Stacked bar plot of the number of TCRs paired by each algorithm

This function plots the number of TCRs paired by each algorithm. It can also plot the number of single-chains (alpha or beta) paired by the algorithms.

Usage

plot_paired(
  data,
  chain = c("paired", "alpha", "beta"),
  samples = NULL,
  color_scheme = NULL
)

Arguments

data

a TIRTLseqDataSet object or a data frame created using get_pair_stats()

chain

the TCR chain to plot (default is "paired")

samples

(optional) the samples to include in the plot (default is all)

color_scheme

(optional) the color scheme for the plot

Value

a ggplot object with a stacked bar chart of the number of pairs called for each sample by each algorithm.

See also

Other qc: get_all_tcrs(), get_pair_stats(), get_paired_by_read_fraction_range(), plot_n_reads(), plot_num_partners(), 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(), 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(ts_data)