metasnf (version 2.1.2)

similarity_matrix_heatmap: Plot heatmap of similarity matrix

Description

Plot heatmap of similarity matrix

Usage

similarity_matrix_heatmap(
  similarity_matrix,
  order = NULL,
  cluster_solution = NULL,
  scale_diag = "mean",
  log_graph = TRUE,
  cluster_rows = FALSE,
  cluster_columns = FALSE,
  show_row_names = FALSE,
  show_column_names = FALSE,
  data = NULL,
  left_bar = NULL,
  right_bar = NULL,
  top_bar = NULL,
  bottom_bar = NULL,
  left_hm = NULL,
  right_hm = NULL,
  top_hm = NULL,
  bottom_hm = NULL,
  annotation_colours = NULL,
  min_colour = NULL,
  max_colour = NULL,
  split_vector = NULL,
  row_split = NULL,
  column_split = NULL,
  ...
)

Value

Returns a heatmap (class "Heatmap" from package ComplexHeatmap) that displays the similarities between observations in the provided matrix.

Arguments

similarity_matrix

A similarity matrix

order

Vector of numbers to reorder the similarity matrix (and data if provided). Overwrites ordering specified by cluster_solution param.

cluster_solution

Row of a solutions data frame or column of a transposed solutions data frame.

scale_diag

Method of rescaling matrix diagonals. Can be "none" (don't change diagonals), "mean" (replace diagonals with average value of off-diagonals), or "zero" (replace diagonals with 0).

log_graph

If TRUE, log transforms the graph.

cluster_rows

Parameter for ComplexHeatmap::Heatmap.

cluster_columns

Parameter for ComplexHeatmap::Heatmap.

show_row_names

Parameter for ComplexHeatmap::Heatmap.

show_column_names

Parameter for ComplexHeatmap::Heatmap.

data

A data frame containing elements requested for annotation.

left_bar

Named list of strings, where the strings are features in df that should be used for a barplot annotation on the left of the plot and the names are the names that will be used to caption the plots and their legends.

right_bar

See left_bar.

top_bar

See left_bar.

bottom_bar

See left_bar.

left_hm

Like left_bar, but with a heatmap annotation instead of a barplot annotation.

right_hm

See left_hm.

top_hm

See left_hm.

bottom_hm

See left_hm.

annotation_colours

Named list of heatmap annotations and their colours.

min_colour

Colour used for the lowest value in the heatmap.

max_colour

Colour used for the highest value in the heatmap.

split_vector

A vector of partition indices.

row_split

Standard parameter of ComplexHeatmap::Heatmap.

column_split

Standard parameter of ComplexHeatmap::Heatmap.

...

Additional parameters passed into ComplexHeatmap::Heatmap.

Examples

# \donttest{
my_dl <- data_list(
    list(
        data = expression_df,
        name = "expression_data",
        domain = "gene_expression",
        type = "continuous"
    ),
    list(
        data = methylation_df,
        name = "methylation_data",
        domain = "gene_methylation",
        type = "continuous"
    ),
    uid = "patient_id"
)

sc <- snf_config(my_dl, n_solutions = 10)

sol_df <- batch_snf(my_dl, sc, return_sim_mats = TRUE)

sim_mats <- sim_mats_list(sol_df)

similarity_matrix_heatmap(
    sim_mats[[1]],
    cluster_solution = sol_df[1, ]
)
# }