plot_singlescan {cape}

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