plot.netgwasmap | R Documentation |
Plot the graph associated with constructed linkage map via function netmap
.
## 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, ... )
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.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 |
... |
ONLY applicable when |
Pariya Behrouzi and Ernst C. Wit
Maintainer: Pariya Behrouzi pariya.behrouzi@gmail.com
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.
netmap
, buildMap
.
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