Bar plot of the fraction of paired single chains by frequency

This function returns a bar plot of the fraction of single-chains (alpha or beta, default is beta) that were paired within different frequency ranges (default is [10^-1, 10^-2], [10^-2, 10^-3], ... , [10^-5,10^-6], [10^-6, 0]) for each sample.

Usage

plot_paired_by_read_fraction_range(
  data,
  chain = c("beta", "alpha"),
  cutoffs = 10^(-6:-1),
  freq = FALSE,
  samples = NULL,
  color_scheme = NULL
)

Arguments

data

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

chain

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

cutoffs

a vector of cutoffs for the read fraction ranges

freq

if TRUE, plot the number of pairs, if FALSE plot the fraction paired (default is FALSE, plot the fraction paired)

samples

(optional) the samples to include in the plot

color_scheme

(optional) the color scheme to use in the plot

Value

a ggplot object with the bar plot of fraction of paired chains by frequency

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_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_by_read_fraction_range(ts_data, chain = "beta")