Plot clusters of similar TCRs

plot_clusters() plots TCRs that were previously clustered by the cluster_tcrs() function.

Usage

plot_clusters(
  obj,
  n_clusters = 10,
  seed = 1234,
  annotation_cols = c("cluster", "source"),
  color_col = "cluster"
)

Arguments

obj

an object returned by the cluster_tcrs() function

n_clusters

the number of clusters to plot (default 10)

seed

a number to use as the seed. Using the same number across multiple runs allows for reproducible results.

annotation_cols

columns to use for heatmap annotations (default is the cluster and the source, i.e. your data or vdj-db)

color_col

a column to use to color nodes in the network visualization (default is "cluster")

Value

Currently returns a list with three items: $umap - a umap visualization of the TCRs from the top clusters

$graph - a graph/network visualization of TCRs from the top clusters

$heatmap - a heatmap visualization of TCRs from the top clusters

Details

The function currently returns a list with a UMAP plot, a graph/network plot, and a heatmap.

See also

cluster_tcrs(), TCRdist()

Other plotting: plot_clone_size_across_samples(), plot_clonotype_indices(), plot_diversity(), plot_n_reads(), plot_num_partners(), plot_paired(), plot_paired_by_read_fraction_range(), plot_paired_vs_rank(), plot_pairs_with_eachother(), plot_ranks(), plot_read_fraction_vs_pair_status(), plot_sample_overlap(), plot_sample_vs_sample()

Examples

# example code
# paired = load_tirtlseq("your_directory/")
# obj = cluster_tcrs(paired)
# plot_clusters(obj)