SangerAlignment-class-generateReportSA: generateReportSA

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

generateReportSA

Description

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

Usage

## S4 method for signature 'SangerAlignment'
generateReportSA(
  object,
  outputDir,
  includeSangerContig = TRUE,
  includeSangerRead = TRUE,
  colors
)

Arguments

object	A SangerAlignment S4 instance.
outputDir	The output directory of the generated HTML report.
includeSangerContig	The parameter that decides whether to include SangerContig level report. The value is TRUE or FALSE and the default is TRUE.
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.

Value

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

Examples

data("sangerAlignmentData")
## Not run: 
generateReportSA(sangerAlignmentData)
generateReportSA(sangerAlignmentData, colors="cb_friendly")
## End(Not run)

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