A point plot of read fraction vs. rank for the most frequent alpha/beta chains

This function creates two point plots (alpha left, beta right) of the n_max most frequent single-chains found in a sample.

This function creates a plot similar to plot_pairs_with_eachother(), but does not mirror the alpha chains plot and add connections between paired alpha and beta chains.

Usage

plot_read_fraction_vs_pair_status(
  data,
  sample,
  chain = c("both", "beta", "alpha"),
  n_max = 100,
  show_num_partners = F,
  color_scheme = NULL
)

Arguments

data

a TIRTLseqDataSet object

sample

the sample to plot (either by number or sample id)

chain

the chain to plot, "alpha", "beta", or "both" (default is "both")

n_max

the number of most frequent single-chains to plot

show_num_partners

whether to show the number of partners for each single-chain (default is FALSE)

color_scheme

(optional) the color scheme for the plot

Value

A ggplot object with the point plot

See also

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_sample_overlap(), 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_read_fraction_vs_pair_status(ts_data, sample = 1, n_max = 100)


plot_read_fraction_vs_pair_status(ts_data, sample = 1, n_max = 100,
show_num_partners = TRUE)