Map founder haplotype effects for a given hotspot.

Usage

hsHapEffects(
  effects,
  tbands,
  chromosome,
  tissue,
  sigLOD,
  hsNum = 1,
  pop = "do",
  founders = NULL,
  palette = NULL,
  topFeats = NULL,
  psave = TRUE,
  pname = NULL,
  outdir = NULL,
  vert = FALSE,
  showTarg = TRUE,
  ...
)

Arguments

effects: Effects object qtl_effects.
tbands: List of transband locations (bands.rna list from transbands function)
chromosome: Chromosome that the transband (hotspot) is present on.
tissue: Tissue that the transband (hotspot) is present in
sigLOD: Significant LOD threshold to use for filtering phenotypes.
hsNum: If there are multiple hotspots on a chromosome, indicate which one. Default is 1.
pop: One of c("do", "cc", "other") to indicate founder population. Default is "do".
founders: If pop == "other", list of founders in haplotype order.
palette: Founder color map.
topFeats: Optional. Top hotspot features based on PCA analysis.
psave: Logical. Save the plot as .png. Default TRUE.
pname: File name to save plot (needs to end in .png). Default is haplotype_effects_<tissue>_transband_<hsNum>_chromosome_<chromosome>.png
outdir: Directory to save plots. Default is NULL.
vert: Logical. Rotate plot to vertical orientation. Default FALSE.
showTarg: Logical. Show target names in resulting plot. Default TRUE.
...: Additional arguments to pass to ComplexHeatmap

Value

List of plots. ht_plot: Plot only, formatted with legend on the left. ht: Original ComplexHeatmap object.