plot_singlescan: Plot results of single-locus scans

Description

This function plots the results of singlescan

Usage

plot_singlescan(
  data_obj,
  singlescan_obj,
  chr = NULL,
  traits = NULL,
  alpha = c(0.01, 0.05),
  standardized = TRUE,
  color_scheme = c("DO/CC", "other"),
  allele_labels = NULL,
  include_covars = TRUE,
  show_selected = FALSE,
  line_type = "l",
  lwd = 1,
  pch = 16,
  cex = 1,
  covar_label_size = 0.7
)

Arguments

data_obj: a Cape object
singlescan_obj: a singlescan object from singlescan
chr: a vector of chromosome names to include in the plot. Defaults to all chromosomes.
traits: a vector of trait names to plot. Defaults to all traits.
alpha: the alpha significance level. Lines for significance values will only be plotted if n_perm > 0 when singlescan was run. And only alpha values specified in singlescan can be plotted.
standardized: If TRUE t statistics are plotted. If FALSE, effect sizes are plotted.
color_scheme: A character value of either "DO/CC" or other indicating the color scheme of main effects. If "DO/CC" allele effects can be plotted with the DO/CC colors.
allele_labels: A vector of labels for the alleles if different than those stored in the data_object.
include_covars: Whether to include covariates in the plot.
show_selected: If TRUE will indicate which markers were selected for the pairscan. In order for these to be plotted, select_markers_for_pairscan must be run first.
line_type: as defined in plot
lwd: line width, default is 1
pch: see the "points()" R function. Default is 16 (a point).
cex: see the "points()" R function. Default is 1.
covar_label_size: default is 0.7