visualize_clusters: Visualize clusters

In hjunwoo/ccfindR: Cancer Clone Finder

Description

Use tSNE to generate two-dimensional map of coefficient matrix.

Usage

visualize_clusters(object, rank, verbose = FALSE, cex = 1,
  cex.names = 0.7, ...)

Arguments

object	scNMF object.
rank	Rank value to extract from object.
verbose	Print tSNE messages.
cex	Symbol size in tSNE plot
cex.names	Font size of labels in count barplot.
...	Other parameters to send to Rtsne.

Details

It retrieves a coefficient matrix H from an object and use its elements to assign each cell into clusters. t-Distributed Stochastic Neighbor Embedding (t-SNE; https://lvdmaaten.github.io/tsne/) is used to visualize the clustering in 2D. Also plotted is the distribution of cell counts for all clusters.

Value

NULL

Examples

set.seed(1)
x <- simulate_data(nfeatures=10,nsamples=c(20,20,60,40,30))
rownames(x) <- seq_len(10)
colnames(x) <- seq_len(170)
s <- scNMFSet(count=x,rowData=seq_len(10),colData=seq_len(170))
s <- vb_factorize(s,ranks=seq(2,5))
visualize_clusters(s,rank=5)

hjunwoo/ccfindR documentation built on Oct. 4, 2019, 10:31 a.m.