densityBeanPlot {minfi} | R Documentation |
Density ‘bean’ plots of methylation Beta values, primarily for QC.
densityBeanPlot(dat, sampGroups = NULL, sampNames = NULL, main = NULL, pal = brewer.pal(8, "Dark2"), numPositions = 10000)
dat |
An |
sampGroups |
Optional sample group labels. See details. |
sampNames |
Optional sample names. See details. |
main |
Plot title. |
pal |
Color palette. |
numPositions |
The density calculation uses |
This function produces the density bean plot component of the QC
report. If sampGroups
is specified, group-specific colors will
be used. For speed reasons the plots are produced using a random
subset of CpG positions. The number of positions used is specified by the
numPositions
option.
No return value. Plots are produced as a side-effect.
Martin Aryee aryee@jhu.edu.
P Kampstra. Beanplot: A boxplot alternative for visual comparison of distributions. Journal of Statistical Software 28, (2008). http://www.jstatsoft.org/v28/c01
qcReport
, mdsPlot
, controlStripPlot
, densityPlot
if (require(minfiData)) { names <- pData(RGsetEx)$Sample_Name groups <- pData(RGsetEx)$Sample_Group par(mar=c(5,6,4,2)) densityBeanPlot(RGsetEx, sampNames=names, sampGroups=groups) }