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Plot read coverage graphs of contigs classified as Prophage-like, Sloping, or HighCovNoPattern

Source: R/plottingTrIdentResultsFunctions.R
plotTrIdentResults.Rd

Plot the read coverages of a contig and its associated pattern-match for Prophage-like, Sloping and HighCovNoPattern classifications. Returns a list of ggplot objects.

Usage

plotTrIdentResults(
  VLPpileup,
  WCpileup,
  TrIdentResults,
  onlyPlot,
  logScale = FALSE,
  saveFilesTo
)

Arguments

VLPpileup

VLP-fraction pileup file generated by mapping sequencing reads from a sample's ultra-purified VLP-fraction mapped to the sample's whole-community metagenome assembly. The pileup file MUST have the following format: * V1: Contig accession * V2: Mapped read coverage values averaged over 100 bp windows * V3: Starting position (bp) of each 100 bp window. Restarts from 0 at the start of each new contig. * V4: Starting position (bp) of each 100 bp window. Does NOT restart at the start of each new contig.

WCpileup

A whole-community pileup file generated by mapping sequencing reads from a sample's whole-community mapped to the sample's whole-community metagenome assembly. The pileup file MUST have the following format: * V1: Contig accession * V2: Mapped read coverage values averaged over 100 bp windows * V3: Starting position (bp) of each 100 bp window. Restarts from 0 at the start of each new contig. * V4: Starting position (bp) of each 100 bp window. Does NOT restart at the start of each new contig.

TrIdentResults

Output from `TrIdentClassifier()`.

onlyPlot

Optional, use to 'only plot' the contigs classified as either "Prophage-like", "Sloping", or "HighCovNoPattern".

logScale

TRUE or FALSE, display VLP-fraction read coverage in log10 scale. Default is FALSE.

saveFilesTo

Optional, Provide a path to the directory you wish to save output to. A folder will be made within the provided directory to store results.

Value

Large list containing ggplot objects

Examples

data("VLPFractionSamplePileup")
data("WholeCommunitySamplePileup")
data("TrIdentSampleOutput")

patternMatches <- plotTrIdentResults(
  VLPpileup = VLPFractionSamplePileup,
  WCpileup = WholeCommunitySamplePileup,
  TrIdentResults = TrIdentSampleOutput
)