In sagrudd/nanopoRe: Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
)
library(nanopoRe)
library(knitr)
library(emojifont)
init()
setOutputFormat("file")

# this is not a promethION dataset - but we need a dataset for vignette testing
# at TRAVIS - don't see case for adding another 5Mb file that is essentially
# the same as MinION dataset below (other than additional channel data ...)
seqsumFile <- system.file("extdata", "sequencing_summary.txt.bz2", 
    package = "nanopoRe")

importSequencingSummary(seqsumFile)

include_graphics( SequenceSummaryExecutiveSummary() )

include_graphics( SequencingSummaryPassGauge() )

include_graphics( SequencingSummaryChannelActivity() )

include_graphics( SequenceSummaryBasicInfoPlot() )

include_graphics( SequencingSummaryWeightedReadLength() )

include_graphics( SequencingSummaryReadLengthHistogram() )

include_graphics( SequencingSummaryReadQualityHistogram() )

include_graphics( SequencingSummaryReadLengthQualityDensity(binFilter=5) )

include_graphics( SequencingSummaryTemporalThroughput() )

include_graphics( SequencingSummaryCumulativeBases() )

include_graphics( SequencingSummaryCumulativeReads() )

include_graphics( SequencingSummarySpeedPlot() )

include_graphics( SequencingSummaryActiveChannelPlot() )

if (SequencingSummaryHasBarcodeInfo()) {
    include_graphics( SequenceSummaryBarcodeInfoGraphic() )
}

if (SequencingSummaryHasBarcodeInfo()) {
    SequenceSummaryBarcodeTable()
}

if (SequencingSummaryHasBarcodeInfo()) {
    include_graphics( SequenceSummaryBarcodeHistogram() )
}

sagrudd/nanopoRe documentation built on June 7, 2020, 10:20 p.m.