Line plot of clonotype rank vs. read fraction for each sample

plot_ranks() returns a line plot of TCR rank vs. read fraction for a given sample.

Usage

plot_ranks(
  data,
  chain = c("beta", "alpha"),
  column = "readFraction",
  color_scheme = NULL
)

rank_plot(...)

Arguments

data

a TIRTLseqDataSet object

chain

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

column

the variable to plot (default is "readFraction")

color_scheme

(optional) the color scheme for the plot

Value

a ggplot object with the rank 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_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_ranks(ts_data, chain = "beta")