generateEPG: Generate EPG

In strvalidator: Process Control and Validation of Forensic STR Kits

Generate EPG

Description

Visualizes an EPG from DNA profiling data.

Usage

generateEPG(
  data,
  kit,
  title = NULL,
  wrap = TRUE,
  boxplot = FALSE,
  peaks = TRUE,
  collapse = TRUE,
  silent = FALSE,
  ignore.case = TRUE,
  at = 0,
  scale = "free",
  limit.x = TRUE,
  label.size = 3,
  label.angle = 0,
  label.vjust = 1,
  label.hjust = 0.5,
  expand = 0.1,
  debug = FALSE
)

Arguments

data	data frame containing at least columns 'Sample.Name', 'Allele', and 'Marker'.
kit	string or integer representing the STR typing kit.
title	string providing the title for the EPG.
wrap	logical TRUE to wrap by dye.
boxplot	logical TRUE to plot distributions of peak heights as boxplots.
peaks	logical TRUE to plot peaks for distributions using mean peak height.
collapse	logical TRUE to add the peak heights of identical alleles peaks within each marker. NB! Removes off-ladder alleles.
silent	logical FALSE to show plot.
ignore.case	logical FALSE for case sensitive marker names.
at	numeric analytical threshold (Height <= at will not be plotted).
scale	character "free" free x and y scale, alternatively "free_y" or "free_x".
limit.x	logical TRUE to fix x-axis to size range. To get a common x scale set scale="free_y" and limit.x=TRUE.
label.size	numeric for allele label text size.
label.angle	numeric for allele label print angle.
label.vjust	numeric for vertical justification of allele labels.
label.hjust	numeric for horizontal justification of allele labels.
expand	numeric for plot are expansion (to avoid clipping of labels).
debug	logical for printing debug information to the console.

Details

Generates a electropherogram like plot from 'data' and 'kit'. If 'Size' is not present it is estimated from kit information and allele values. If 'Height' is not present a default of 1000 RFU is used. Off-ladder alleles can be plotted if 'Size' is provided. There are various options to customize the plot scale and labels. It is also possible to plot 'distributions' of peak heights as boxplots.

Value

ggplot object.

strvalidator documentation built on July 26, 2023, 5:45 p.m.