plot.netgwasmap {netgwas}

plot for S3 class "netgwasmap"

Description

Plot the graph associated with constructed linkage map via function netmap.

Usage

## S3 method for class 'netgwasmap'
plot(x, vis= NULL, layout= NULL, vertex.size= NULL, label.vertex =
		"none", label.size= NULL, vertex.color= NULL, edge.color = "gray29",
		sel.ID = NULL, ... )

Arguments

x

An object from "netgwasmap" class.

vis

Visualizing in four options: (i) "summary" plots the related network, conditional dependence relationships between markers before and after ordering markers; (ii) "interactive" plots the associated network, where it opens a new windows with interactive graph drawing facility; (iii) "unordered markers" plots the conditional dependence relationships between markers before ordering markers; (iv) "ordered markers" plots conditional dependence relationships between markers after ordering markers. Default is "summary".

layout

The vertex placement algorithm which is according to igraph package. The default layout is Fruchterman-Reingold layout. Other possible layouts are, for example, layout_with_kk, circle, and Reingold-Tilford graph in igraph package.

vertex.size

Optional integer to adjust vertex size in graph G. Default is 5.

label.vertex

Assign names to the vertices. There are three options: "none", "some", "all". (i) Specifying "none" omits vertex labels in the graph, (ii) using label.vertex = "some" you need to provide a vector of vertex IDs or a single vertex ID to the sel.ID argument, which you would like to be shown in the graph. label.vertex = "some" is only applicable for vis = "interactive", (iii) Specifying "all" includes all vertex labels in the graph. Default is "none".

label.size

Optional integer to adjust the size of node's label in graph G. Applicable when vertex.label is TRUE. Default is 0.8.

vertex.color

Optional integer vectors giving colors to the vertices.

edge.color

Optional integer vectors giving colors to edges.

sel.ID

ONLY applicable when vis= "interactive". A vector of vertex IDs or a single vertex ID, which you would like to be shown in the graph. ONLY applicable when label.vertex="some".

...

ONLY applicable when vis= "CI". System reserved (No specific usage)

Author(s)

Pariya Behrouzi and Ernst C. Wit
Maintainer: Pariya Behrouzi [e-mail]

References

1. Behrouzi, P., and Wit, E. C. (2018). De novo construction of polyploid linkage maps using discrete graphical models. Bioinformatics.
2. Behrouzi, P., and Wit, E. C. (2017c). netgwas: An R Package for Network-Based Genome-Wide Association Studies. arXiv preprint, arXiv:1710.01236.

See Also

netmap, buildMap.