Plot pairwise epistasis — plot_epistasis • cancereffectsizeR

Visualize pairwise epistatic scaled selection coefficients, as calculated by ces_epistasis() or ces_gene_epistasis(). For each variant, the isolated site effect--the overall scaled selection at the site without regard for the mutation status of the other site--is also depicted.

Usage

plot_epistasis(
  epistatic_effects,
  pairs_per_row = 8,
  x_title = "Site pairs",
  variant_label_size = 6.5,
  dodge_labels = "auto",
  alternating_colors = c("#7cb4de", "#7DD3AF"),
  schematic_label_size = 2.5,
  significance_levels = c(0.05, 0.01, 0.001),
  significance_cols = list(A_change = "p_A_change", B_change = "p_B_change", model =
    "p_epistasis"),
  inference_floor = 0.001
)

Arguments

epistatic_effects: Epistatic effects inference table, as produced by ces_epistasis() or ces_gene_epistasis().
pairs_per_row: How many epistatic pairs to show in each plot row. The provided value is incremented if need to prevent the legend schematic from being isolated on its own row.
x_title: X-axis label. Set NULL for no label.
variant_label_size: Text size for the variant labels.
dodge_labels: TRUE/FALSE on using n.dodge (height staggering) on variant labels. Defaults to "auto"; you can try setting manually if labels are not looking good.
alternating_colors: Colors, provided as character vector, to use on epistatic effect arrows. It's recommended to supply one or two colors, but more will work.
schematic_label_size: Text size of labels in the schematic.
significance_levels: A vector of 1-3 distinct numeric values on (0, 1) in descending order to use for significance annotations.
significance_cols: A named list of column names that give significance values for nonzero change in selection for each pair of sites A and B, and for the performance of the epistatic selection model over a model that ignores epistatic interactions. List elements must be named A_change (default "p_A_change") B_change ("p_B_change"), and model ("p_epistasis"). The purpose of this option is to support the use of different columns when multiple testing correction is performed.
inference_floor: Numeric value of the optimization floor used in epistatic effect inference. Typically, should be left at the default value, which matches cancereffectsizeR epistatic inference defaults. For plot legibility, there will be a dashed horizontal line in the output plot, higher than inference_floor and lower than any non-minimized parameter inference, which indicates that all arrows pointing below the line have estimates at the optimization floor.7CB4DE (old) c("#8dbee2", "#a3d8c2")

Details

Variant pairs for which the epistatic selection model is not significantly better than a no-epistasis model (in which ces_A0 = ces_A_on_B and ces_B0 = ces_B_on_A) are depicted with faded arrows; the threshold is p_epistasis < .05 (or, instead of p_epistasis, whatever corrected significance column is specified with significance_cols).