plot_cluster {musicatk} | R Documentation

## Visualize clustering results

### Description

The clustering results can be visualized on a UMAP panel. Three different types of plots can be generated using this function: cluster-by-signature plot, cluster-by-annotation plot, and a single UMAP plot.

### Usage

    plot_cluster(result, clusters, group = "signature", annotation = NULL)

### Arguments

`result` | A `musica_result` object generated by a mutational discovery or prediction tool. A two-dimensional UMAP has to be stored in this object.
`clusters` | The result generated from cluster_exposure function.
`group` | A single character string indicating the grouping factor. Possible options are: "signature" (columns are signatures in a grid), "annotation" (columns are sample annotation), and "none" (a single UMAP plot). Default is "signature".
`annotation` | Column name of annotation.

### Value

Generate a ggplot object.

### See Also

create_umap

### Examples

    set.seed(123)
    data(res_annot)
    #Get clustering result
    clust_out <- cluster_exposure(result = res_annot, nclust = 2)
    #UMAP
    create_umap(result = res_annot)
    #generate cluster X signature plot
    plot_cluster(result = res_annot, clusters = clust_out, group = "signature")
    #generate cluster X annotation plot
    plot_cluster(result = res_annot, clusters = clust_out, group = "annotation",
                annotation = "Tumor_Subtypes")
    #generate a single UMAP plot
    plot_cluster(result = res_annot, clusters = clust_out, group = "none")

[Package musicatk version 1.2.0 Index]