Visualize clustering results

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.

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

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.

plotly

If TRUE, the plot will be made interactive using plotly.

Value

Generate a ggplot or plotly object.

See also

create_umap

Examples

set.seed(123)
data(res_annot)
#Get clustering result
clust_out <- cluster_exposure(result = res_annot, nclust = 2)
#> Metric: 'euclidean'; comparing: 7 vectors.
#> Warning: FANNY algorithm has not converged in 'maxit' = 10 iterations
#UMAP
create_umap(result = res_annot)
#> The parameter 'n_neighbors' cannot be bigger than the total number of samples. Setting 'n_neighbors' to 7.
#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")