Plot peaks associated with specific genes.

Usage

peak_plot(
  mapping,
  tissue,
  pheno,
  pop = "do",
  outdir = NULL,
  pname = NULL,
  psave = TRUE,
  chromosome = NULL,
  effects = FALSE,
  founders = NULL,
  palette = NULL
)

Arguments

mapping: Mapping list from mapQTL, or full path to .rds containing one.
tissue: Tissue to derive plots from
pheno: Phenotype to plot
pop: One of c("do", "cc", "other") to indicate founder population. Default is "do".
outdir: Directory to save plots. Default is NULL.
pname: File name to save plot (needs to end in .png).
psave: Logical. Save the plot as .png. Default TRUE.
chromosome: Chromosome that the peaks is present on.
effects: Logical. Plotting effects on chromosome. Default is FALSE.
founders: If pop == "other", list of founders in haplotype order.
palette: Founder color map (> 8 founders).

Value

Plot of phenotype specific peaks, or phenotype specific peak with effects