create_html_report: Create the Ribo-seQC analysis report in html

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

Create the Ribo-seQC analysis report in html

Description

This function creates the Ribo-seQC html report based on the Ribo-seQC analysis files generated with RiboseQC_analysis.

Usage

create_html_report(input_files, input_sample_names, output_file,
  extended = F)

Arguments

input_files	Character vector with full paths to data files generated with RiboseQC_analysis. Must be of same length as input_sample_names.
input_sample_names	Character vector containing input names (max. 5 characters per name). Must be of same length as input_files.
output_file	String; full path to html report file.
extended	creates a large html report including codon occupancy for each read length. Defaults to FALSE

Details

This function creates the html report visualizing the RiboseQC analysis data.

Input are two lists of the same length:

a) input_files: list of full paths to one or multiple input files (Ribo-seQC analysis files generated with RiboseQC_analysis) and

b) input_sample_names: list of corresponding names describing the file content in max. 5 characters (these are used as names in the report).

For the report, a RMarkdown file is rendered as html document, saved as output_file.

Additionally, all figures in the report are saved as PDF figures in an extra folder in the same directory as the report html file.

Example:
output_file <- "\mydir\myreport.html" will generate the html report \mydir\myreport.html and the folder \mydir\myreport_plots\ for the RDS object files to be stored in.

Value

The function saves the html report file with the file path output_file and a folder containing all figures shown in the html report as RDS object files (located in the same directory as the html report).

Author(s)

Dominique Sydow, [e-mail]

See Also

plot_read_biotype_dist_1, plot_read_biotype_dist_2, plot_read_length_dist, plot_read_length_dist_by_biotype, plot_read_biotype_dist_by_length, get_metagene_data, plot_metagene_hm_rmd, plot_metagene_hm, plot_metagene_bar_rmd, plot_metagene_bar, plot_frame_dist_boxplot_rmd, plot_frame_dist_boxplot, get_rl_and_cutoffs, get_default_rl_selection, get_top50_mapping, get_top50_cds_genes, get_top50_all_genes, get_codon_usage_data, plot_codon_usage_positional_rmd, plot_codon_usage_positional, plot_codon_usage_bulk_rmd, plot_codon_usage_bulk

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