Description Usage Arguments Details Value Author(s) References See Also Examples
Given RFLP data is plotted where the samples are sorted according to the corresponding dendrogram.
1 2 3 4 |
x |
data.frame with RFLP data; see |
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 |
hclust.method |
method used for hierarchical clustering;
see |
mar.bottom |
bottom margin of the plot; see |
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, |
xlab |
passed to function |
ylab |
passed to function |
ylim |
passed to function |
... |
additional arguments passed to function |
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.
invisible
Fabienne Flessa Fabienne.Flessa@uni-bayreuth.de,
Alexandra Kehl Alexandra.Kehl@botgarten.uni-tuebingen.de,
Matthias Kohl Matthias.Kohl@stamats.de
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | 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)
|
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