assoc_pval_heatmap: Heatmap of pairwise associations between features

In metasnf: Meta Clustering with Similarity Network Fusion

Heatmap of pairwise associations between features

Description

Heatmap of pairwise associations between features

Usage

assoc_pval_heatmap(
  correlation_matrix,
  scale_diag = "max",
  cluster_rows = TRUE,
  cluster_columns = TRUE,
  show_row_names = TRUE,
  show_column_names = TRUE,
  show_heatmap_legend = FALSE,
  confounders = NULL,
  out_of_models = NULL,
  annotation_colours = NULL,
  labels_colour = NULL,
  split_by_domain = FALSE,
  dl = NULL,
  significance_stars = TRUE,
  slice_font_size = 8,
  ...
)

Arguments

correlation_matrix	Matrix containing all pairwise association p-values. The recommended way to obtain this matrix is through the calc_assoc_pval function.
scale_diag	Parameter that controls how the diagonals of the correlation_matrix are adjusted in the heatmap. For best viewing, this is set to "max", which will match the diagonals to whichever pairwise association has the highest p-value.
cluster_rows	Parameter for ComplexHeatmap::Heatmap. Will be ignored if split_by_domain is also provided.
cluster_columns	Parameter for ComplexHeatmap::Heatmap. Will be ignored if split_by_domain is also provided.
show_row_names	Parameter for ComplexHeatmap::Heatmap.
show_column_names	Parameter for ComplexHeatmap::Heatmap.
show_heatmap_legend	Parameter for ComplexHeatmap::Heatmap.
confounders	A named list where the elements are columns in the correlation_matrix and the names are the corresponding display names.
out_of_models	Like confounders, but a named list of out of model measures (who are also present as columns in the correlation_matrix).
annotation_colours	Named list of heatmap annotations and their colours.
labels_colour	Vector of colours to use for the columns and rows of the heatmap.
split_by_domain	The results of dl_var_summar - a data frame that has the domain of every feature in the plotted data. columns of the correlation_matrix. Will be used to "slice" the heatmap into visually separated sections.
dl	A nested list of input data from data_list().
significance_stars	If TRUE (default), plots significance stars on heatmap cells
slice_font_size	Font size for domain separating labels.
...	Additional parameters passed into ComplexHeatmap::Heatmap.

Value

Returns a heatmap (class "Heatmap" from package ComplexHeatmap) that displays the pairwise associations between features from the provided correlation_matrix.

Examples

#data_list <- data_list(
#    list(income, "household_income", "demographics", "ordinal"),
#    list(pubertal, "pubertal_status", "demographics", "continuous"),
#    list(fav_colour, "favourite_colour", "demographics", "categorical"),
#    list(anxiety, "anxiety", "behaviour", "ordinal"),
#    list(depress, "depressed", "behaviour", "ordinal"),
#    uid = "unique_id"
#)
#
#assoc_pval_matrix <- calc_assoc_pval_matrix(data_list)
#ap_heatmap <- assoc_pval_heatmap(assoc_pval_matrix)

metasnf documentation built on April 3, 2025, 5:40 p.m.