immuneSIM (version 0.8.7)

plot_repertoire_A_vs_B: Comparative plots of main repertoire features of two input repertoires (length distribution, amino acid frequency, VDJ usage, kmer occurrence)

Description

Comparative plots of main repertoire features of two input repertoires (length distribution, amino acid frequency, VDJ usage, kmer occurrence)

Usage

plot_repertoire_A_vs_B(repertoire_A, repertoire_B,
  names_repertoires = c("Repertoire_A", "Repertoire_B"),
  length_aa_plot = 14, output_dir = "", verbose = TRUE)

Arguments

repertoire_A

An annotated AIRR-compliant immuneSIM repertoire.

(http://docs.airr-community.org/en/latest/)

repertoire_B

An annotated AIRR-compliant immuneSIM repertoire.

names_repertoires

A vector containing two strings denoting the names of the repertoires / repertoire descriptions.

length_aa_plot

Defines sequence length for which the amino acid frequency plot will be made.

output_dir

String containing full path of desired output folder. If empty, figures will be output in tempdir().

verbose

Determines whether messages on plot locations are output to user. (Default: TRUE)

Value

TRUE (plots saved as pdfs into subfolder 'figures')

Examples

# NOT RUN {
repertoire_A <- list_example_repertoires[["example_repertoire_A"]]
repertoire_B <- list_example_repertoires[["example_repertoire_B"]]
plot_repertoire_A_vs_B(
repertoire_A,
repertoire_B,
c("Sim_repertoire_1","Sim_repertoire_2"),
length_aa_plot = 14,
output_dir="")
# }