plot-methods {lumi} | R Documentation |
Creating quality control plots of a LumiBatch object
## S4 method for signature 'LumiBatch, missing': plot(x, what = c("density", "boxplot", "pair", "MAplot", "sampleRelation", "outlier", "cv"), main, ...)
x |
a LumiBatch object returned by lumiQ |
what |
one of the six kinds of QC plots |
main |
the title of the QC plot |
... |
additional parameters for the corresponding QC plots |
The parameter "what" of plot
function controls the type of QC plots, which includes:
hist-methods
boxplot-methods
pairs-methods
MAplot-methods
plotSampleRelation
detectOutlier
estimateLumiCV
LumiBatch-class
, hist-methods
, boxplot-methods
, MAplot-methods
,
pairs-methods
, plotSampleRelation
, estimateLumiCV
, detectOutlier
## load example data data(example.lumi) ## Quality control estimation lumi.Q <- lumiQ(example.lumi) ## summary summary(lumi.Q) ## plot the density plot(lumi.Q, what='density') ## plot the pairwise sample correlation plot(lumi.Q, what='pair') ## plot the pairwise MAplot plot(lumi.Q, what='MAplot') ## sample relations plot(lumi.Q, what='sampleRelation', method='mds', color=c('100US', '95US:5P', '100US', '95US:5P')) ## detect outlier based on the distance to the mean profile plot(lumi.Q, what='outlier') ## Density plot of coefficient of variance plot(lumi.Q, what='cv')