SangerContig-class-generateReportSC {sangeranalyseR} | R Documentation |
A SangerContig method which generates final reports of the SangerContig instance.
## S4 method for signature 'SangerContig' generateReportSC( object, outputDir, includeSangerRead = TRUE, colors, navigationAlignmentFN = NULL )
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 |
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. |
The output absolute path to the SangerContig's HTML file.
data("sangerContigData") ## Not run: generateReportSC(sangerContigData) generateReportSC(sangerContigData, colors="cb_friendly") ## End(Not run)