color_patterns_set {qtl2ggplot}

Set up colors for patterns or points

Description

Set up colors for patterns or points

Usage

color_patterns_set(
  scan1output,
  snpinfo,
  patterns,
  col,
  pattern,
  show_all_snps,
  col_hilit,
  drop_hilit,
  maxlod
)

Arguments

scan1output

output of linear mixed model for phename (see scan1)

snpinfo

Data frame with snp information

patterns

Connect SDP patterns: one of c("none","all","hilit").

col

Color of other points, or colors for patterns

pattern

allele pattern as of form AB:CDEFGH

show_all_snps

show all SNPs if TRUE

col_hilit

Color of highlighted points

drop_hilit

SNPs with LOD score within this amount of the maximum SNP association will be highlighted.

maxlod

Maximum LOD for drop of drop_hilit

Value

list of col and pattern.