plot.iC10 | R Documentation |
Plot results of the iC10 classifier, in two different formats: either the signatures of the training set or the signatures of the new data classified.
## S3 method for class 'iC10'
plot(x, sample.name=1, newdata = NULL,...)
x |
An object of |
sample.name |
Number of sample to plot (if |
newdata |
An object result to call to |
... |
Additional arguments passed to |
Two types of plots can be produced. If newdata
is NULL, a panel 6x2 is drawn with the 10 profiles
of the signatures of the training set and the profile of the features of sample.name
and the
distribution of the probabilities of classification to each iC10 for that sample.
If newdata
is not nutll, a panel 6x2 (with the 11th panel empty) is drawn with the 10 profiles of
newdata
samples and their distribution into the clusters.
The features are sorted by type: copy number (if available) are drawn in grey, and then expression, each
of them are sorted by genomic position.
A 6x2 plot is produced.
Oscar M Rueda
Ali HR et al. Genome-driven integrated classification of breast cancer validated in over 7,500 samples. Genome Biology 2014; 15:431. Curtis et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 2012; 486:346-352.
iC10
require(iC10TrainingData)
data(train.CN)
data(train.Exp)
features <- matchFeatures(Exp=train.Exp, Exp.by.feat="probe")
features <- normalizeFeatures(features, "scale")
res <- iC10(features)
plot(res, sample.name=10)
plot(res, newdata=features)
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