metasnf (version 2.1.2)

plot.snf_config: Heatmap for visualizing an SNF config

Description

Create a heatmap where each row corresponds to a different set of hyperparameters in an SNF config object. Numeric parameters are scaled normalized and non-numeric parameters are added as heatmap annotations. Rows can be reordered to match prior meta clustering results.

Usage

# S3 method for snf_config
plot(
  x,
  order = NULL,
  hide_fixed = FALSE,
  show_column_names = TRUE,
  show_row_names = TRUE,
  rect_gp = grid::gpar(col = "black"),
  colour_breaks = c(0, 1),
  colours = c("black", "darkseagreen"),
  column_split_vector = NULL,
  row_split_vector = NULL,
  column_split = NULL,
  row_split = NULL,
  column_title = NULL,
  include_weights = TRUE,
  include_settings = TRUE,
  ...
)
config_heatmap(
  x,
  order = NULL,
  hide_fixed = FALSE,
  show_column_names = TRUE,
  show_row_names = TRUE,
  rect_gp = grid::gpar(col = "black"),
  colour_breaks = c(0, 1),
  colours = c("black", "darkseagreen"),
  column_split_vector = NULL,
  row_split_vector = NULL,
  column_split = NULL,
  row_split = NULL,
  column_title = NULL,
  include_weights = TRUE,
  include_settings = TRUE,
  ...
)
# S3 method for settings_df
plot(
  x,
  order = NULL,
  hide_fixed = FALSE,
  show_column_names = TRUE,
  show_row_names = TRUE,
  rect_gp = grid::gpar(col = "black"),
  colour_breaks = c(0, 1),
  colours = c("black", "darkseagreen"),
  column_split_vector = NULL,
  row_split_vector = NULL,
  column_split = NULL,
  row_split = NULL,
  column_title = NULL,
  include_weights = TRUE,
  include_settings = TRUE,
  ...
)
# S3 method for weights_matrix
plot(
  x,
  order = NULL,
  hide_fixed = FALSE,
  show_column_names = TRUE,
  show_row_names = TRUE,
  rect_gp = grid::gpar(col = "black"),
  colour_breaks = c(0, 1),
  colours = c("black", "darkseagreen"),
  column_split_vector = NULL,
  row_split_vector = NULL,
  column_split = NULL,
  row_split = NULL,
  column_title = NULL,
  include_weights = TRUE,
  include_settings = TRUE,
  ...
)

Value

Returns a heatmap (class "Heatmap" from package ComplexHeatmap) that displays the scaled values of the provided SNF config.

Arguments

x

An snf_config class object.

order

Numeric vector indicating row ordering of SNF config.

hide_fixed

Whether fixed parameters should be removed.

show_column_names

Whether show column names.

show_row_names

Whether show row names.

rect_gp

Graphic parameters for drawing rectangles (for heatmap body). The value should be specified by gpar and fill parameter is ignored.

colour_breaks

Numeric vector of breaks for the legend.

colours

Vector of colours to use for the heatmap. Should match the length of colour_breaks.

column_split_vector

Vector of indices to split columns by.

row_split_vector

Vector of indices to split rows by.

column_split

Split on columns. For heatmap splitting, please refer to https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-split .

row_split

Same as split.

column_title

Title on the column.

include_weights

If TRUE, includes feature weights of the weights matrix into the config heatmap.

include_settings

If TRUE, includes columns from the settings data frame into the config heatmap.

...

Additional parameters passed to ComplexHeatmap::Heatmap.

Examples

dl <- 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"
)

sc <- snf_config(
    dl,
    n_solutions = 10,
    dropout_dist = "uniform"
)

plot(sc)