[Seqinr-commits] r1544 - pkg/man

[noreply at r-forge.r-project.org]

Author: lobry
Date: 2009-02-04 14:54:23 +0100 (Wed, 04 Feb 2009)
New Revision: 1544

Added:
   pkg/man/plotabif.Rd
Log:
new plot function for ABIF data

Added: pkg/man/plotabif.Rd
===================================================================
--- pkg/man/plotabif.Rd	                        (rev 0)
+++ pkg/man/plotabif.Rd	2009-02-04 13:54:23 UTC (rev 1544)
@@ -0,0 +1,72 @@
+\name{plotabif}
+\alias{plotabif}
+\title{Electrophoregram plot for ABIF data}
+\description{
+  Simple chromatogram plot for data imported with the \code{\link{read.abif}} function.
+}
+\usage{
+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(0, 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,
+  ...)
+}
+\arguments{
+  \item{abifdata}{the result returned by \code{\link{read.abif}}}
+  \item{chanel}{the dye number}
+  \item{tmin}{scaled starting time for the time axis}
+  \item{tmax}{scaled ending time for the time axis}
+  \item{tscale}{scale factor for the time axis}
+  \item{yscale}{scale factor for the y-axis (RFU)}
+  \item{type}{type of line drawing forwarded to \code{\link{plot}}}
+  \item{las}{orientation of axis labels forwarded to \code{\link{plot}}}
+  \item{xlab}{x-axis label forwarded to \code{\link{plot}}}
+  \item{ylab}{y-axis label forwarded to \code{\link{plot}}}
+  \item{irange}{indices of data to be plotted}
+  \item{x}{values used for the x-axis}
+  \item{xlim}{limits for the x-axis forwarded to \code{\link{plot}}}
+  \item{chanel.names}{numbers extensions used for the DATA}
+  \item{DATA}{names of the DATA components}
+  \item{y}{values used for the y-axis}
+  \item{ylim}{limits for the y-axis forwarded to \code{\link{plot}}}
+  \item{dyn}{dye name}
+  \item{main}{title for the plot forwarded to \code{\link{plot}}}
+  \item{calibr}{an optional calibration function to convert time into bp}
+  \item{ladder.bp}{an optional ladder scale in bp (calibr must be provided)}
+  \item{allele.names}{name of the dataset with allele names}
+  \item{ladder.lab}{logical: should allele names be added on plot}
+  \item{...}{arguments forwarded to \code{\link{plot}}}
+}
+\references{
+  \code{citation("seqinr")}
+}
+\author{J.R. Lobry}
+\seealso{
+  function \code{\link{read.abif}} to import files in ABIF format, 
+  data \code{\link{gs500liz}} for internal size standards,
+  data \code{\link{identifiler}} for allele names in the allelic ladder,
+  data \code{\link{JLO}} for an example of an individual sample file,
+  data \code{\link{ECH}} for an example of an allelic lader.
+}
+\examples{
+data(ECH)
+plotabif(ECH,chanel = 1, tmin = 3.2, tmax = 6.1)
+}
+