plot.exstra_score: Plot ECDF curves from an exstra_score object

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

Plot ECDF curves from an exstra_score object

Description

Plot ECDF curves from an exstra_score object

Usage

## S3 method for class 'exstra_score'
plot(
  x,
  loci = NULL,
  sample_col = NULL,
  refline = TRUE,
  ylab = "Fn(x)",
  verticals = TRUE,
  pch = 19,
  xlim,
  ylim = c(0, 1),
  alpha_control = 0.5,
  alpha_case = NULL,
  xlinked = "all",
  xlinked.safe = TRUE,
  x_upper_missing = 150,
  main = NULL,
  ...
)

Arguments

x	exstra_score object.
loci	character; Only plot at the loci specified/ No effect if NULL.
sample_col	Specify the colours for the given samples as a named character vector. names() are sample names, while the values are characters specifying colours. If specified, other samples are black by default, but may have an alpha value less than 1 for transparency.
refline	logical; if TRUE, then vertical lines are drawn indicating the reference size. This does not take into account mismatches in the STR, or false repeat hits.
ylab	Label for the y-axis.
verticals	logical; if TRUE, vertical lines are drawn at steps. See plot.stepfun.
pch	numeric; the plotting character size.
xlim	numeric of length 2; the x-limits for the plot.
ylim	numeric of length 2; the y-limits for the plot.
alpha_control	Transparency alpha value for the control samples.
alpha_case	Transparency alpha value for the case samples. No effect if NULL.
xlinked	If not "all", limits X chromosome loci to only "male" or "female" samples. Can also filter on only samples with "known" or "missing" sex.
xlinked.safe	logical; if TRUE when xlinked is filtering on "male" or "female", an error will be raised if any samples have an undefined sex. If FALSE, samples with missing sex will also be filtered when xlinked is "male" or "female".
x_upper_missing	If xlim is not specified, then loci with no data will have this upper x-axis limit.
main	Plot title.
...	Further arguments to the plot.ecdf function.

Examples

plot(exstra_wgs_pcr_2["HD"])

plot(exstra_wgs_pcr_2, "HD", sample_col = c("WGSrpt_10" = "red", "WGSrpt_12" = "blue"))

# X-linked disorder, show male samples only:
plot(exstra_wgs_pcr_2, "SBMA", xlinked = "male")

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