plot_diagnostic: Generate diagnostic plots

In amandamok/choros: Bias Correction for Ribosome Profiling Data

Generate diagnostic plots

Description

This function generates diagnostic plots: RPF density at the start codon; RPF density at the stop codon; histogram of RPF lengths; heatmap of RPF counts by RPF length and frame

Input '.bam' file must contain 'tag.ZW' of posterior weights computed from 'RSEM'

Usage

plot_diagnostic(
  bam_fname,
  transcript_length_fname,
  plot_title = "",
  start_min = -20,
  start_max = 5,
  stop_min = -5,
  stop_max = 20,
  length_min = 15,
  length_max = 35
)

Arguments

bam_fname	character; file path to .bam alignment file
transcript_length_fname	character; file path to transcriptome lengths file
plot_title	character; title for diagnostic plot
start_min	integer; 5'-most position to include in plot, relative to start codon
start_max	integer; 3'-most position to include in plot, relative to start codon
stop_min	integer; 5'-most position to include in plot, relative to stop codon
stop_max	integer; 3'-most position to include in plot, relative to stop codon
length_min	integer; minimum RPF length
length_max	integer; maximum RPF length

Value

A patchwork object of diagnostic plots

amandamok/choros documentation built on March 15, 2023, 7:57 p.m.