Electrophoregram plot for ABIF data
Simple chromatogram plot for data imported with the read.abif function.
plotabif(abifdata,
chanel = 1,
tmin = 1/tscale,
tmax = abifdata$Data[["SCAN.1"]]/tscale,
tscale = 1000,
yscale = 1000, type = "l", las = 1,
xlab = paste("Time", tscale, sep = "/"),
ylab = paste("RFU", yscale, sep = "/"),
irange = (tmin*tscale):(tmax*tscale),
x = irange/tscale,
xlim = c(tmin, tmax),
chanel.names = c(1:4,105),
DATA = paste("DATA", chanel.names[chanel], sep = "."),
y = abifdata$Data[[DATA]][irange]/yscale,
ylim = c(min(y), max(y)),
dyn = abifdata$Data[[paste("DyeN", chanel, sep = ".")]],
main = paste(deparse(substitute(abifdata)), chanel, dyn, sep = " ; "),
calibr = NULL,
ladder.bp = NULL,
allele.names = "identifiler",
ladder.lab = TRUE,
...)abifdata |
the result returned by |
chanel |
the dye number |
tmin |
scaled starting time for the time axis |
tmax |
scaled ending time for the time axis |
tscale |
scale factor for the time axis |
yscale |
scale factor for the y-axis (RFU) |
type |
type of line drawing forwarded to |
las |
orientation of axis labels forwarded to |
xlab |
x-axis label forwarded to |
ylab |
y-axis label forwarded to |
irange |
indices of data to be plotted |
x |
values used for the x-axis |
xlim |
limits for the x-axis forwarded to |
chanel.names |
numbers extensions used for the DATA |
DATA |
names of the DATA components |
y |
values used for the y-axis |
ylim |
limits for the y-axis forwarded to |
dyn |
dye name |
main |
title for the plot forwarded to |
calibr |
an optional calibration function to convert time into bp |
ladder.bp |
an optional ladder scale in bp (calibr must be provided) |
allele.names |
name of the dataset with allele names |
ladder.lab |
logical: should allele names be added on plot |
... |
arguments forwarded to |
Returns invisibly its local graphical parameter settings.
J.R. Lobry
citation("seqinr")
function read.abif to import files in ABIF format,
data gs500liz for internal size standards,
data identifiler for allele names in the allelic ladder,
data JLO for an example of an individual sample file,
data ECH for an example of an allelic lader.
data(ECH) plotabif(ECH,chanel = 1, tmin = 3.2, tmax = 6.1)
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