visualize_clusters {ccfindR} | R Documentation

## Visualize clusters

### 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)

[Package ccfindR version 1.6.0 Index]