Manhattan plot of p-values — plot_manhattan • geneference

Plots a Manhattan plot with only the SNPs that have a p-value of at most 0.1.

plot_manhattan(
  dataset,
  P,
  SNP = SNP,
  causal = causal,
  line_color = "cornflowerblue",
  line_type = "dashed",
  save_plot_path = FALSE,
  plot_filename = "manhattan_plot.png"
)

Arguments

dataset	data imported to R by `load_results()`.
P	column containing p-values to be plotted. State in the format dataset$P_value.
SNP	column containing the SNP values. If loaded with `load_results()` can be left default otherwise state in the format dataset$SNP.
causal	column containing the causal values. If created created with `augment_results()` can be left default, otherwise state in the format dataset$causal.
line_color	color of the lines.
line_type	the type of the lines.
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

All points above the upper dashed line show SNPs that are significant at 0.05 significance level with Bonferroni-correction. Points above the lower dashed line show SNPs that are significant at a 0.05 significance level.
The color of the point show whether or not they are truly causal for the phenotype.
The user must run some analysis with analysis_association() and load the data with load_results(). Furthermore, augment_results() must be run where the user should create a 'causal' column from the true effect sizes.