similarity_matrix_heatmap: Plot heatmap of similarity matrix
In metasnf: Meta Clustering with Similarity Network Fusion

similarity_matrix_heatmap

R Documentation

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,
  ...
)

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.

Value

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

Examples


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, ]
)

metasnf documentation built on June 8, 2025, 12:47 p.m.