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 )
The result generated from cluster_exposure function.
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".
Column name of annotation.
If TRUE, the plot will be made interactive using plotly.
Generate a ggplot or plotly object.
set.seed(123) data(res_annot) #Get clustering result clust_out <- cluster_exposure(result = res_annot, nclust = 2)#>#> Warning: FANNY algorithm has not converged in 'maxit' = 10 iterations#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")