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_list = NULL,
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
Vector containing cluster assignments.
- 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_list
A nested list of input data from
generate_data_list().- data
A dataframe 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.