.