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