Plot an individual peak or Principal Component of a hotspot.

Usage

hsPeakPlot(
  mapping,
  feats,
  tbands,
  chromosome,
  tissue,
  candidateMed = NULL,
  hsNum = 1,
  color = "#0073C2FF",
  pc = FALSE,
  wag = FALSE,
  sigLOD,
  topPC = 0.5,
  psave = TRUE,
  pname = NULL,
  outdir = NULL,
  ...
)

Arguments

mapping: Mapping list from mapQTL.
feats: List of phenotypes to include. Individual/Candidate Mediator Only: Local to hotspot. PC: Targets of hotspot.
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.
candidateMed: Dataframe of candidate mediator information (can be from annotations). Columns must include "id", "symbol", "start", "end".
hsNum: If there are multiple hotspots on a chromosome, indicate which one. Default is 1.
color: Plot color. Default is "#0073C2FF".
pc: Logical. Plot the first principal component of the targets. Default FALSE.
wag: Logical. Include tailWag effects plot in final. Default is FALSE.
sigLOD: Significant LOD threshold to use for filtering phenotypes.
topPC: Proportion of top hotspot contributers to be identified with Principal Component Analysis. Default is 0.5.
psave: Logical. Save the plot as .png. Default TRUE.
pname: File name to save plot (needs to end in .png).
outdir: Directory to save plots. Default is NULL.
...: Additional arguments

Value

ggplot/patchwork object: Peak plot (with or without phenotype effects). If plotting the Principal Component of the hotspot, also includes a list of the top proportion of phenotypes contributing to the hotspot.