R: Plot the density distributions for correlation object(s)
plot.Corr
R Documentation
Plot the density distributions for correlation object(s)
Description
Plot the density distributions for a given Corr object or list of Corr objects.
The method can be used as object specific as well as static. In the latter case
the method can accept a list of Corr objects using Corr$plot(corrList) call signature.
Usage
## S3 method for class 'Corr'
plot(x, dataList=NULL, title="nonparametric density fit", lineColors=NULL, lineStyles=NULL, lineWidths=2, verbose=FALSE, cex.main=1.2, cex.lab=1, cex.axis=1, cex.legend=1, par.zoom=1, ...)
Arguments
dataList
the list of Corr objects (used if static version of method invoked).
Default is $NULL.
title
main plot title. Default is 'nonparametric density fit'.
lineColors
the vector of line colors (recycled if necessary)
for plotting the distributions of different Corr objects.
If NULL (default), the predefined set of colors is used.
lineStyles
the vector of line styles (recycled if necessary)
for plotting the distributions of different Corr objects.
If NULL (default), the predefined set of line styles is used.
lineWidths
the vector of line widths (recycled if necessary)
for plotting the distributions of different Corr objects. Default is 2.
verbose
if TRUE enables diagnostic messages.Default is FALSE.
cex.main
Main title font size. Default is 1.2.
cex.lab
X and Y titles font size. Default is 1.
cex.axis
X and Y axis labels font size. Default is 1.
cex.legend
font size for the plot legend. Default is 1.
par.zoom
graphics parameters zoom factor. Scales the graphical parameters like cex, lwd, mai etc.
Used to plot into the file based device with dimensions 'zoom' times bigger than for on-screen device.
...
additional graphical parameters
Author(s)
Alex Lisovich, Roger Day
See Also
For more information see Corr.
Examples
examples$corr$plot();
#create a set of corr. objects for a given DB subset treating subset
#as a full group and then plot the correlation densities including union
corrSet<-examples$jointUniquePairs$getCorr(examples$corr,
groups=c("union","EnVision_Q","NetAffx_Q","DAVID_Q","EnVision_Q"),
full.group=TRUE,verbose=TRUE);
Corr$plot(corrSet);
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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> library(IdMappingAnalysis)
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.20.0 (2016-02-17) successfully loaded. See ?R.oo for help.
Attaching package: 'R.oo'
The following objects are masked from 'package:methods':
getClasses, getMethods
The following objects are masked from 'package:base':
attach, detach, gc, load, save
Loading required package: rChoiceDialogs
Loading required package: rJava
Attaching package: 'rJava'
The following object is masked from 'package:R.oo':
clone
This is rChoiceDialogs 1.0.6 2014-09-05
This is IdMappingAnalysis 1.16.0 2013-05-24
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/IdMappingAnalysis/plot.Corr.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.Corr
> ### Title: Plot the density distributions for correlation object(s)
> ### Aliases: plot.Corr Corr.plot plot,Corr-method
> ### Keywords: internal methods
>
> ### ** Examples
>
> examples$corr$plot();
>
> #create a set of corr. objects for a given DB subset treating subset
> #as a full group and then plot the correlation densities including union
> corrSet<-examples$jointUniquePairs$getCorr(examples$corr,
+ groups=c("union","EnVision_Q","NetAffx_Q","DAVID_Q","EnVision_Q"),
+ full.group=TRUE,verbose=TRUE);
creating matching correlations ...
Subsetting JointUniquePairs object by < EnVision_Q NetAffx_Q DAVID_Q EnVision_Q >
Subsetting JointUniquePairs object by < EnVision_Q NetAffx_Q DAVID_Q EnVision_Q >
union
EnVision_Q
NetAffx_Q
DAVID_Q
EnVision_Q
> Corr$plot(corrSet);
>
>
>
>
>
> dev.off()
null device
1
>