plot_multi: Multiple STR score ECDF plots

In bahlolab/exSTRa: Expanded STR algorithm: detecting expansions in Illumina sequencing data

Multiple STR score ECDF plots

Description

Allows plotting the STR scores of many loci with legend. Plots may be written directly to PDF files.

Usage

plot_multi(
  strscore,
  prefix = "exSTRa_plot",
  dir = "images/",
  plot_cols = NULL,
  color_only = NULL,
  plot_types = 1,
  alpha_control = 0.5,
  alpha_case = NULL,
  legend = TRUE,
  legend_control = TRUE,
  controls_label = "controls",
  cases_label = "cases",
  custom_legend = NULL,
  ...
)

Arguments

strscore	exstra_score object.
prefix	File name prefix.
dir	Output directory for PDF plots.
plot_cols	If a named vector, colours to use for each sample (names) for all loci. Unspecified samples are treated as controls. May be a named (loci) list with named vectors as above for specific locus colours.
color_only	List (named with loci) of a character vectors of samples to color at each locus.
plot_types	vector; Specify the plot output device. May have multiple of the following options if these are desired. Set to: 1 for current device, 2 for output to a single PDF file with multiple pages (when >1 locus), and 3 for a PDF file per locus.
alpha_control	Transparency alpha value for control samples.
alpha_case	Transparency alpha value for case samples.
legend	logical; if TRUE, include a legend.
legend_control	logical; if TRUE, include generic control specification in legend.
controls_label	character; a generic label in the legend for controls.
cases_label	character; a generic label for case samples in the legend.
custom_legend	A named (sample) vector of colors, for the legend.
...	Further arguments to plot.exstra_score

Examples

# Plot 4 loci
par(mfrow = c(2, 2))
plot_multi(exstra_wgs_pcr_2[c("HD", "SCA6", "FRDA", "SCA1")], alpha_case = 0.2)

bahlolab/exSTRa documentation built on Sept. 17, 2022, 5:08 p.m.