RFLPrefplot {RFLPtools} | R Documentation |
Given RFLP samples are plotted together with reference samples and sorted by their distance to the reference sample.
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, ...)
x |
data.frame with RFLP data; e.g. |
ref |
data.frame with RFLP reference data; e.g. |
distfun |
function computing the distance with default |
nrBands |
if not missing, then only samples with the specified number of bands are considered. |
mar.bottom |
bottom margin of the plot; see |
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, |
xlab |
passed to function |
ylab |
passed to function |
ylim |
passed to function |
... |
additional arguments passed to function |
Given RFLP samples are plotted together with reference samples and sorted by their distance to the reference sample.
invisible
Fabienne Flessa Fabienne.Flessa@uni-bayreuth.de,
Alexandra Kehl Alexandra.Kehl@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.
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)