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Scatterplot of TCR clone read fraction of clones between two samples

plot_sample_vs_sample.Rd

[Experimental] plot_sample_vs_sample() returns a scatterplot of read frequencies of TCRs between two samples.

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

Usage

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

chain

which chain to plot, alpha or beta (default is beta)

log2fc_cutoff

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

sem_cutoff

the standard-error of the mean (SEM) to use as a cutoff in calling clones expanded or contracted (default is 2.5)

pseudo1

the pseudocount to add to read frequency of the first sample (default is 10^-6).

pseudo2

the pseudocount to add to read frequency of the second sample (default is 10^-6).

labelx

the label for the x-axis

labely

the label for the y-axis

return_data

if TRUE, return the data frame used to make the plot rather than the plot itself.

smooth_sem

if "window", then SEM values for clones will be smoothed by comparing to other clones within a window of similar frequencies. Otherwise, no smoothing. (default is "window")

window_size

the number of similar clones to include within a window.

end_window_size

the number of clones to include in a window at the ends (most and least frequent)

highlight_clones

a vector of nucleotides of clones to highlight

highlight_color

a color for highlighted clones

interactive

whether to return an interactive plot (default FALSE)

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.

If return_data is TRUE, the data frame used to make the plot is returned instead of the plot.

See also

Other longitudinal: plot_clone_size_across_samples()

Examples

folder = system.file("extdata/SJTRC_TIRTL_seq_longitudinal",
  package = "TIRTLtools")
sjtrc = load_tirtlseq(folder,
  meta_columns = c("marker", "timepoint", "version"), sep = "_",
  verbose = FALSE)

plot_sample_vs_sample(sjtrc$data$cd8_tp1_v2, sjtrc$data$cd8_tp2_v2, chain = "beta")
#> Warning: Ignoring unknown aesthetics: text