Stacked bar chart with fractions of reads attributed to the most frequent clonotypes

plot_clonotype_indices() creates a stacked bar chart containing the fraction of reads for the top 10 most frequent clonotypes, the 11th to 100th most frequent clonotypes, the 101st to 1000th most frequent, and so on, for each sample in the dataset.

Usage

plot_clonotype_indices(
  data,
  chain = c("beta", "alpha"),
  cutoffs = 10^(1:5),
  group_col = NULL,
  label_col = "Sample",
  flip = FALSE,
  return_data = FALSE,
  color_scheme = NULL
)

Arguments

data

a TIRTLseqDataSet object

chain

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

cutoffs

the indices used for the end of each group in the bar chart. The default is 10^(1:5), i.e. the 10th most-frequent clone, the 100th most-frequent clone, the 1,000th, the 10,000th, and the 100,000th.

group_col

(optional) if supplied, a column of the metadata that will be used to group samples

label_col

(optional) labels for the samples

flip

(optional) if TRUE, flip the x and y-axes (default is FALSE)

return_data

(optional) if TRUE, return the data used to make the plot (default is FALSE)

color_scheme

(optional) a color scheme to use

Value

Returns a stacked bar chart of relative frequencies of most-frequent clonotypes. If return_data is TRUE, the data frame used to create the plot is returned instead.

See also

diversity(), plot_diversity()

Other diversity: calculate_diversity(), get_all_div_metrics(), plot_diversity()

Examples

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

plot_clonotype_indices(data, chain = "beta")