plot_pairscan: Plot the result of the pairwise scan

Description

This function plots the results of the pairwise scan. It plots a matrix of the the interactions between all pairs of markers.

Usage

plot_pairscan(
  data_obj,
  pairscan_obj,
  phenotype = NULL,
  standardized = FALSE,
  show_marker_labels = FALSE,
  show_chr = TRUE,
  label_chr = TRUE,
  show_alleles = TRUE,
  allele_labels = NULL,
  pos_col = "brown",
  neg_col = "blue",
  color_scheme = c("DO/CC", "other"),
  pdf_label = "Pairscan.Regression.pdf"
)

Value

Plots to a pdf

Arguments

data_obj: a Cape object
pairscan_obj: a pairscan object from pairscan
phenotype: The names of the phenotypes to be plotted. If NULL, all phenotypes are plotted.
standardized: If TRUE, the standardized effects are plotted. IF FALSE, the effect sizes are plotted.
show_marker_labels: If TRUE marker labels are plotted along the axes. If FALSE, they are omitted.
show_chr: If TRUE, the chromosome boundaries are shown
label_chr: If TRUE, the chromosomes are labeled
show_alleles: If TRUE, the allele of each marker is indicated by color.
allele_labels: Labels for the alleles if other than those stored in the data object.
pos_col: The color to use for positive main effects and interactions must be one of "green", "purple", "red", "orange", "blue", "brown", "yellow", "gray" see get_color
neg_col: The color to use for negative main effects and interactions takes the same values as pos_col.
color_scheme: either "DO/CC" or "other". "DO/CC" uses the official "DO/CC" colors for the DO/CC alleles http://www.csbio.unc.edu/CCstatus/index.py?run=AvailableLines.information "other" uses an unrelated color palette for multiple alleles.
pdf_label: Label for the resulting file. Defaults to "Pairscan.Regression.pdf" if plotting to pdf, "Pairscan.Regression.jpg" otherwise.