RFLPplot: Function to plot RFLP data.

In RFLPtools: Tools to Analyse RFLP Data

Description

Given RFLP data is plotted where the samples are sorted according to the corresponding dendrogram.

Usage

RFLPplot(x, nrBands, nrMissing, distfun = dist, 
         hclust.method = "complete", mar.bottom = 5, 
         cex.axis = 0.5, colBands, xlab = "", 
         ylab = "molecular weight", ylim, ...)

Arguments

x	data.frame with RFLP data; see RFLPdata.
nrBands	if not missing, then only samples with the specified number of bands are considered.
nrMissing	if not missing, then it is assumed that some bands may be missing. That is, all samples with number of bands in nrBands, nrBands+1, ..., nrBands+nrMissing are considered.
distfun	function computing the distance with default dist; see dist.
hclust.method	method used for hierarchical clustering; see hclust.
mar.bottom	bottom margin of the plot; see par.
cex.axis	size of the x-axis annotation.
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

RFLP data is plotted. The samples are sorted according to the corresponding dendrogram which is computed via function hclust.

The option to specify nrMissing may be useful, if gel image quality is low, and the detection of bands is doubtful.

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

RFLPdata, dist

Examples

data(RFLPdata)
par(mfrow = c(1,2))
plot(hclust(RFLPdist(RFLPdata, nrBands = 3)), cex = 0.7)
RFLPplot(RFLPdata, nrBands = 3, mar.bottom = 6, cex.axis = 0.8)

par(mfrow = c(1,2))
plot(hclust(RFLPdist2(RFLPdata, nrBands = 9, nrMissing = 1)), cex = 0.7)
RFLPplot(RFLPdata, nrBands = 9, nrMissing = 1, mar.bottom = 6, cex.axis = 0.8)


distfun <- function(x) dist(x, method = "maximum")
par(mfrow = c(1,2))
plot(hclust(RFLPdist(RFLPdata, nrBands = 3, distfun = distfun), 
            method = "average"), cex = 0.7, cex.lab = 0.7)
RFLPplot(RFLPdata, nrBands = 3, distfun = distfun, hclust.method = "average", 
         mar.bottom = 6, cex.axis = 0.8)

Example output

Loading required package: RColorBrewer

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