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Heatmap of pairwise associations between features

Source: R/heatmaps.R
assoc_pval_heatmap.Rd

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)