similarity_matrix_heatmap {metasnf} | 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_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 |
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 |
column_split |
Standard parameter of |
... |
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.