plot_pairscan {cape}

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"
)

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.

Value

Plots to a pdf