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

In PACVr: Plastome Assembly Coverage Visualization

Description

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

Usage

PACVr.complete(
  gbk.file,
  bam.file,
  windowSize = 250,
  logScale = FALSE,
  threshold = 0.5,
  syntenyLineType = 1,
  relative = TRUE,
  textSize = 0.5,
  delete = TRUE,
  output = NA
)

Arguments

gbk.file	a character vector that specifies the name of, and path to, the GenBank input file
bam.file	a character vector 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
syntenyLineType	a numeric value of 1, 2 or 3 that specifies the line type for visualizing IR gene synteny; 1 = ribbon lines, 2 = solid lines, 3 = no line
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
delete	the decision to delete temporary files upon program execution
output	a character vector that specifies the name of, and path to, the output file

Examples

## Not run: 
gbkFile <- system.file("extdata", 
                       "NC_045072/NC_045072.gb", 
                       package="PACVr")
bamFile <- system.file("extdata", 
                       "NC_045072/NC_045072_PlastomeReadsOnly.sorted.bam", 
                       package="PACVr")
outFile <- paste(tempdir(), "/NC_045072__all_reads.pdf", sep="")
PACVr.complete(gbk.file=gbkFile, bam.file=bamFile, windowSize=250,
               threshold=0.5, syntenyLineType=1, relative=TRUE, textSize=0.5, 
               delete=TRUE, output=outFile
               
## End(Not run)

PACVr documentation built on Nov. 23, 2020, 1:07 a.m.