PACVr (version 1.0.11)

PACVr.complete: Execute the complete pipeline of PACVr

Description

This function executes the complete pipeline of PACVr via a single command.

Usage

PACVr.complete(
  gbkFile,
  bamFile,
  windowSize = 250,
  logScale = FALSE,
  threshold = 0.5,
  IRCheck = NA,
  relative = TRUE,
  textSize = 0.5,
  tabularCovStats = FALSE,
  output = NA
)

Value

A file in pdf format containing a circular visualization of the input plastid genome and its sequence reads. As a function, returns 0 in case of visualization success.

Arguments

gbkFile

a character string that specifies the name of, and path to, the GenBank input file; alternatively, a character string of GenBank data

bamFile

a character string that specifies the name of, and path to, the BAM input file

windowSize

a numeric value that specifies window size in which the coverage is calculated

logScale

a boolean that specifies if the coverage depth is to be log-transformed before visualizing it

threshold

a numeric value that specifies the threshold for plotting coverage depth bars in red as opposed to the default black

IRCheck

a numeric value that specifies if tests for IRs of input genome should be performed, and - if IRs are present - which line type to be used for visualizing gene synteny between IRs; 0 = IR presence test but no synteny visualization, 1 = IR presence test and synteny visualization, with ribbon lines between IRs, 2 = IR presence test and synteny visualization, with solid lines between IRs, otherwise = neither IR presence test nor synteny visualization

relative

a boolean that specifies whether the threshold is a relative value of the average coverage instead of an absolute value

textSize

a numeric value that specifies the relative font size of the text element in the visualization

tabularCovStats

a boolean, that when TRUE, generates additional files with detailed genomic region information

output

a character string that specifies the name of, and path to, the output file

Examples

if (FALSE) {
gbkFile <- system.file("extdata", "NC_045072/NC_045072.gb", package="PACVr")
bamFile <- system.file("extdata", "NC_045072/NC_045072_subsampled.bam", package="PACVr")
outFile <- paste(tempdir(), "/NC_045072__all_reads.pdf", sep="")
PACVr.complete(gbkFile=gbkFile, bamFile=bamFile, windowSize=250, logScale=FALSE,
               threshold=0.5, IRCheck=1, relative=TRUE, textSize=0.5,
               tabularCovStats=FALSE, output=outFile)
}
if (FALSE) {
gbkFile <- system.file("extdata", "MG936619/MG936619.gb", package="PACVr")
bamFile <- system.file("extdata", "MG936619/MG936619_subsampled.bam", package="PACVr")
outFile <- paste(tempdir(), "/MG936619_CoverageViz.pdf", sep="")
PACVr.complete(gbkFile=gbkFile, bamFile=bamFile, windowSize=50, logScale=FALSE,
               threshold=0.5, IRCheck=NA, relative=TRUE, textSize=0.5,
               tabularCovStats=FALSE, output=outFile)
}