LLRplot: Scatter Plot of Pair LLRs

In sequoia: Pedigree Inference from SNPs

Scatter Plot of Pair LLRs

Description

Plot LLR(rely/U) against LLR(relx/U), for one combination of relationships, colour coded by fcl & top.

Usage

LLRplot(relx, rely, LLRU, fcl, top, RelCol, bgcol, Tassign = 0.5, Tfilter = -2)

Arguments

relx	relationship to plot on the x-axis. One of 'PO', 'FS', 'HS', 'GP', 'FA', or 'HA'.
rely	relationship to plot on the y-axis; as relx.
LLRU	matrix with log10-likelihoods, already scaled by LL(U) for each pair.
fcl	focal relationship, sets outer circle colour of points.
top	most likely relationship, sets inner filling colour of points.
RelCol	named character vector with colours to use per relationship.
bgcol	do background colour TRUE/FALSE.
Tassign	assignment threshold, shown as grey square in bottom-left corner and band along the diagonal.
Tfilter	filter threshold, shown as dark grey square in bottom-left.

Details

The background of the plot is coloured to match relx (bottom triangle) and rely (upper triangle).

sequoia documentation built on Sept. 8, 2023, 5:29 p.m.