plot.fsa: Plot method for "fsa" objects
In FSAtools: Fragment Analysis and Capillary Sequencing Tool Kit

plot.fsa

R Documentation

Plot method for "fsa" objects

Description

Plots a fsa object. For each selected channel, a line is drawn bewteen measured fluorescence intensities (y axis) along the electrophoresis time (x axis).

Usage

## S3 method for class 'fsa'
plot(x, units = NA, channels = NA, chanColors = NA, ladder = TRUE,
    offScaleCol = "#FF0000", offScalePch = "+", offScaleCex = 0.4, bg = "white",
    fg = "black", title = "", title.adj = 0, title.line = NA, xlab = NA,
    ylab = "Intensity", xlim = NA, ylim = NA, xaxt = "s", yaxt = "s", bty = "o",
    xaxp = NA, nticks = 5, all.bp = TRUE, peaks.alpha = 48L, peaks.srt = 30,
    peaks.adj = c(0, 0), peaks.cex = 1.3, peaks.font = 2, legend.x = "topleft", ...)

Arguments

`x`	The `fsa` object to plot.
`units`	Single character value, the unit to use on x axis. "index" uses the raw index contained in files, "bp" usess base pair estimations but needs the object to be aligned first using `align.fsa`. `NA` will select "bp" if `x` is aligned, "index" elsewhere.
`channels`	Character or integer vector, the channels to plot. If `NA`, all channels are selected.
`chanColors`	Character vector defining colors to use to plot channels. Can be named according to channel names stored in `x`, or parallel with `channels` (first color for first channel, etc, no recycling). If `NA`, colors stored in `x` are used. See the `col` argument in `par` for further details on allowed values.
`ladder`	Single logical value, whether to add an x axis with size ladder peaks or not. Raises a warning if `x` was not aligned before plotting.
`offScaleCol`	To be passed to `points` for off-scale value plot (see `par` for allowed values).
`offScalePch`	To be passed to `points` for off-scale value plot (see `par` for allowed values).
`offScaleCex`	To be passed to `points` for off-scale value plot (see `par` for allowed values).
`bg`	See `par` for further details.
`fg`	See `par` for further details. This value is also used for col.axis, col.lab, col.main and col.sub graphical parameters.
`title`	Single character value, the main title to print on the plot.
`title.adj`	To be passed as `adj` to `title`.
`title.line`	To be passed as `line` to `title`.
`xlab`	See `plot` for further details. If `NA`, `units` is used.
`ylab`	See `plot` for further details.
`xlim`	See `plot` for further details. If `NA`, `x` range is used.
`ylim`	See `plot` for further details. If `NA`, `x` range is used.
`xaxt`	See `par` for further details.
`yaxt`	See `par` for further details.
`bty`	See `par` for further details.
`xaxp`	See `par` for further details. If `NA`, a suitable value is computed.
`nticks`	Single integer value. When `xaxp` is `NA` and `units` is "bp", this values fixes the interval between X axis labels.
`all.bp`	Single logical value, whether to force an unlabeled axis tick at each bp when `units` is "bp" or not.
`peaks.alpha`	Single integer value, the alpha channel to add to peak colors to make a background (255 is no transparency at all, 0 is invisible).
`peaks.srt`	To be passed as `srt` to `text` while printing peak names.
`peaks.adj`	To be passed as `adj` to `text` while printing peak names.
`peaks.cex`	To be passed as `cex` to `text` while printing peak names.
`peaks.font`	To be passed as `font` to `text` while printing peak names.
`legend.x`	To be passed as `x` to `legend`.
`...`	Further arguments to be passed to `plot`.

Value

Invisibly returns TRUE on success.

Author(s)

Sylvain Mareschal

Examples

  # Example FSA file provided
  fsa <- read.fsa(system.file("extdata/fsa_GEP/A5918.fsa", package="FSAtools"))
  
  # Plot whole profile
  plot(fsa)
  
  # Plot subset of the profile (time index)
  plot(fsa, units="index", xlim=c(4000,5000))
  
  # Plot subset of the profile (base pairs)
  fsa <- align.fsa(fsa)
  plot(fsa, units="bp", xlim=c(80,130))

FSAtools documentation built on Aug. 19, 2023, 1:06 a.m.