Plot true genetic liabilities against posterior mean genetic liabilities

Source: R/visualisations.R

Creates a scatterplot of genetic liability against posterior mean genetic liability.

plot_pmgl_vs_true(
  dataset,
  line_color = "black",
  line_type = "dashed",
  label_size = 3,
  save_plot_path = FALSE,
  plot_filename = "posterior_liabilities.png"
)

Arguments

dataset

data imported to R by load_phenotypes().
line_color

color of identity line.
line_type

type of identity line.
label_size

the size of the boxes.
save_plot_path

if FALSE, return the function returns a ggplot object. Else a path of the directory to save the plot to.
plot_filename

name of the file to be saved, including file extension. Must be either .pdf, .png or .jpeg

Value

Either returns a ggplot object or saves the plot to save_plot_path and returns NULL.

Details

Visualises how well the posterior mean genetic liabilities fit the genetic liabilities. An identity line is included to help see if the genetic liabilities are balanced above and below for each posterior mean genetic liability. Furthermore, the color and labels show each configuration class, which is detailed in vignette("liability-distribution").
This function requires the user to run assign_ltfh_phenotype(), and then association_analysis(pheno_name = "LTFH_pheno"). Data is loaded with load_phenotypes().
vignette("ggplot2-specs", package = "ggplot2") details the usage of aesthetic parameters in ggplot2.