plot_frame_dist_boxplot: Plot frame coverage of 5'-site profiles

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

Plot frame coverage of 5'-site profiles

Description

This function plots the frame coverage of 5'-site profiles, i.e. the fraction of reads (their 5' end) in frame 0, 1, and 2 (defined by start codon), as boxplots (per-frame distributions over all transcripts) for individual read lengths as well as for all read lengths summarized.

Usage

plot_frame_dist_boxplot(analysis_frame_cutoff, comp, sample = "",
  output_rds_path = "")

Arguments

analysis_frame_cutoff	Object containing statistics on frame coverage (per originating compartment and read length) generated by RiboseQC_analysis. Example: res_all$selection_cutoffs$analysis_frame_cutoff
comp	String for originating compartment Check for available originating compartments in the data set using: names(res_all$profiles_fivepr$five_prime_subcodon)
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.

Details

This plot is used in the Ribo-seQC report in section 4.2.1.

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.