R: Plot the correlation densities of the empirical fit, mixture...
mixture.plot.JointUniquePairs
R Documentation
Plot the correlation densities of the empirical fit, mixture fit and each
of the mixture components for a mixture object derived from JointUniquePairsand Corr objects
Description
Plot the correlation densities of the empirical fit, mixture fit and each of the mixture components
for a mixture object derived from UniquePairsMatch and Corr objects with optional subsetting
by a group of ID Maps. This is achived by first creating a mixture model from the JointUniquePairs
and Corr objects with optional subsetting by a group of ID Maps encapsulated within the and then calling the MixtureObject.plot()
on a resulting Mixture object.
Usage
## S3 method for class 'JointUniquePairs'
mixture.plot(this, corr, idMapNames=NULL, subsetting=FALSE, G=c(1:5), verbose=FALSE, ...)
Arguments
corr
Corr object.
idMapNames
If not NULL, defines the subset of ID Maps from JointUniquePairs
on which the full event group is to be formed. Default is NULL.
subsetting
If TRUE, uses Corr subset to compute the mixture model or uses
the original Corr otherwise. Default is FALSE.
G
The number of mixture model components. If a numeric vector,
the optimal mixture model is computed. Default is c(1:5).
verbose
If TRUE enables diagnostic messages. Default is FALSE.
...
Additional graphical parameters
Value
The Mixture object plotted
Author(s)
Alex Lisovich, Roger Day
See Also
For more information see JointUniquePairs.
Examples
#plot the results of mixture fit for a given DB subset and a Corr object (corr.spearman)
mixtureSet<-examples$jointUniquePairs$mixture.plot(examples$corr,
idMapNames=c("NetAffx_Q","DAVID_Q","EnVision_Q"),
subsetting=TRUE,G=c(1:5),verbose=TRUE);
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(IdMappingAnalysis)
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.20.0 (2016-02-17) successfully loaded. See ?R.oo for help.
Attaching package: 'R.oo'
The following objects are masked from 'package:methods':
getClasses, getMethods
The following objects are masked from 'package:base':
attach, detach, gc, load, save
Loading required package: rChoiceDialogs
Loading required package: rJava
Attaching package: 'rJava'
The following object is masked from 'package:R.oo':
clone
This is rChoiceDialogs 1.0.6 2014-09-05
This is IdMappingAnalysis 1.16.0 2013-05-24
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/IdMappingAnalysis/mixture.plot.JointUniquePairs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mixture.plot.JointUniquePairs
> ### Title: Plot the correlation densities of the empirical fit, mixture fit
> ### and each of the mixture components for a mixture object derived from
> ### JointUniquePairsand Corr objects
> ### Aliases: mixture.plot.JointUniquePairs JointUniquePairs.mixture.plot
> ### mixture.plot,JointUniquePairs-method
> ### Keywords: internal methods
>
> ### ** Examples
>
> #plot the results of mixture fit for a given DB subset and a Corr object (corr.spearman)
> mixtureSet<-examples$jointUniquePairs$mixture.plot(examples$corr,
+ idMapNames=c("NetAffx_Q","DAVID_Q","EnVision_Q"),
+ subsetting=TRUE,G=c(1:5),verbose=TRUE);
Subsetting JointUniquePairs object by < NetAffx_Q DAVID_Q EnVision_Q >
computing mixture model for 1 2 3 4 5 components...
>
>
>
>
>
> dev.off()
null device
1
>