plot_repertoire_A_vs_B: Comparative plots of main repertoire features of two input...

Description Usage Arguments Value Examples

View source: R/plot_repertoire_A_vs_B.R

Description

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

Usage

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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

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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="")

immuneSIM documentation built on Sept. 27, 2019, 5:02 p.m.