visualize_clusters {ccfindR} | R Documentation |
Use tSNE to generate two-dimensional map of coefficient matrix.
visualize_clusters(object, rank, verbose = FALSE, cex = 1, cex.names = 0.7, ...)
object |
|
rank |
Rank value to extract from |
verbose |
Print tSNE messages. |
cex |
Symbol size in tSNE plot |
cex.names |
Font size of labels in count barplot. |
... |
Other parameters to send to |
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.
NULL
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)