A step plot of the cumulative number of paired/unpaired alpha/beta chains among the most frequent chains

The function creates a stepped line plot of the cumulative number of paired/unpaired alpha or beta chains (default is both) among the n_max most frequent chains.

Usage

plot_paired_vs_rank(
  data,
  sample,
  y_axis = c("n_not_paired", "n_paired"),
  chain = c("both", "beta", "alpha"),
  n_max = 100,
  color_scheme = NULL
)

Arguments

data

a TIRTLseqDataSet object

sample

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

y_axis

whether to plot the cumulative number of paired or un-paired single-chains (default is "n_not_paired")

chain

the TCR chain to plot (default is both alpha and beta)

n_max

the number of most frequent single-chains to plot

color_scheme

(optional) the color scheme for the plot

Value

A ggplot object with the 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_pairs_with_eachother(), plot_ranks(), plot_read_fraction_vs_pair_status(), 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_paired_vs_rank(ts_data, sample = 1, y_axis = "n_not_paired", chain = "both", n_max = 100)


plot_paired_vs_rank(ts_data, sample = 1, y_axis = "n_paired", chain = "both", n_max = 100)