visualize_CELP: visualize_CELP

In goodarzilab/Ribolog: Logistic-regression-based analysis of ribosome profiling data

visualize_CELP

Description

Function to visualize translational stalling (CELP bias) overlaid on observed and corrected read counts.

Usage

visualize_CELP(tr_codon_read_count_loess_corrected_list, transcript,
  panel_rows = 1, panel_cols = 1, from_codon = NULL,
  to_codon = NULL, outfile = NULL)

Arguments

tr_codon_read_count_loess_corrected_list	A list of codon level read counts for all samples and transcripts. It is the second element of a tr_codon_bias_coeff_corrected_count object produced by CELP_bias. It has the following structure: list$<sample.name>$<transcript.ID> data.frame: [1] codon_number [2] codon_type [3] aa_type [4] observed_count [5] bias_coefficient [8] corrected_count.
transcript	Name of the transcript to be plotted
panel_rows	Number of rows in the case of plotting multiple samples on one page. Default: 1.
panel_cols	Number of columns in the case of plotting multiple samples on one page. Default: 1.
from_codon	Plot starts from this codon. Use this and to_codon to zoom in on particular regions of the transcript. Default: NULL (plot starts at the start codon).
to_codon	Plot ends with this codon. Use this and from_codon to zoom in on particular regions of the transcript. Default: NULL (plot stops at the stop codon).
outfile	Path and name of the output pdf file. If it is not provided, plots will be printed to standard output. Default: NULL.

Details

This function plots the CELP bias coefficient as a curve overlaid on barplots of observed read counts upward (positive y) and corrected read counts downward (in the nominal negative y range). This allows visual inspection of the prominent bias positions and a comparison of read count heterogeneity along the transcript before and after CELP bias correction.

Examples

visualize_CELP(tr_codon_bias_coeff_loess_corrected_count_LMCN$tr_codon_read_count_loess_corrected, "ENST00000000233", "<file.path>/ENST00000000233.CELP.bias.plots.pdf")
visualize_CELP(tr_codon_bias_coeff_loess_corrected_count_LMCN$tr_codon_read_count_loess_corrected, "ENST00000000233", panel_rows = 2, panel_cols = 4, "<file.path>/ENST00000000233.CELP.bias.all.in.one.page.plots.pdf")

goodarzilab/Ribolog documentation built on Oct. 7, 2022, 10:14 p.m.