SangerContig-class-generateReportSC: generateReportSC

In roblanf/sangeranalyseR: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

generateReportSC

Description

A SangerContig method which generates final reports of the SangerContig instance.

Usage

## S4 method for signature 'SangerContig'
generateReportSC(
  object,
  outputDir,
  includeSangerRead = TRUE,
  colors,
  navigationAlignmentFN = NULL
)

Arguments

object	A SangerContig S4 instance.
outputDir	The output directory of the generated HTML report.
includeSangerRead	The parameter that decides whether to include SangerRead level report. The value is TRUE or FALSE and the default is TRUE.
colors	A vector for users to set the colors of (A, T, C, G, else). There are three options for users to choose from. 1. "default": (green, blue, black, red, purple). 2. "cb_friendly": ((0, 0, 0), (199, 199, 199), (0, 114, 178), (213, 94, 0), (204, 121, 167)). 3. Users can set their own colors with a vector with five elements.
navigationAlignmentFN	The internal parameter passed to HTML report. Users should not modify this parameter on their own.

Value

The output absolute path to the SangerContig's HTML file.

Examples

data("sangerContigData")
## Not run: 
generateReportSC(sangerContigData)
generateReportSC(sangerContigData, colors="cb_friendly")
## End(Not run)

roblanf/sangeranalyseR documentation built on April 15, 2024, 12:44 a.m.