Package 'PACVr'

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)

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Export the custom environment 'RCircos.Env'

Description

This function exports the custom environment 'RCircos.Env' used by RCircos.

Details

PACVr employs RCircos as its visualization engine. In its operation, RCircos defines a custom environment (called 'RCircos.Env') and reads/writes variables to this environment from various of its functions. In order to make this environment accessible to RCircos within PACVr and, simultaneously, fulfil the requirements of CRAN, this export command was created. For more information, please see the Stackoverflow post at https://stackoverflow.com/questions/56875962/r-package-transferring-environment-from-imported-package.

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