Plot the optimal graph by model selection
# S3 method for select
plot(x, vis= NULL, xlab= NULL, ylab= NULL, n.var= NULL, vertex.label= FALSE
, ..., layout= NULL, label.vertex= "all", vertex.size= NULL, vertex.color= "red",
edge.color= "gray29", sel.label= NULL)An object with S3 class "select"
Visualizing the selected graph using two options: (i) "CI": plotting conditional independence (CI) relationships between variables, and (ii) "interactive": plotting the conditional independence network, where opens a new windows with interactive graph drawing facility. Default is "CI".
ONLY applicable when vis= "CI".
ONLY applicable when vis= "CI".
ONLY applicable when vis= "CI". A vector containing number of: phenotypes, markers in each chromosome, and environment variables. For example, the CviCol dataset, which is provided in the package, contain 5 chromosomes which the total number of markers is \(p = 90\), where the first 24 markers belong into chromosome 1, the next 14 markers into chromosome 2, ..., and chromosome 5 contains 19 markers. Thus, n.var = c(24,14,17,16,19). If n.var = NULL, in the graph visualization all markers are represented as same color.
ONLY applicable when vis= "CI". Assign names to the vertices. Default is FALSE.
ONLY applicable when vis= "CI". System reserved (No specific usage)
ONLY applicable when vis= "interactive". The layout specification. Some graph layouts examples: layout_with_fr, layout_in_circle, layout_as_tree, and layout.fruchterman.reingold. The default layout is layout_with_fr.
ONLY applicable when vis= "interactive". Assign names to the vertices. There are three options: "none", "some", "all". Specify "none" to omit vertex labels in the graph; using label.vertex = "some" you must provide a vector of vertex IDs or a single vertex ID to the sel.label argument, which you would like to be shown in the graph. Specify "all" to include all vertex labels in the graph. Default is "all".
Optional. The size of vertices in the graph visualization. The default value is 7.
ONLY applicable when vis= "interactive". Optional vector (or a color name) giving the colors of the vertices. The default is "red"
ONLY applicable when vis= "interactive". Optional. The default is "gray".
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".
An object with S3 class "select" is returned:
Plot of a selected graph, when vis= "CI".
Conditional independence (CI) relationships between variables, when vis= "CI"
Interactive plot of a selected graph with .eps format, when vis= "interactive"
Behrouzi, P., and Wit, E. C. (2017c). netgwas: An R Package for Network-Based Genome-Wide Association Studies. arXiv preprint, arXiv:1710.01236.