PACVr.complete: Execute the complete pipeline of 'PACVr'

In michaelgruenstaeudl/PACVr: Plastome Assembly Coverage Visualization

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
)

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

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.

Examples

## Not run: 
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)

## End(Not run)
## Not run: 
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)

## End(Not run)

michaelgruenstaeudl/PACVr documentation built on June 14, 2025, 11:06 p.m.