Stacked bar plot of the fraction of alpha/beta chains with different numbers of partners

plot_num_partners() creates bar plots for alpha and beta chains showing how many partners they are paired with by the MAD-HYPE and/or T-shell algorithms.

Usage

plot_num_partners(
  data,
  group_col = NULL,
  fraction = TRUE,
  include_non_functional = FALSE,
  max_partners = 5,
  samples = NULL,
  return_data = FALSE,
  color_scheme = NULL
)

Arguments

data

a TIRTLseqDataSet object

group_col

a column of the metadata to use to group multiple samples into one bar plot The default is NULL, which uses the sample id.

fraction

whether to plot the fraction of chains or the total number of chains (default is TRUE, i.e. plot fractions)

include_non_functional

whether to include chains with non-functional cdr3 sequences when tabulating the output.

max_partners

the maximum number of partners, N, to include in the plots. All chains with more than N partners will be grouped together under the ">N" category.

samples

(optional) which samples to plot

return_data

if TRUE, return the data used to make the plots

color_scheme

the color scheme to use for the plot

Value

A bar chart (ggplot object) with facets (sub-plots) for each sample. If return_data is TRUE, the data frame used to create the plot is returned instead.

Details

For each sample, the function creates stacked bar charts for alpha and beta chains, showing the proportion of them (among all called pairs) that are paired with 1 chain, 2 chains, 3 chains, etc.

See also

identify_non_functional_seqs()

Other qc: get_all_tcrs(), get_pair_stats(), get_paired_by_read_fraction_range(), plot_n_reads(), plot_paired(), 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_num_partners(ts_data)