plotLD: Plot LD square

In mklarqvist/rtomahawk: Tools for computing, querying and storing linkage-disequilibrium data

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

plotLD(x = "twk", from = "ANY", to = "ANY", colors = "ANY",
  bg = "ANY", opacity = "ANY", upper = "logical",
  lower = "logical", 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.
upper	Plot only the upper triangular of values.
lower	Plot only the lower triangular of values.
really	Logical flag to prevent plotting too many points. Set this to TRUE at your own peril.

Author(s)

Marcus D. R. Klarqvist <[e-mail]> | <https://mdrk.me>

See Also

twk_data, twk_header, twk_filter, and twk

Examples

# This example assumes you have a Tomahawk file called "1kgp3_chr6.two" in
# your current working directory.
f<-setFilters(minR2=0.1)
twk<-openTomahawkOutput("1kgp3_chr6.two")
y<-readRecords(twk,f,"6:5e6-10e6",really=TRUE)
plotLD(y, ylim=c(5e6, 10e6), xlim=c(5e6, 10e6))
plotLD(y, ylim=c(5e6, 10e6), xlim=c(5e6, 10e6), upper = TRUE)
plotLD(y, ylim=c(5e6, 10e6), xlim=c(5e6, 10e6), lower = TRUE)

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