plot_singlescan: Plot results of single-locus scans
In cape: Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

plot_singlescan

R Documentation

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