generateEPG {strvalidator}

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.