[ RDocumentation ](/)

Moon  [ ](https://github.com/datacamp/rdocumentation-2.0) [ Learn R
](https://www.datacamp.com/learn/r)

Search all packages and functions

[ micropan  (version  1.0  ) ](/packages/micropan/versions/1.0)

#  plot.Binomix: Plotting and printing ` Binomix ` objects

##  Description

Generic functions for plotting and printing the content of a ` Binomix `
object.

##  Usage

    
    
    "plot"(x, type="pan", cex=2, ncomp=NA, ...)
    "summary"(object, ...)
    "str"(object, ...)

##  Arguments

x

A ` Binomix ` object, see below.

object

A ` Binomix ` object, see below.

type

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.

cex

Plot symbol scaling.

ncomp

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.

...

Optional graphical arguments.

##  Details

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
](/link/binomixEstimate?package=micropan&version=1.0) ` for more details. The
` [ plot.Binomix ](/link/plot.Binomix?package=micropan&version=1.0) ` 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
](/link/summary.Binomix?package=micropan&version=1.0) ` function will print
the estimated core size and pan-genome size for the optimal component model.
The ` [ str.Binomix ](/link/str.Binomix?package=micropan&version=1.0) `
function will simply print the number of models fitted in the ` Binomix `
object.

##  See Also

` [ binomixEstimate ](/link/binomixEstimate?package=micropan&version=1.0) ` .

##  Examples

[ Run this code
](https://www.datacamp.com/datalab/preview?_tag=rdocs&rdocsPath=packages%2Fmicropan%2Fversions%2F1.0%2Ftopics%2Fplot.Binomix&utm_source=r-docs&utm_medium=docs&utm_term=plot.Binomix&utm_content=run_example_in_datalab)

    
    
    # See examples in the Help-file for binomixEstimate.
    

Run the code above in your browser using  [ DataLab
](https://www.datacamp.com/datalab/preview?_tag=rdocs&rdocsPath=packages%2Fmicropan%2Fversions%2F1.0%2Ftopics%2Fplot.Binomix&utm_source=r-docs&utm_medium=docs&utm_term=plot.Binomix&utm_content=run_example_in_datalab)

Powered by  [ DataCamp ](https://www.datacamp.com/)