plot-methods {lumi} | R Documentation |
Creating quality control plots of a ExpressionSet object
## S4 method for signature 'ExpressionSet,missing' plot(x, what = c("density", "boxplot", "pair", "MAplot", "sampleRelation", "outlier", "cv"), main, ...)
x |
a ExpressionSet object returned by |
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:
density: the density plot of the chips, see hist-methods
boxplot: box plot of the chip intensities, see boxplot-methods
pair: the correlation among chips, plot as a hierarchical tree, see pairs-methods
MAplot: the MAplot between chips, see MAplot-methods
sampleRelation: plot the sample relations. See plotSampleRelation
outlier: detect the outliers based on the sample distance to the center. See
detectOutlier
cv: the density plot of the coefficients of variance of the chips. See 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')