plot_variant_influences {cape}

Plot cape coefficients

Description

This function plots the the cape coefficients between pairs of markers as a heat map. The interactions are shown in the main part of the heatmap while the main effects are shown on the right hand side. Directed interactions are read from the y axis to the x axis. For example an interaction from marker1 to marker2 will be shown in the row corresponding to marker1 and the column corresponding to marker2. Similarly, if marker1 has a main effect on any traits, these will be shown in the row for marker1 and the trait columns.

Usage

plot_variant_influences(
  data_obj,
  p_or_q = 0.05,
  min_std_effect = 0,
  plot_all_vals = FALSE,
  standardize = FALSE,
  color_scheme = c("DO/CC", "other"),
  pos_col = "brown",
  neg_col = "blue",
  not_tested_col = "lightgray",
  show_marker_labels = FALSE,
  show_chr = TRUE,
  label_chr = TRUE,
  show_alleles = TRUE,
  scale_effects = c("log10", "sqrt", "none"),
  pheno_width = NULL,
  covar_width = NULL,
  covar_labels = NULL,
  phenotype_labels = NULL,
  show_not_tested = TRUE
)

Arguments

data_obj

a Cape object

p_or_q

A threshold indicating the maximum p value (or q value if FDR was used) of significant interactions and main effects

min_std_effect

An optional filter. The plot will exclude all pairs with standardized effects below the number set here.

plot_all_vals

If TRUE will plot all values regardless of significant

standardize

Whether to plot effect sizes (FALSE) or standardized effect sizes (TRUE)

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.

pos_col

The color to use for positive main effects and interactions must be one of "green", "purple", "red", "orange", "blue", "brown", "yellow", "gray" see get_color

neg_col

The color to use for negative main effects and interactions takes the same values as pos_col.

not_tested_col

The color to use for marker pairs not tested. Takes the same values as pos_col and neg_col

show_marker_labels

Whether to write the marker labels on the plot

show_chr

Whether to show chromosome boundaries

label_chr

Whether to label chromosomes if plotted

show_alleles

If TRUE, the allele of each marker is indicated by color.

scale_effects

One of "log10", "sqrt", "none." If some effects are very large, scaling them can help show contrasts between smaller values. The default is no scaling.

pheno_width

Each marker and trait gets one column in the matrix. If there are many markers, this makes the effects on the traits difficult to see. pheno_width increases the number of columns given to the phenotypes. For example, if pheno_width = 11, the phenotypes will be shown 11 times wider than individual markers.

covar_width

See pheno_width. This is the same effect for covariates.

covar_labels

Labels for covariates if different from those stored in the data object.

phenotype_labels

Labels for traits if different from those stored in the data object

show_not_tested

Whether to color the marker pairs that were not tested. If FALSE, they will not be colored in.

Value

This function invisibly returns the variant influences matrix. shown in the heat map.