generateReport {sangeranalyseR} | R Documentation |
A method which generates final reports of the SangerRead, SangerContig, and SangerAlignment instance.
generateReport( object, outputDir = NULL, includeSangerContig = TRUE, includeSangerRead = TRUE, colors = "default", ... )
object |
A SangerRead, SangerContig, or 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. |
... |
Further generateReportSR, generateReportSC, and generateReportSA related parameters. |
A SangerRead
, SangerContig
, or SangerAlignment
object.
Kuan-Hao Chao
data(sangerReadFData) data(sangerContigData) data(sangerAlignmentData) ## Not run: generateReport(sangerReadFData) generateReport(sangerReadFData, colors="cb_friendly") generateReport(sangerContigData) generateReport(sangerContigData, colors="cb_friendly") generateReport(sangerAlignmentData) generateReport(sangerAlignmentData, colors="cb_friendly") ## End(Not run)