plot.nem {nem} | R Documentation

## plot nested effect model

### Description

plot graph of nested effect model, the marginal likelihood distribution or the posterior position of the effected genes

### Usage

            ## S3 method for class 'nem':
            plot(x, what="graph", remove.singletons=FALSE, PDF=FALSE, filename="nemplot.pdf", thresh=0, transitiveReduction=FALSE, ...)

### Arguments

`x` | nem object to plot
`what` | (i), "graph", (ii) "mLL" = likelihood distribution, (iii) "pos" = posterior position of effected genes
`remove.singletons` | remove unconnected nodes from the graph plot
`PDF` | output as PDF-file
`filename` | filename of PDF-file
`thresh` | if x has a real valued adjacency matrix (weight matrix), don't plot edges with weight <= thresh
`transitiveReduction` | plot a transitively reduced graph
`...` | other arguments to pass

### Value

none

### Author(s)

Florian Markowetz <URL: http://genomics.princeton.edu/~florian>, Holger Froehlich

### See Also

`nem`, `score`

[Package nem version 2.4.0 Index]