Binomix objectsGeneric functions for Binomix objects.
# S3 method for Binomix
plot(x, type = "pan", cex = 2, ncomp = NA,
show.bar = TRUE, ...)# S3 method for Binomix
summary(object, ...)
A Binomix object, see below.
Type of plot, default is type="pan" which means the pie chart shows distribution over the entire pan-genome. The alternative is type="single" which means the pie chart will show the distribution within a single (average) genome.
Plot symbol scaling.
Which model to display. You can override the display of the optimal (minimum BIC) model by specifying the number of components here, e.g. ncomp=5 will always display the model with 5 components regardless of its BIC value.
Logical indicating if a colorbar should be displayed next to the pie.
Optional graphical arguments.
A Binomix object, see below.
A Binomix object contains a series of fitted binomial mixture models. It is a small
(S3) extension to a list, having two components. These are named BIC.table and
Mix.list, see binomixEstimate for more details.
The plot.Binomix function will display a Binomix object as a pie chart. Only
the model with the smallest BIC-criterion value is displayed. The BIC-criterion is used to rank the
various fitted models, and minimum BIC is an objective criterion for finding the best model complexity.
Each sector of the pie chart is a component, the color of the sector indicates its detection probability
and the size of the sector its mixing proportion. This pie chart illustrates how gene clusters are
distributed within the pan-genome. Sectors of (dark) blue color are highly conserved gene clusters
(core genes), sectors of greenish colors are medium conserved clusters (shell genes) and sectors of
orange/pink colors are non-conserved clusters (cloud genes).
The summary.Binomix function will print the estimated core size and pan-genome size for
the optimal component model.
# NOT RUN {
# See examples in the Help-file for binomixEstimate.
# }
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