plotLDTriangular: Plot LD triangle

Description Usage Arguments Author(s) See Also Examples

Description

Some additional details about this S4 generic and its methods. The extra blank line between this section and the title is critical for roxygen2 to differentiate the title from the description section.

Usage

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plotLDTriangular(x = "twk", from = "ANY", to = "ANY",
  orientation = "numeric", colors = "ANY", bg = "ANY",
  opacity = "ANY", annotate = "logical", really = "logical", ...)

Arguments

x

Input Tomahawk class.

from

Start position in base-pairs.

to

End position in base-pairs.

colors

Vector of colors used to plot with. These are different from col as these colors are internally parsed to add opacity.

opacity

Logical flag/numerical value controlling opacity levels of colors. If set to the logical FALSE, colours will have a uniform opacity of 1. If set to a numerical value, colours will uniformly share that opacity level. If unset, opacity will be a gradient from [0.1, 1] starting at R2 > 0.1.

annotate

Logical flag for setting header title and subtitle overlay on plot.

really

Logical flag to prevent plotting too many points. Set this to TRUE at your own peril.

Author(s)

Marcus D. R. Klarqvist <mk819@cam.ac.uk> | <https://mdrk.me>

See Also

twk_data, twk_header, twk_filter, and twk

Examples

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# This example assumes you have a Tomahawk file called "1kgp3_chr6.two" in
# your current working directory.
f<-setFilters(minR2=0.5)
twk<-openTomahawkOutput("1kgp3_chr6.two")
y<-readRecords(twk,f,"6:5e6-10e6",really=TRUE)
plotLDTriangular(y, ylim=c(0, 500e3), xlim=c(6e6, 7e6))

mklarqvist/rtomahawk documentation built on May 16, 2019, 5:01 a.m.