om_reads_cov_plot: Plot Reads coverage distribution

In bioShaun/omplotr: store plot functions & themes for onmath projects

Plot Reads coverage distribution

Description

Plot bwa mapping coverage summrized by samtools

Usage

om_reads_cov_plot(coverage_table, sample_limit, max_depth, out_prefix = NULL)

Arguments

coverage_table	coverage stats table of all samples
sample_limit	sample number limit to show detail inform of each sample
max_depth	Sequencing depth limit to show in plot
out_prefix	output file prefix, default is NULL, don't output file

Details

Mapping coverage of each sample is generated by samtools stats sorted.bam;

Then extracted using grep

grep ^COV| cut -f 3,4

Examples

cov_stats <- system.file("extdata", "all_sample.genome.cov.xls", package = "omplotr")

# show coverage summary
om_reads_cov_plot(cov_stats, 5, 100)
# show detail sample information
om_reads_cov_plot(cov_stats, 10, 100)

bioShaun/omplotr documentation built on June 11, 2025, 7:48 a.m.