plot_codon_usage_bulk: Plot bulk codon usage bar plots

In ohlerlab/RiboseQC: RiboseQC, a Comprehensive Ribo-Seq Analysis Tool

Plot bulk codon usage bar plots

Description

This function plots the codon usage summed up over all positions* (bulk codon usage) as bar plot for a specific data type, originating compartment, and read length, as well as based on a user-defined genetic code.

* Information on positions included in analysis:
Based on P-site corrected reads, the codon usage within CDS regions for protein coding genes is examplatory calculated

• for the first 11 codons of the CDS (referred to as start),

• for 11 codons from the middle of the CDS (referred to as middle), and

• for the last 11 codons of the CDS (referred to as stop).

Usage

plot_codon_usage_bulk(codon_usage_data, sample = "",
  output_rds_path = "")

Arguments

sample	String; sample name (selected from the input names given in the input_sample_names parameter of create_html_report).
output_rds_path	String; full path to output folder for RDS object files created by this function. Defaults to NOT save RDS; to save RDS, provide path to destination folder.
codon_usage_bulk_data	List containing codon usage bulk data and meta data, generated by get_codon_usage_data.

Value

This function returns a plot that can be integrated in the html report and that can be saved as RDS object file.

Author(s)

Dominique Sydow, [e-mail]

See Also

create_html_report

ohlerlab/RiboseQC documentation built on Aug. 15, 2023, 7:30 a.m.