plotChipLayout: Function to Plot the Layout of an Illumina BeadChip

In beadarray: Quality assessment and low-level analysis for Illumina BeadArray data

Description

Using the values obtained from a sentrix descriptor object generated by simpleXMLparse, a plot is generated showing samples and sections.

Usage

plotChipLayout(SD, subsC = NULL, sampC = NULL, sectC = NULL, desectC = "red", markC = "white", main = NULL, samplab = NULL, sectlab = NULL)

Arguments

SD	A sentrix descriptor object such as that generated by simpleXMLparse from an Illumina sdf file
subsC	The colour for the array substrate. Will be extracted from the sentrix descriptor object if null.
sampC	The colour for the samples. Will be extracted from the sentrix descriptor object if null.
sectC	The colour for the sections. Will be extracted from the sentrix descriptor object if null.
desectC	The colour with which to outline the decode sections
markC	The colour for plotting decoding and analytical markers
main	A title to give the figure (e.g. chip name)
samplab	labels for the samples. Will be extracted from the sentrix descriptor object if null.
sectlab	labels for the sections (if appropriate). Will be extracted from the sentrix descriptor object if null.

Value

returns a plot to the current device (recommend this is tall and thin)

Author(s)

Andy Lynch

Examples

## SD<-simpleXMLparse(mysdf)
## plotChipLayout(SD)

beadarray documentation built on Nov. 8, 2020, 4:51 p.m.