Plot the Hotspot Z-score matrix

Heatmap of the pairwise gene-gene Z-scores. With module membership from generate_hotspot_membership() the plot keeps the top_k largest modules, orders genes within each module by hierarchical clustering and separates and labels the module blocks, so the block structure is actually readable. Without membership every gene is shown in the order it comes in.

Usage

# S3 method for class 'Hotspot'
plot(x, top_k = 5L, max_genes = 500L, seed = 42L, ...)

Arguments

x

A Hotspot object.

top_k

Integer. Number of modules to keep, ranked by gene count. Set to NULL to keep all of them. Ignored when no membership has been computed. Defaults to 5L.

max_genes

Integer. Maximum number of genes to plot. Above this a subsample is drawn, allocated across the kept modules in proportion to their size. Set to NULL to disable. Defaults to 500L.

seed

Integer. Seed for reproducible subsampling.

...

Further arguments (currently unused).

Value

A ggplot2::ggplot object.

Examples

# gene-gene Z-scores ordered by module membership
sc <- demo_single_cells()
hs <- hotspot_gene_cor_sc(sc, .verbose = FALSE)
hs <- generate_hotspot_membership(hs)
plot(hs)


unlink(sc@dir_data, recursive = TRUE, force = TRUE)