R: Electrophoregram plot for ABIF data

plotabif {seqinr} | R Documentation

## Electrophoregram plot for ABIF data

### Description

Simple chromatogram plot for data imported with the `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(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,
      ...)

### Arguments

`abifdata` | the result returned by `read.abif`
`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 `plot`
`las` | orientation of axis labels forwarded to `plot`
`xlab` | x-axis label forwarded to `plot`
`ylab` | y-axis label forwarded to `plot`
`irange` | indices of data to be plotted
`x` | values used for the x-axis
`xlim` | limits for the x-axis forwarded to `plot`
`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 `plot`
`dyn` | dye name
`main` | title for the plot forwarded to `plot`
`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 `plot`

### Value

Returns invisibly its local graphical parameter settings.

### Author(s)

J.R. Lobry

### References

`citation("seqinr")`

### See Also

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.

### Examples

    data(ECH)
    plotabif(ECH,chanel = 1, tmin = 3.2, tmax = 6.1)

[Package seqinr version 3.4-5 Index]