igraph.qtlnet {qtlnet}

qtlnet plot using igraph

Description

Plot inferred causal network using igraph package.

Usage

igraph.qtlnet(x, edges, loci.list,
  pheno.color = "green", qtl.color = "red", vertex.color,
  include.qtl = TRUE, ...)
## S3 method for class 'qtlnet'
plot(x, ...)

Arguments

x

Object of class qtlnet.

edges

Data frame with first two columns being cause and effect directed phenotype pairs. Typically determined as averaged.net element from call to summary.qtlnet.

loci.list

List of character names of loci by phenotype. Typically determined by call to loci.qtlnet.

pheno.color, qtl.color

Name of color to use for phenotypes and QTLs, respectively.

vertex.color

Vertex colors in order of pheno-pheno edged augmented by loci.list, by default determined by pheno.color and qtl.color.

include.qtl

Include QTL in graph if TRUE and loci.list is not NULL.

...

Additional arguments passed to called routines.

Details

Uses the igraph package to create graph objects. These can be exported to a variety of other modern graphics packages. graph.qtlnet is synonymous with igraph.qtlnet.

Value

Object of class graph created using graph.data.frame.

Author(s)

Brian S. Yandell and Elias Chaibub Neto

References

Chaibub Neto E, Keller MP, Attie AD, Yandell BS (2010) Causal Graphical Models in Systems Genetics: a unified framework for joint inference of causal network and genetic architecture for correlated phenotypes. Ann Appl Statist 4: 320-339. http://www.stat.wisc.edu/~yandell/doc/2010/92.AnnApplStat.pdf

See Also

summary.qtlnet, loci.qtlnet, graph.data.frame, tkplot

Examples

Pscdbp.graph <- igraph.qtlnet(Pscdbp.qtlnet)
Pscdbp.graph
## Not run: 
tkplot(Pscdbp.graph)

## End(Not run)