cell_map: Plot heatmap of clustering coefficient matrix

In ccfindR: Cancer Clone Finder

Description

Retrieve a coefficient matrix H derived from factorization by rank value and generate heatmap of its elements.

Usage

cell_map(object, rank, main = "Cells", ...)

Arguments

object	Object of class scNMFSet.
rank	Rank value for which the cell map is to be displayed. The object must contain the corresponding slot: one element of coeff(object)[[k]] for which ranks(object)[[k]]==rank.
main	Title of plot.
...	Other arguments to be passed to heatmap, image, and plot.

Value

NULL

Examples

set.seed(1)
x <- simulate_data(nfeatures=10,nsamples=c(20,20,60))
rownames(x) <- seq_len(10)
colnames(x) <- seq_len(100)
s <- scNMFSet(count=x,rowData=seq_len(10),colData=seq_len(100))
s <- vb_factorize(s,ranks=seq(2,5))
plot(s)
cell_map(s, rank=3)

ccfindR documentation built on Nov. 8, 2020, 5:12 p.m.