| 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-methodsboxplot-methodspairs-methodsMAplot-methodsplotSampleRelationdetectOutlierestimateLumiCV
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')