Scatterplot of TCR clone read fraction of clones between two samples

plot_sample_vs_sample() returns a scatterplot of read frequencies of TCRs between two samples

Usage

plot_sample_vs_sample(
  data1,
  data2,
  chain = c("beta", "alpha"),
  log2fc_cutoff = 3,
  sem_cutoff = 2.5,
  smooth_sem = c("window", "none"),
  window_size = 30,
  end_window_size = 5,
  pseudo1 = 1e-06,
  pseudo2 = 1e-06,
  labelx = "Frequency on timepoint 1",
  labely = "Frequency on timepoint 2",
  return_data = FALSE
)

Arguments

data1

a list of three data frames (alpha, beta, and paired) for one sample

data2

a list of three data frames (alpha, beta, and paired) for one sample

log2_cutoff

the log2 fold-change cutoff to call a TCR up- or down-regulated (default 1.5)

Value

A scatterplot (ggplot object) with read frequencies (proportions), colored by whether each TCR is up-regulated, down-regulated, or neither, given the log2 fold-change cutoff.

Details

The function labels each TCR as up-regulated, down-regulated, or stable, based on the log2 fold-change cutoff supplied (default 1.5).

See also

Other plotting: plot_clone_size_across_samples(), plot_clonotype_indices(), plot_clusters(), plot_diversity(), plot_n_reads(), plot_num_partners(), 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()

Examples

# example code