strength.viewer {bnviewer}

Interactive Bayesian Network Strength Viewer

Description

Show the strength of the probabilistic relationships expressed by the arcs of a Bayesian network, and use model averaging to build a network containing only the significant arcs.

Usage

strength.viewer(
  bayesianNetwork,
  bayesianNetwork.boot.strength,
  bayesianNetwork.background = NULL,
  bayesianNetwork.arc.strength.threshold.expression = NULL,
  bayesianNetwork.arc.strength.threshold.expression.color = NULL,
  bayesianNetwork.arc.strength.threshold.alternative.color = NULL,
  bayesianNetwork.arc.strength.label = FALSE,
  bayesianNetwork.arc.strength.label.prefix = "",
  bayesianNetwork.arc.strength.label.color = NULL,
  bayesianNetwork.arc.strength.tooltip = FALSE,
  bayesianNetwork.edge.scale.min = 1,
  bayesianNetwork.edge.scale.max = 5,
  bayesianNetwork.edge.scale.label.min = 14,
  bayesianNetwork.edge.scale.label.max = 14,
  bayesianNetwork.title = "",
  bayesianNetwork.subtitle = "",
  bayesianNetwork.footer = "",
  bayesianNetwork.enabled.interactive.mode = FALSE,
  bayesianNetwork.layout = "default",
  bayesianNetwork.width = "100%",
  bayesianNetwork.height = "500px",
  node.shape = NULL,
  node.label.prefix = "",
  node.colors = list(),
  node.font = list(),
  node.size = 10,
  edges.smooth = TRUE,
  edges.dashes = FALSE,
  edges.colors = list(),
  edges.width = 1,
  options.highlightNearest = TRUE,
  options.nodesIdSelection = FALSE,
  clusters.legend.title = "",
  clusters.legend.options = list(),
  clusters = list()
)

Arguments

bayesianNetwork

A Bayesian Network structure from Averaged Network

bayesianNetwork.boot.strength

A nonparametric bootstrap to assess arc strength and direction

bayesianNetwork.background

Bayesian network background

bayesianNetwork.arc.strength.threshold.expression

Logical expression of the force threshold of the arcs of the Bayesian network

bayesianNetwork.arc.strength.threshold.expression.color

Color applied to logical expression of the force threshold of the arcs of the Bayesian network

bayesianNetwork.arc.strength.threshold.alternative.color

Alternative color to logical expression of the force threshold of the arcs of the Bayesian network

bayesianNetwork.arc.strength.label

Enable Bayesian Network arc strength label

bayesianNetwork.arc.strength.label.prefix

Include Bayesian Network arc strength label prefix

bayesianNetwork.arc.strength.label.color

Set Bayesian Network arc strength label color

bayesianNetwork.arc.strength.tooltip

Enable Bayesian Network arc strength tooltip

bayesianNetwork.edge.scale.min

Set bayesian Network edge scale minimum

bayesianNetwork.edge.scale.max

Set bayesian Network edge scale maximum

bayesianNetwork.edge.scale.label.min

Set bayesian Network edge scale label minimum

bayesianNetwork.edge.scale.label.max

Set bayesian Network edge scale label maximum

bayesianNetwork.title

: String. Bayesian Network title

bayesianNetwork.subtitle

: String. Bayesian Network subtitle

bayesianNetwork.footer

: String. Bayesian Network footer

bayesianNetwork.enabled.interactive.mode

: Boolean. Enabled interactive viewer mode.

bayesianNetwork.layout

: String. A layout of a Bayesian Network

1. layout_on_sphere

2. layout_on_grid

3. layout_in_circle

4. layout_as_star

5. layout_as_tree

6. layout_with_sugiyama

7. layout_with_kk

8. layout_with_dh

9. layout_with_lgl

10. layout_with_mds

11. layout_with_gem

12. layout_nicely

13. layout_components

14. layout_hierarchical_direction_UD

15. layout_hierarchical_direction_DU

16. layout_hierarchical_direction_LR

17. layout_hierarchical_direction_RL

bayesianNetwork.width

: String. Bayesian Network width

bayesianNetwork.height

: String. Bayesian Network height

node.shape

: String. A node shape of a Bayesian Network

1. dot (default)

2. circle

3. ellipse

4. database

5. diamond

6. square

7. triangle

8. box

9. star

10. text

node.label.prefix

: String. Adds a prefix to the node label

node.colors

: String | named list. Color for the node. Can be 'rgba(120,32,14,1)', '#97C2FC' (hexa notation on 7 char without transparency) or 'red'. Can be just one color, or a list with several elements:

1. "background" : String. Default to '#97C2FC'. Background color for the node.

2. "border" : String. Default to '#2B7CE9'. Border color for the node.

3. "highlight" : String | named list, Color of the node when selected.

   1. "background" : String. Default to '#97C2FC'. Background color for the node when selected.

   2. "border" : String. Default to '#2B7CE9'. Border color for the node when selected.

node.font

Node Font : Array. Example list(color = "black", face="Arial")

node.size

Integer. Node Size.

edges.smooth

: Boolean. When true, the edge is drawn as a dynamic quadratic bezier curve.

edges.dashes

: Array or Boolean. Default to false. When true, the edge will be drawn as a dashed line.

edges.colors

: Named list or String. Default to named list. Color information of the edge in every situation. Can be 'rgba(120,32,14,1)', '#97C2FC' (hexa notation on 7 char without transparency) or 'red'.

• "color" : String. Default to '#848484. The color of the edge when it is not selected or hovered over (assuming hover is enabled in the interaction module).

• "highlight " : String. Default to '#848484'. The color the edge when it is selected.

• "hover" : String. Default to '#848484'. The color the edge when the mouse hovers over it (assuming hover is enabled in the interaction module).

• "inherit" : String or Boolean. Default to 'from'. When color, highlight or hover are defined, inherit is set to false! Supported options are: true, false, 'from','to','both'.

• "opacity" : Number. Default to 1.0. It can be useful to set the opacity of an edge without manually changing all the colors. The allowed range of the opacity option is between 0 and 1.

edges.width

: Number. Default to 1. Sets edge width.

options.highlightNearest

: Boolean. Default to true. Highlight nearest when clicking a node.

options.nodesIdSelection

: Boolean. Default to false. Add an id node selection creating an HTML select element.

clusters.legend.title

: Array. Get details in the example.

clusters.legend.options

: Array of Array. Get details in the example.

clusters

: Array of Array. Get details in the example.

References

See online documentation http://robsonfernandes.net/bnviewer

Examples

library(bnlearn)
library(bnviewer)

bayesianNetwork.boot.strength = boot.strength(coronary, R = 20, algorithm = "hc")

avg.bayesianNetwork = averaged.network(bayesianNetwork.boot.strength, threshold = 0.2)

strength.viewer(
  avg.bayesianNetwork,
  bayesianNetwork.boot.strength,
  bayesianNetwork.background = "white",
  bayesianNetwork.arc.strength.threshold.expression = c("@threshold > 0 & @threshold < 0.5",
                                                        "@threshold >= 0.5 & @threshold < 0.6",
                                                        "@threshold >= 0.6 & @threshold <= 1"),

  bayesianNetwork.arc.strength.threshold.expression.color  = c("red", "yellow", "green"),
  bayesianNetwork.arc.strength.threshold.alternative.color =  "white",

  bayesianNetwork.arc.strength.label = TRUE,
  bayesianNetwork.arc.strength.label.prefix = "",
  bayesianNetwork.arc.strength.label.color = "black",

  bayesianNetwork.arc.strength.tooltip = TRUE,

  bayesianNetwork.edge.scale.min = 1,
  bayesianNetwork.edge.scale.max = 3,

  bayesianNetwork.edge.scale.label.min = 14,
  bayesianNetwork.edge.scale.label.max = 14,

  bayesianNetwork.width = "100%",
  bayesianNetwork.height = "800px",
  bayesianNetwork.layout = "layout_with_sugiyama",
  node.colors = list(background = "#97c2fc",
                     border = "#2b7ce9",
                     highlight = list(background = "#e91eba",
                                      border = "#2b7ce9")),

  node.font = list(color = "black", face="Arial"),
  edges.dashes = FALSE,

  bayesianNetwork.title="Bayesian Network Strength Analysis - Coronary",
  bayesianNetwork.subtitle = "Coronary heart disease data set",
  bayesianNetwork.footer = "Fig. 1 - Layout with Sugiyama"
)