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Last data update: 2014.03.03

R: Plots the content of a 'DataGeNET.Psy' or 'JaccardIndexPsy'...

plot,DataGeNET.Psy,ANY-method

R Documentation

Plots the content of a `DataGeNET.Psy` or `JaccardIndexPsy` object.

Description

This functions llows to create a variety of plots for DataGeNEt.Psy and JaccardIndexPsy objects.

Usage

## S4 method for signature 'DataGeNET.Psy,ANY'
plot(x, y,
  layout = igraph::layout.fruchterman.reingold, type = "disease",
  verbose = FALSE, ...)

Arguments

`x`	Object of class `DataGeNET.Psy`
`y`	NOT USED
`layout`	Function to design the location of the different nodes. By default `layout.fruchterman.reingold` from `igraph` is used.
`type`	Type of the drawn chart. By default it is `"disease"` but it also can be `"individual"`, `"disease"`, `"disease class"`, `"venn"`, `"barplot"`, `"heatmapGenes"`, `"heatmapScore"` or `"heatmap"`.
`verbose`	By default `FALSE`. If set to `TRUE` information on the drawing process will be shown.
`...`	Passed to inner functions for different plots.

Value

A plot for DataGeNET.Psy.

Examples

data(qr)
plot(qr) # for all-disease plot
plot(qr, type = 'disease class') # for MPI plot

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(psygenet2r)
Loading required package: VennDiagram
Loading required package: grid
Loading required package: futile.logger
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/psygenet2r/plot-DataGeNET.Psy-ANY-method.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot,DataGeNET.Psy,ANY-method
> ### Title: Plots the content of a 'DataGeNET.Psy' or 'JaccardIndexPsy'
> ###   object.
> ### Aliases: plot,DataGeNET.Psy,ANY-method
> 
> ### ** Examples
> 
> data(qr)
> plot(qr) # for all-disease plot
> plot(qr, type = 'disease class') # for MPI plot
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>