Plot the overlap/agreement between samples (in terms of most frequent clones)

This function returns a heatmap showing the overlap among the most frequent n_seq TCRs (default is n_seq=200) among pairs of samples in a dataset.

Usage

plot_sample_overlap(
  data,
  chain = c("paired", "alpha", "beta"),
  n_seq = 200,
  show_row_names = FALSE,
  show_column_names = FALSE,
  label_col = "Sample",
  title = "",
  return_data = FALSE,
  cluster_rows = TRUE,
  cluster_cols = TRUE
)

sample_overlap(...)

Arguments

data

the dataset, an object loaded using the load_tirtlseq() function

chain

which chain to plot: either paired or alpha-/beta-pseudobulk. (default "paired")

n_seq

the number of most frequent TCR sequences to use (default 200)

show_row_names

whether to show row names for the heatmap (default FALSE)

show_column_names

whether to show column names for the heatmap (default FALSE)

label_col

a column of the metadata to use as labels for rows and columns (default "Sample", uses the sample_id)

title

a title for the heatmap

return_data

whether to return the data used for plotting (a matrix with the overlap values) instead of a heatmap (default is FALSE)

cluster_rows

whether to cluster the rows of the heatmap (default TRUE)

cluster_cols

whether to cluster the columns of the heatmap (default TRUE)

Value

A heatmap with hierarchically clustered rows and columns showing the number of TCRs shared between each pair of samples, among their top N most frequent TCRs.

If return_data is TRUE, a matrix of overlap values will be returned instead.

See also

load_tirtlseq()

Other qc: get_all_tcrs(), get_pair_stats(), get_paired_by_read_fraction_range(), 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(), summarize_data()

Examples

folder = system.file("extdata/SJTRC_TIRTL_seq_longitudinal", package = "TIRTLtools")
ts_data = load_tirtlseq(folder, meta_columns = c("marker", "timepoint", "version"), sep = "_", verbose = FALSE)

plot_sample_overlap(ts_data, chain = "beta")

plot_sample_overlap(ts_data, chain = "alpha")

plot_sample_overlap(ts_data, chain = "paired")