plot.fsa: Plot method for "fsa" objects

In MLPA: Multiplex Ligation-Dependent Probe Amplification Data Analysis

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 = "", xlab = NA, ylab = "Intensity", xlim = NA, ylim = NA,
    xaxt = "s", yaxt = "s", bty = "o", xaxp = NA, nticks = 5, all.bp = TRUE, ...)

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.
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.
...	Further arguments to be passed to plot.

Author(s)

Sylvain Mareschal

See Also

read.fsa

Examples

  # Example FSA file provided
  fsa <- read.fsa(system.file("extdata/fsa/A5918.fsa", package="MLPA"))
  
  # 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))

MLPA documentation built on May 2, 2020, 1:06 a.m.