plotReadCategoryCounts: Plot the proportion of template, complement and 2D reads...

In grimbough/IONiseR: Quality Assessment Tools for Oxford Nanopore MinION data

Description

Generates a bar plot showing the breakdown of read types found in a set of fast5 files. There is a strict hierarchy to the types of read that can be found in a fast5 file. A full 2D read requires both a complement and template strand to have been read correctly. Similarly, a complement strand can only be present if the template was read successfully. Finally, you can encounter a file containing now called bases on either strand. Here we visualise the total number of fast5 files, along with the counts containing each of the categories above. For an ideal dataset all four bars will be the same height. This is unlikely, but the drop between bars can give some indication of data quality.

Usage

plotReadCategoryCounts(summaryData)

Arguments

summaryData

Object of class Fast5Summary.

Value

Returns an object of class gg representing the plot.

Examples

if( require(minionSummaryData) ) {
   data(s.typhi.rep2, package = 'minionSummaryData')
   plotReadCategoryCounts( s.typhi.rep2 )
}

grimbough/IONiseR documentation built on Sept. 24, 2020, 11:32 a.m.