plot.select {nutriNetwork}

Plot function for S3 class "select"

Description

Plot the optimal graph by model selection

Usage

## S3 method for class 'select'
plot(x, vis= NULL, xlab= NULL, ylab= NULL, n.mem= NULL, 
vertex.label= FALSE, ..., layout= NULL, label.vertex= "all", 
vertex.size= NULL, vertex.color= NULL, edge.color= "gray29", sel.nod.label= NULL,
label.size = NULL, w.btw= 800, w.within = 10, sign.edg= TRUE, edge.width= NULL, 
edge.label= NULL, max.degree= NULL, layout.tree= NULL, root.node= NULL,   
degree.node= NULL, curve= FALSE, pos.legend= "bottomleft", cex.legend= 0.8, 
iterl = NULL, temp = NULL, tk.width = NULL, tk.height= NULL)

Arguments

x

An object with S3 class "select"

vis

Visualizing the results as a graph (network) or as a matrix. There are 4 options to visulize the selected graph: (i) "CI": plotting conditional independence (CI) relationships between variables, (ii) "interactive": plotting the conditional independence network, where opens a new windows with interactive graph drawing facility, and (iii) "parcor.network": plots the estimated graph based on partial correlation values. (iv) "parcor.interactive": plots the estimated graph based on partial correlation matrix with an interactive graph drawing facility. Default is "CI".
Also, there are 3 options to visulaze the selected graph as a matrix: (i) vis= "image.parcorMatrix" plots the image of partial correlation matrix, (ii) vis = "image.adj" draws the adjacency matrix (only presence and absence of links), (iii) vis = "image.precision" plots the selected precision matrix.

xlab

ONLY applicable when vis = "CI", "image.parcorMatrix", "image.adj", or "image.precision".

ylab

ONLY applicable when vis = "CI", "image.parcorMatrix", "image.adj", or "image.precision".

n.mem

A vector of memberships. For example, the vfit dataset that is provided in the package contains 3 different groups, where the first 7 variables are general covariates (e.g. age, sex, BMI, and etc.), the next 17 variables belong to nutrient (e.g. vitamins B6, B12, C, D, and etc.), and the last 5 variables belong to physical performance and muscle strength. Thus, n.mem = c(7, 17, 5). If n.mem = NULL and vis = "CI" all vertices are coloured the same.

vertex.label

ONLY applicable when vis= "CI". Assign names to the vertices. Default is FALSE.

...

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

layout

ONLY applicable when vis= "interactive" or "parcor.network". 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.

label.vertex

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".

vertex.size

Optional. The size of vertices in the graph visualization. The default value is 7.

vertex.color

ONLY applicable when vis= "interactive" or "parcor.network". Optional vector (or a color name) giving the colors of the vertices. The default is "red"

edge.color

ONLY applicable when vis= "interactive". Optional. The default is "gray".

sel.nod.label

ONLY applicable when vis= "interactive" or "parcor.network". 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".

label.size

ONLY applicable for vis= "interactive" or vis= "parcor.network". The font size of the vertex labels.

w.btw

Distance between nodes from different memberships of n.mem in layout.

w.within

Distance of nodes within one membership of n.mem in layout.

sign.edg

Optional. ONLY applicable when vis= "parcor.network". If TRUE then edges are colored as red and blue, where red stands for positive and blue negative partial correlation values. If FASLE all edeges are colored as gray. Default is TRUE.

edge.width

Optional. ONLY applicable when vis= "parcor.network". Based on the strength of partial correlation values, edges will shown with different line type. Default is FALSE.

edge.label

Optional. ONLY applicable when vis= "parcor.network". If TRUE then the partial correlation values will be shown on top of each edge. Default is FALSE.

max.degree

Optional. ONLY applicable when vis= "parcor.network". A number showing degree of a node. This can be used to print those vertex labels that the correspondence vertex have at least e.g. 1 degree.

layout.tree

Optional. ONLY applicable when vis= "parcor.network". If TRUE then it uses layout_as_tree from igraph package. Default is FALSE.

root.node

Optional. ONLY applicable when vis= "parcor.network". The index of the root vertex or root vertices. If this is a non-empty vector then the supplied vertex ids are used as the roots of the trees . If it is an empty vector, then the root vertices are automatically calculated based on topological sorting, performed with the opposite mode than the mode argument. After the vertices have been sorted, one is selected from each component.

degree.node

Optional. ONLY applicable when vis= "parcor.network". It is related to the vertex label degree. It controls the position of the labels with respect to the vertices. Value are for example -pi/2, 0, pi/2, pi sets above, to the right, below, to the left of a node, respectively.

curve

Optional. ONLY applicable when vis= "parcor.network". Edge curvature, range between 0 and 1 (FALSE sets it to 0, TRUE to 0.5). Default is FALSE.

pos.legend

Applicable when vis= "parcor.network" or vis= "CI". The x and y co-ordinates to be used to position the legend. They can be specified by keywords like "topright", "topleft", and etc. Default is "bottomleft".

cex.legend

Applicable when vis= "parcor.network" or vis= "CI".

iterl

Optional. ONLY applicable when vis= "parcor.interactive". integer scalar, the number of iterations to perform for layout_with_fr layout.

temp

Optional. ONLY applicable when vis= "parcor.interactive". Real scalar, the start temperature for layout_with_fr layout.

tk.width

Optional. The size of the drawing area of interactive plot.

tk.height

Optional. The size of the drawing area of interactive plot.

Value

An object with S3 class "select" is returned:

network

Plot of a selected graph, when vis= "CI".

adjacency

Conditional independence (CI) relationships between variables, when vis= "CI"

network

Interactive plot of a selected graph with .eps format, when vis= "interactive"

Author(s)

Pariya Behrouzi
Maintainer: Pariya Behrouzi [e-mail]

References

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

select

Examples

    
    
data(vfit)
out <- nutriNetwork(vfit)
sel <- selectnet(out)
plot(sel, vis= "image.parcorMatrix")