plot_fsa: FSAPlot: plot_fsa

In joshuakrobertson/FSAPlot: FSAPlot: a tool for visualising microsatellite amplicons

Description

A function to plot fsa files produce from an ABI analyser and rendered into a data.frame using the read_fsa function. Plots are produced using ggplot2 by Hadley Wickham.

Usage

plot_fsa(fsa, dye, title = TRUE, x_limits)

Arguments

fsa	A data.frame containing microsatellite fragment lengths and relative fluoresence produced using read_fsa.
dye	Fluorescent dye bound to loci that one wishes to view. Only 6FAM, HEX, NED, or ROX are supported. This call can either be a single dye or a vector of multiple dyes. No default is provided.
title	An argument defining whether the title of the fsa file is to be given at the head of a given plot. This argument must by TRUE or FALSE.
x_limits	A vector of length 2 defining the basepair range to be viewed. Default is 100 to 500

Details

The default ladder for fragment length calibration is GS500. Note that only data.frames produced by read_fsa may be plotted with this function.

Examples

source = "/home/fish332_microsat.fsa"
Peak_Dat = read_fsa(File = source, Lad_Chan = 4, Range = c(50:80))
plot_fsa(Peak_Dat, dye = c("6FAM", "NED"), title = TRUE, x_limits = c(50,80))

joshuakrobertson/FSAPlot documentation built on June 27, 2020, 1:18 a.m.